Genome-Wide Prediction of Intrinsic Disorder; Sequence Alignment of Intrinsically Disordered Proteins

ERIC Educational Resources Information Center

Midic, Uros

2012-01-01

Intrinsic disorder (ID) is defined as a lack of stable tertiary and/or secondary structure under physiological conditions in vitro. Intrinsically disordered proteins (IDPs) are highly abundant in nature. IDPs possess a number of crucial biological functions, being involved in regulation, recognition, signaling and control, e.g. their functional…

The Subfascial Approach to Primary and Secondary Breast Augmentation with Autologous Fat Grafting and Form-Stable Implants.

PubMed

Sampaio Goes, João Carlos; Munhoz, Alexandre Mendonça; Gemperli, Rolf

2015-10-01

This article presents an overview of the subfascial approach to primary and secondary breast augmentation with form-stable implants associated with autologous fat grafting. Although breast augmentation is a well-studied procedure, there are few previous reports concerning the subfascial technique and, especially, this technique associated with lipofilling. Consequently, the authors present their experience with a form-stable, anatomically shaped silicone gel breast implant, which has recently been approved in the United States following FDA clinical trials. Primary and secondary breast augmentations using form-stable implants resulted in satisfactory outcomes. Copyright © 2015 Elsevier Inc. All rights reserved.

Comprehensive computational design of ordered peptide macrocycles

PubMed Central

Hosseinzadeh, Parisa; Bhardwaj, Gaurav; Mulligan, Vikram Khipple; Shortridge, Matthew D.; Craven, Timothy W.; Pardo-Avila, Fátima; Rettie, Stephen A.; Kim, David E.; Silva, Daniel-Adriano; Ibrahim, Yehia M.; Webb, Ian K.; Cort, John R.; Adkins, Joshua N.; Varani, Gabriele; Baker, David

2018-01-01

Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with L-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of L- and D-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods. PMID:29242347

Structural modeling of the N-terminal signal–receiving domain of IκBα

PubMed Central

Yazdi, Samira; Durdagi, Serdar; Naumann, Michael; Stein, Matthias

2015-01-01

The transcription factor nuclear factor-κB (NF-κB) exerts essential roles in many biological processes including cell growth, apoptosis and innate and adaptive immunity. The NF-κB inhibitor (IκBα) retains NF-κB in the cytoplasm and thus inhibits nuclear localization of NF-κB and its association with DNA. Recent protein crystal structures of the C-terminal part of IκBα in complex with NF-κB provided insights into the protein-protein interactions but could not reveal structural details about the N-terminal signal receiving domain (SRD). The SRD of IκBα contains a degron, formed following phosphorylation by IκB kinases (IKK). In current protein X-ray structures, however, the SRD is not resolved and assumed to be disordered. Here, we combined secondary structure annotation and domain threading followed by long molecular dynamics (MD) simulations and showed that the SRD possesses well-defined secondary structure elements. We show that the SRD contains 3 additional stable α-helices supplementing the six ARDs present in crystallized IκBα. The IκBα/NF-κB protein-protein complex remained intact and stable during the entire simulations. Also in solution, free IκBα retains its structural integrity. Differences in structural topology and dynamics were observed by comparing the structures of NF-κB free and NF-κB bound IκBα-complex. This study paves the way for investigating the signaling properties of the SRD in the IκBα degron. A detailed atomic scale understanding of molecular mechanism of NF-κB activation, regulation and the protein-protein interactions may assist to design and develop novel chronic inflammation modulators. PMID:26157801

Use of conserved key amino acid positions to morph protein folds.

PubMed

Reddy, Boojala V B; Li, Wilfred W; Bourne, Philip E

2002-07-15

By using three-dimensional (3D) structure alignments and a previously published method to determine Conserved Key Amino Acid Positions (CKAAPs) we propose a theoretical method to design mutations that can be used to morph the protein folds. The original Paracelsus challenge, met by several groups, called for the engineering of a stable but different structure by modifying less than 50% of the amino acid residues. We have used the sequences from the Protein Data Bank (PDB) identifiers 1ROP, and 2CRO, which were previously used in the Paracelsus challenge by those groups, and suggest mutation to CKAAPs to morph the protein fold. The total number of mutations suggested is less than 40% of the starting sequence theoretically improving the challenge results. From secondary structure prediction experiments of the proposed mutant sequence structures, we observe that each of the suggested mutant protein sequences likely folds to a different, non-native potentially stable target structure. These results are an early indicator that analyses using structure alignments leading to CKAAPs of a given structure are of value in protein engineering experiments. Copyright 2002 Wiley Periodicals, Inc.

Advances in single-molecule magnet surface patterning through microcontact printing.

PubMed

Mannini, Matteo; Bonacchi, Daniele; Zobbi, Laura; Piras, Federica M; Speets, Emiel A; Caneschi, Andrea; Cornia, Andrea; Magnani, Agnese; Ravoo, Bart Jan; Reinhoudt, David N; Sessoli, Roberta; Gatteschi, Dante

2005-07-01

We present an implementation of strategies to deposit single-molecule magnets (SMMs) using microcontact printing microCP). We describe different approaches of microCP to print stripes of a sulfur-functionalized dodecamanganese (III, IV) cluster on gold surfaces. Comparison by atomic force microscopy profile analysis of the patterned structures confirms the formation of a chemically stable single layer of SMMs. Images based on chemical contrast, obtained by time-of-flight secondary ion mass spectrometry, confirm the patterned structure.

Determination of Trophic Structure in Selected Freshwater Ecosystems by using Stable Isotope Analysis

PubMed Central

Zainordin, ‘Amila Faqhira; Ab Hamid, Suhaila

2017-01-01

Stable isotope analysis has been used extensively to establish trophic relationships in many ecosystems. Present study utilised stable isotope signatures of carbon and nitrogen to identify trophic structure of aquatic food web in river and rice field ecosystems in Perak, northern peninsular Malaysia. The mean δ13C values of all producers ranged from −35.29 ± 0.21 to −26.00 ± 0.050‰. The greatest δ15N values noted was in zenarchopterid fish with 9.68 ± 0.020‰. The δ15N values of aquatic insects ranged between 2.59 ± 0.107 in Elmidae (Coleoptera) and 8.11 ± 0.022‰ in Nepidae (Hemiptera). Correspondingly, with all the δ13C and δ15N values recorded, it can be deduced that there are four trophic levels existed in the freshwater ecosystems which started with the producer (plants), followed by primary consumer (aquatic insects and non-predatory fish), secondary consumer (invertebrate predators) and lastly tertiary consumer (vertebrate predators). PMID:28890758

Group 6 metal pentacarbonyl complexes of air-stable primary, secondary, and tertiary ferrocenylethylphosphines.

PubMed

Rabiee Kenaree, Amir; Sauvé, Ethan R; Ragogna, Paul J; Gilroy, Joe B

2016-02-21

The synthesis and characterization of a series of Group 6 metal pentacarbonyl complexes of air stable primary, secondary, and tertiary phosphines containing ferrocenylethyl substituents are reported [M(CO)5L: M = Cr, Mo, W; L = PH2(CH2CH2Fc), PH(CH2CH2Fc)2, P(CH2CH2Fc)3]. The structure and composition of the complexes were confirmed by multinuclear NMR spectroscopy, IR and UV-Vis absorption spectroscopy, mass spectrometry, X-ray crystallography, and elemental analysis. The solid-state structural data reported revealed trends in M-C and M-P bond lengths that mirrored those of the atomic radii of the Group 6 metals involved. UV-Vis absorption spectroscopy and cyclic voltammetry highlighted characteristics consistent with electronically isolated ferrocene units including wavelengths of maximum absorption between 435 and 441 nm and reversible one-electron (per ferrocene unit) oxidation waves between 10 and -5 mV relative to the ferrocene/ferrocenium redox couple. IR spectroscopy confirmed that the σ donating ability of the phosphines increased as ferrocenylethyl substituents were introduced and that the tertiary phosphine ligand described is a stronger σ donor than PPh3 and a weaker σ donor than PEt3, respectively.

Stable solidification of silica-based ammonium molybdophosphate by allophane: Application to treatment of radioactive cesium in secondary solid wastes generated from fukushima.

PubMed

Wu, Yan; Lee, Chuan-Pin; Mimura, Hitoshi; Zhang, Xiaoxia; Wei, Yuezhou

2018-01-05

Silica-based ammonium molybdophosphate (AMP/SiO 2 ) is an absorbent material that can effectively remove Cs from radioactive-contaminated wastewater (RCW) generated by Fukushima nuclide accident. Pressing/sintering method was used for final disposal of secondary waste (spent absorbent) to achieve the volume reduction of AMP-Cs/SiO 2 (AMP/SiO 2 saturation adsorption of Cs) and stable solidification of Cs by adding natural allophane. The structure of AMP-Cs completely collapsed at approximately 700°C, and most Mo and P species in AMP sublimed. The optimal sintering temperature was estimated as 900°C. The stable crystalline phase of Cs 4 Al 4 Si 20 O 48 was recrystallized by the reaction of Cs 2 O, Al 2 O 3 , and SiO 2 , and the immobilization ratio of Cs was approximately 100%. The leachability of Cs from the sintered product in distilled water was approximately 0.41%. The high immobilization and low leachability of Cs were attributed to the excellent solidification properties of the sintered products of AMP-Cs/SiO 2 -allophane. Copyright © 2017 Elsevier B.V. All rights reserved.

Structures and Free Energy Landscapes of the A53T Mutant-Type α-Synuclein Protein and Impact of A53T Mutation on the Structures of the Wild-Type α-Synuclein Protein with Dynamics

PubMed Central

2013-01-01

The A53T genetic missense mutation of the wild-type α-synuclein (αS) protein was initially identified in Greek and Italian families with familial Parkinson’s disease. Detailed understanding of the structures and the changes induced in the wild-type αS structure by the A53T mutation, as well as establishing the direct relationships between the rapid conformational changes and free energy landscapes of these intrinsically disordered fibrillogenic proteins, helps to enhance our fundamental knowledge and to gain insights into the pathogenic mechanism of Parkinson’s disease. We employed extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations to determine the secondary and tertiary structural properties as well as the conformational free energy surfaces of the wild-type and A53T mutant-type αS proteins in an aqueous solution medium using both implicit and explicit water models. The confined aqueous volume effect in the simulations of disordered proteins using an explicit model for water is addressed for a model disordered protein. We also assessed the stabilities of the residual secondary structure component interconversions in αS based on free energy calculations at the atomic level with dynamics using our recently developed theoretical strategy. To the best of our knowledge, this study presents the first detailed comparison of the structural properties linked directly to the conformational free energy landscapes of the monomeric wild-type and A53T mutant-type α-synuclein proteins in an aqueous solution environment. Results demonstrate that the β-sheet structure is significantly more altered than the helical structure upon A53T mutation of the monomeric wild-type αS protein in aqueous solution. The β-sheet content close to the mutation site in the N-terminal region is more abundant while the non-amyloid-β component (NAC) and C-terminal regions show a decrease in β-sheet abundance upon A53T mutation. Obtained results utilizing our new theoretical strategy show that the residual secondary structure conversion stabilities resulting in α-helix formation are not significantly affected by the mutation. Interestingly, the residual secondary structure conversion stabilities show that secondary structure conversions resulting in β-sheet formation are influenced by the A53T mutation and the most stable residual transition yielding β-sheet occurs directly from the coil structure. Long-range interactions detected between the NAC region and the N- or C-terminal regions of the wild-type αS disappear upon A53T mutation. The A53T mutant-type αS structures are thermodynamically more stable than those of the wild-type αS protein structures in aqueous solution. Overall, the higher propensity of the A53T mutant-type αS protein to aggregate in comparison to the wild-type αS protein is related to the increased β-sheet formation and lack of strong intramolecular long-range interactions in the N-terminal region in comparison to its wild-type form. The specific residual secondary structure component stabilities reported herein provide information helpful for designing and synthesizing small organic molecules that can block the β-sheet forming residues, which are reactive toward aggregation. PMID:23607785

Structures and free energy landscapes of the A53T mutant-type α-synuclein protein and impact of A53T mutation on the structures of the wild-type α-synuclein protein with dynamics.

PubMed

Coskuner, Orkid; Wise-Scira, Olivia

2013-07-17

The A53T genetic missense mutation of the wild-type α-synuclein (αS) protein was initially identified in Greek and Italian families with familial Parkinson's disease. Detailed understanding of the structures and the changes induced in the wild-type αS structure by the A53T mutation, as well as establishing the direct relationships between the rapid conformational changes and free energy landscapes of these intrinsically disordered fibrillogenic proteins, helps to enhance our fundamental knowledge and to gain insights into the pathogenic mechanism of Parkinson's disease. We employed extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations to determine the secondary and tertiary structural properties as well as the conformational free energy surfaces of the wild-type and A53T mutant-type αS proteins in an aqueous solution medium using both implicit and explicit water models. The confined aqueous volume effect in the simulations of disordered proteins using an explicit model for water is addressed for a model disordered protein. We also assessed the stabilities of the residual secondary structure component interconversions in αS based on free energy calculations at the atomic level with dynamics using our recently developed theoretical strategy. To the best of our knowledge, this study presents the first detailed comparison of the structural properties linked directly to the conformational free energy landscapes of the monomeric wild-type and A53T mutant-type α-synuclein proteins in an aqueous solution environment. Results demonstrate that the β-sheet structure is significantly more altered than the helical structure upon A53T mutation of the monomeric wild-type αS protein in aqueous solution. The β-sheet content close to the mutation site in the N-terminal region is more abundant while the non-amyloid-β component (NAC) and C-terminal regions show a decrease in β-sheet abundance upon A53T mutation. Obtained results utilizing our new theoretical strategy show that the residual secondary structure conversion stabilities resulting in α-helix formation are not significantly affected by the mutation. Interestingly, the residual secondary structure conversion stabilities show that secondary structure conversions resulting in β-sheet formation are influenced by the A53T mutation and the most stable residual transition yielding β-sheet occurs directly from the coil structure. Long-range interactions detected between the NAC region and the N- or C-terminal regions of the wild-type αS disappear upon A53T mutation. The A53T mutant-type αS structures are thermodynamically more stable than those of the wild-type αS protein structures in aqueous solution. Overall, the higher propensity of the A53T mutant-type αS protein to aggregate in comparison to the wild-type αS protein is related to the increased β-sheet formation and lack of strong intramolecular long-range interactions in the N-terminal region in comparison to its wild-type form. The specific residual secondary structure component stabilities reported herein provide information helpful for designing and synthesizing small organic molecules that can block the β-sheet forming residues, which are reactive toward aggregation.

Invasive Mussels Alter the Littoral Food Web of a Large Lake: Stable Isotopes Reveal Drastic Shifts in Sources and Flow of Energy

PubMed Central

Ozersky, Ted; Evans, David O.; Barton, David R.

2012-01-01

We investigated how establishment of invasive dreissenid mussels impacted the structure and energy sources of the littoral benthic food web of a large temperate lake. We combined information about pre- and postdreissenid abundance, biomass, and secondary production of the littoral benthos with results of carbon and nitrogen stable isotope analysis of archival (predreissenid) and recent (postdreissenid) samples of all common benthic taxa. This approach enabled us to determine the importance of benthic and sestonic carbon to the littoral food web before, and more than a decade after dreissenid establishment. Long term dreissenid presence was associated with a 32-fold increase in abundance, 6-fold increase in biomass, and 14-fold increase in secondary production of the littoral benthos. Dreissenids comprised a large portion of the post-invasion benthos, making up 13, 38, and 56% of total abundance, biomass, and secondary production, respectively. The predreissenid food web was supported primarily by benthic primary production, while sestonic material was relatively more important to the postdreissenid food web. The absolute importance of both sestonic material and benthic primary production to the littoral benthos increased considerably following dreissenid establishment. Our results show drastic alterations to food web structure and suggest that dreissenid mussels redirect energy and material from the water column to the littoral benthos both through biodeposition of sestonic material as well as stimulation of benthic primary production. PMID:23284673

Sequential protein unfolding through a carbon nanotube pore

NASA Astrophysics Data System (ADS)

Xu, Zhonghe; Zhang, Shuang; Weber, Jeffrey K.; Luan, Binquan; Zhou, Ruhong; Li, Jingyuan

2016-06-01

An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of the nanopore interface thus facilitate the formation of stable ``unfoldon'' motifs above the nanotube aperture that can exist in the absence of specific native contacts with the other secondary structure. Destruction of these unfoldons gives rise to distinct force peaks in our simulations, providing us with a sensitive probe for studying the kinetics of serial unfolding events. Our detailed analysis of nanopore-mediated protein unfolding events not only provides insight into how related processes might proceed in the cell, but also serves to deepen our understanding of structural arrangements which form the basis for protein conformational stability.An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of the nanopore interface thus facilitate the formation of stable ``unfoldon'' motifs above the nanotube aperture that can exist in the absence of specific native contacts with the other secondary structure. Destruction of these unfoldons gives rise to distinct force peaks in our simulations, providing us with a sensitive probe for studying the kinetics of serial unfolding events. Our detailed analysis of nanopore-mediated protein unfolding events not only provides insight into how related processes might proceed in the cell, but also serves to deepen our understanding of structural arrangements which form the basis for protein conformational stability. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr00410e

Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding.

PubMed

Yang, A S; Hitz, B; Honig, B

1996-06-21

The stability of beta-turns is calculated as a function of sequence and turn type with a Monte Carlo sampling technique. The conformational energy of four internal hydrogen-bonded turn types, I, I', II and II', is obtained by evaluating their gas phase energy with the CHARMM force field and accounting for solvation effects with the Finite Difference Poisson-Boltzmann (FDPB) method. All four turn types are found to be less stable than the coil state, independent of the sequence in the turn. The free-energy penalties associated with turn formation vary between 1.6 kcal/mol and 7.7 kcal/mol, depending on the sequence and turn type. Differences in turn stability arise mainly from intraresidue interactions within the two central residues of the turn. For each combination of the two central residues, except for -Gly-Gly-, the most stable beta-turn type is always found to occur most commonly in native proteins. The fact that a model based on local interactions accounts for the observed preference of specific sequences suggests that long-range tertiary interactions tend to play a secondary role in determining turn conformation. In contrast, for beta-hairpins, long-range interactions appear to dominate. Specifically, due to the right-handed twist of beta-strands, type I' turns for -Gly-Gly- are found to occur with high frequency, even when local energetics would dictate otherwise. The fact that any combination of two residues is found able to adopt a relatively low-energy turn structure explains why the amino acid sequence in turns is highly variable. The calculated free-energy cost of turn formation, when combined with related numbers obtained for alpha-helices and beta-sheets, suggests a model for the initiation of protein folding based on metastable fragments of secondary structure.

Effect of Anions on Nanofiber Formation of β-sheet Propensity Amphiphile Peptide

NASA Astrophysics Data System (ADS)

Shamsudeen, H.; Tan, H. L.; Eshak, Z.

2018-05-01

Peptide self-assembly forms different nanostructures under simple alteration in the solution environment. Understanding the mechanism of the assembly will help us to control and tailor functional nanomaterials. This study aims to investigate the influence of anions on the self-assembly morphology and shape using a synthetic peptide of FFFFKK. Circular Dichoism (CD) and Environmental Scanning Electron Microscope (ESEM) were used to determine the secondary structure and self-assembly morphology, while Image J imaging software was used to measure diameter size. In the absence of anion, FFFFKK formed anti-parallel β-sheet that adopted sizeable fibrillar structure with a minimal increment over the first 7 hours of assembly. Irregular structure was observed in the presence of Iodide ion (I-) with a less stable secondary structure such as β-turn and β-loop. In the presence of perchlorate ion (ClO4 -), needle-like structure was observed with predominantly β-sheet structure. Our study showed that peptide morphology can be controlled by using different anions with careful selection of amino acid residues in peptide sequence.

Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure

PubMed Central

Shen, Manli; Bellaousov, Stanislav; Hiller, Michael; de La Grange, Pierre; Creamer, Trevor P.; Malina, Orit; Sperling, Ruth; Mathews, David H.; Stoilov, Peter; Stamm, Stefan

2013-01-01

The serotonin receptor 2C plays a central role in mood and appetite control. It undergoes pre-mRNA editing as well as alternative splicing. The RNA editing suggests that the pre-mRNA forms a stable secondary structure in vivo. To identify substances that promote alternative exons inclusion, we set up a high-throughput screen and identified pyrvinium pamoate as a drug-promoting exon inclusion without editing. Circular dichroism spectroscopy indicates that pyrvinium pamoate binds directly to the pre-mRNA and changes its structure. SHAPE (selective 2′-hydroxyl acylation analysed by primer extension) assays show that part of the regulated 5′-splice site forms intramolecular base pairs that are removed by this structural change, which likely allows splice site recognition and exon inclusion. Genome-wide analyses show that pyrvinium pamoate regulates >300 alternative exons that form secondary structures enriched in A–U base pairs. Our data demonstrate that alternative splicing of structured pre-mRNAs can be regulated by small molecules that directly bind to the RNA, which is reminiscent to an RNA riboswitch. PMID:23393189

Opposite consequences of two transcription pauses caused by an intrinsic terminator oligo(U): antitermination versus termination by bacteriophage T7 RNA polymerase.

PubMed

Lee, Sooncheol; Kang, Changwon

2011-05-06

The RNA oligo(U) sequence, along with an immediately preceding RNA hairpin structure, is an essential cis-acting element for bacterial class I intrinsic termination. This sequence not only causes a pause in transcription during the beginning of the termination process but also facilitates transcript release at the end of the process. In this study, the oligo(U) sequence of the bacteriophage T7 intrinsic terminator Tφ, rather than the hairpin structure, induced pauses of phage T7 RNA polymerase not only at the termination site, triggering a termination process, but also 3 bp upstream, exerting an antitermination effect. The upstream pause presumably allowed RNA to form a thermodynamically more stable secondary structure rather than a terminator hairpin and to persist because the 5'-half of the terminator hairpin-forming sequence could be sequestered by a farther upstream sequence via sequence-specific hybridization, prohibiting formation of the terminator hairpin and termination. The putative antiterminator RNA structure lacked several base pairs essential for termination when probed using RNases A, T1, and V1. When the antiterminator was destabilized by incorporation of IMP into nascent RNA at G residue positions, antitermination was abolished. Furthermore, antitermination strength increased with more stable antiterminator secondary structures and longer pauses. Thus, the oligo(U)-mediated pause prior to the termination site can exert a cis-acting antitermination activity on intrinsic terminator Tφ, and the termination efficiency depends primarily on the termination-interfering pause that precedes the termination-facilitating pause at the termination site.

Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data.

PubMed

Baltzis, Athanasios S; Glykos, Nicholas M

2016-03-01

The villin headpiece helical subdomain (HP36) is one of the best known model systems for computational studies of fast-folding all-α miniproteins. HP21 is a peptide fragment-derived from HP36-comprising only the first and second helices of the full domain. Experimental studies showed that although HP21 is mostly unfolded in solution, it does maintain some persistent native-like structure as indicated by the analysis of NMR-derived chemical shifts. Here we compare the experimental data for HP21 with the results obtained from a 15-μs long folding molecular dynamics simulation performed in explicit water and with full electrostatics. We find that the simulation is in good agreement with the experiment and faithfully reproduces the major experimental findings, namely that (a) HP21 is disordered in solution with <10% of the trajectory corresponding to transiently stable structures, (b) the most highly populated conformer is a native-like structure with an RMSD from the corresponding portion of the HP36 crystal structure of <1 Å, (c) the simulation-derived chemical shifts-over the whole length of the trajectory-are in reasonable agreement with the experiment giving reduced χ(2) values of 1.6, 1.4, and 0.8 for the Δδ(13) C(α) , Δδ(13) CO, and Δδ(13) C(β) secondary shifts, respectively (becoming 0.8, 0.7, and 0.3 when only the major peptide conformer is considered), and finally, (d) the secondary structure propensity scores are in very good agreement with the experiment and clearly indicate the higher stability of the first helix. We conclude that folding molecular dynamics simulations can be a useful tool for the structural characterization of even marginally stable peptides. © 2015 The Protein Society.

Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide

NASA Astrophysics Data System (ADS)

Mu, Yan; Gao, Yi Qin

2007-09-01

We studied the effects of hydrophobicity and dipole-dipole interactions between the nearest-neighbor amide planes on the secondary structures of a model polypeptide by calculating the free energy differences between different peptide structures. The free energy calculations were performed with low computational costs using the accelerated Monte Carlo simulation (umbrella sampling) method, with a bias-potential method used earlier in our accelerated molecular dynamics simulations. It was found that the hydrophobic interaction enhances the stability of α helices at both low and high temperatures but stabilizes β structures only at high temperatures at which α helices are not stable. The nearest-neighbor dipole-dipole interaction stabilizes β structures under all conditions, especially in the low temperature region where α helices are the stable structures. Our results indicate clearly that the dipole-dipole interaction between the nearest neighboring amide planes plays an important role in determining the peptide structures. Current research provides a more unified and quantitative picture for understanding the effects of different forms of interactions on polypeptide structures. In addition, the present model can be extended to describe DNA/RNA, polymer, copolymer, and other chain systems.

JWST testbed telescope: a functionally accurate scaled version of the flight optical telescope element used to develop the flight wavefront sensing and control algorithm

NASA Astrophysics Data System (ADS)

Kingsbury, Lana K.; Atcheson, Paul D.

2004-10-01

The Northrop-Grumman/Ball/Kodak team is building the JWST observatory that will be launched in 2011. To develop the flight wavefront sensing and control (WFS&C) algorithms and software, Ball is designing and building a 1 meter diameter, functionally accurate version of the JWST optical telescope element (OTE). This testbed telescope (TBT) will incorporate the same optical element control capability as the flight OTE. The secondary mirror will be controlled by a 6 degree of freedom (dof) hexapod and each of the 18 segmented primary mirror assemblies will have 6 dof hexapod control as well as radius of curvature adjustment capability. In addition to the highly adjustable primary and secondary mirrors, the TBT will include a rigid tertiary mirror, 2 fold mirrors (to direct light into the TBT) and a very stable supporting structure. The total telescope system configured residual wavefront error will be better than 175 nm RMS double pass. The primary and secondary mirror hexapod assemblies enable 5 nm piston resolution, 0.0014 arcsec tilt resolution, 100 nm translation resolution, and 0.04497 arcsec clocking resolution. The supporting structure (specifically the secondary mirror support structure) is designed to ensure that the primary mirror segments will not change their despace position relative to the secondary mirror (spaced > 1 meter apart) by greater than 500 nm within a one hour period of ambient clean room operation.

Evolutionary conservation of sequence and secondary structures inCRISPR repeats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeatsmore » identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.« less

Microenvironments and Signaling Pathways Regulating Early Dissemination, Dormancy, and Metastasis

DTIC Science & Technology

2015-09-01

hypothesize that after extravasation at secondary site TMEM (S- TMEM), in order to exit dormancy a stable S-TMEM structure needs to be maintained and...by understanding early dissemination and dormancy of DTCs we will find ways to eradicate dormant DTCs and prevent metastasis. 2. KEYWORDS...TMEM, DTC, dormancy, dissemination intravasation, extravasation 3. ACCOMPLISHMENTS:  What were the major goals of the project? Our original specific

Designer bFGF-incorporated d-form self-assembly peptide nanofiber scaffolds to promote bone repair.

PubMed

He, Bin; Ou, Yunsheng; Chen, Shuo; Zhao, Weikang; Zhou, Ao; Zhao, Jinqiu; Li, Hong; Jiang, Dianming; Zhu, Yong

2017-05-01

d-Form and l-form peptide nanofiber scaffolds can spontaneously form stable β-sheet secondary structures and nanofiber hydrogel scaffolds, and hold some promise in hemostasis and wound healing. We report here on the synthetic self-assembling peptide d-RADA16 and l-RADA16 are both found to produce stable β-sheet secondary structure and nanofiber hydrogel scaffolds based on circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM) and rheology analysis etc. d-RADA16 hydrogel and l-RADA16 hydrogel can enhance obvious bone repair in femoral condyle defects of the Sprague-Dawley (SD) rat model compared to PBS treatment. Based on micro-computed tomography (CT), it was revealed that d-RADA16 hydrogel and l-RADA16 hydrogel were capable to obtain the extensive bone healing. Histological evaluation also found that these two hydrogels facilitate the presence of more mature bone tissue within the femoral condyle defects. Additionally, d-RADA16 hydrogel showed some potential in storing and releasing basic-fibroblast growth factor (bFGF) which was able to further promote bone regeneration based on micro-CT analysis. These results indicate that d-form peptide nanofiber hydrogel have some special capacity for bone repair. Copyright © 2016 Elsevier B.V. All rights reserved.

Trajectories of Quality of Life after Hematopoietic Cell Transplantation: Secondary Analysis of BMT CTN 0902 Data

PubMed Central

Jim, Heather S.L.; Sutton, Steven K.; Small, Brent J.; Jacobsen, Paul B.; Wood, William A.; Knight, Jennifer M.; Majhail, Navneet S.; Syrjala, Karen L.; Lee, Stephanie J.

2016-01-01

Summary Quality of life is increasingly recognized as an important secondary endpoint of hematopoietic cell transplantation (HCT). The current study examined the extent to which attrition results in biased estimates of patient quality of life. The study also examined whether patients differ in terms of trajectories of quality of life in the first six months post-transplant. A secondary data analysis was conducted of 701 participants who enrolled in the Blood and Marrow Transplantation Clinical Trials Network (BMT CTN) 0902 trial. Participants completed the SF-36, a measure of quality of life, prior to transplant and 100 and 180 days post-transplant. Results indicated that attrition resulted in slightly biased overestimates of quality of life but the amount of overestimation remained stable over time. Patients could be grouped into three distinct classes based on physical quality of life: 1) low and stable; 2) average and declining, then stable; and 3) average and stable. Four classes of patients emerged for mental quality of life: 1) low and stable; 2) average, improving, then stable; 3) higher than average (by almost 1 SD) and stable; and 4) average and stable. Taken together, these data provide a more comprehensive understanding of quality of life that can be used to educate HCT recipients and their caregivers. PMID:27538374

The mitochondrial genomes of Campodea fragilis and C. lubbocki(Hexapoda: Diplura): high genetic divergence in a morphologically uniformtaxon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Podsiadlowski, L.; Carapelli, A.; Nardi, F.

2005-12-01

Mitochondrial genomes from two dipluran hexapods of the genus Campodea have been sequenced. Gene order is the same as in most other hexapods and crustaceans. Secondary structures of tRNAs reveal specific structural changes in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2. Comparative analyses of nucleotide and amino acid composition, as well as structural features of both ribosomal RNA subunits, reveal substantial differences among the analyzed taxa. Although the two Campodea species are morphologically highly uniform, genetic divergence is larger than expected, suggesting a long evolutionary history under stable ecological conditions.

The crystal structure of the calcium-bound con-G[Q6A] peptide reveals a novel metal-dependent helical trimer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cnudde, Sara E.; Prorok, Mary; Jia, Xaofei

2012-02-15

The ability to form and control both secondary structure and oligomerization in short peptides has proven to be challenging owing to the structural instability of such peptides. The conantokin peptides are a family of {gamma}-carboxyglutamic acid containing peptides produced in the venoms of predatory sea snails of the Conus family. They are examples of short peptides that form stable helical structures, especially in the presence of divalent cations. Both monomeric and dimeric conantokin peptides have been identified and represent a new mechanism of helix association, 'the metallozipper motif' that is devoid of a hydrophobic interface between monomers. In the presentmore » study, a parallel/antiparallel three-helix bundle was identified and its crystal structure determined at high resolution. The three helices are almost perfectly parallel and represent a novel helix-helix association. The trimer interface is dominated by metal chelation between the three helices, and contains no interfacial hydrophobic interactions. It is now possible to produce stable monomeric, dimeric, or trimeric metallozippers depending on the peptide sequence and metal ion. Such structures have important applications in protein design.« less

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.

PubMed

Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

2013-07-01

The design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e. a random seed is progressively adapted to acquire the desired folding properties) and more importantly do not allow the user to control explicitly the nucleotide distribution such as the GC-content in their sequences. However, the latter is an important criterion for large-scale applications as it could presumably be used to design sequences with better transcription rates and/or structural plasticity. In this article, we introduce IncaRNAtion, a novel algorithm to design RNA sequences folding into target secondary structures with a predefined nucleotide distribution. IncaRNAtion uses a global sampling approach and weighted sampling techniques. We show that our approach is fast (i.e. running time comparable or better than local search methods), seedless (we remove the bias of the seed in local search heuristics) and successfully generates high-quality sequences (i.e. thermodynamically stable) for any GC-content. To complete this study, we develop a hybrid method combining our global sampling approach with local search strategies. Remarkably, our glocal methodology overcomes both local and global approaches for sampling sequences with a specific GC-content and target structure. IncaRNAtion is available at csb.cs.mcgill.ca/incarnation/. Supplementary data are available at Bioinformatics online.

Three-dimensional imaging of cholesterol and sphingolipids within a Madin-Darby canine kidney cell

DOE PAGES

Yeager, Ashley N.; Weber, Peter K.; Kraft, Mary L.

2016-01-08

Metabolic stable isotope incorporation and secondary ion mass spectrometry(SIMS) depth profiling performed on a Cameca NanoSIMS 50 were used to image the 18O-cholesterol and 15N-sphingolipid distributions within a portion of a Madin-Darby canine kidney (MDCK) cell. Three-dimensional representations of the component-specific isotope distributions show clearly defined regions of 18O-cholesterol and 15N-sphingolipid enrichment that seem to be separate subcellular compartments. Furthermore, the low levels of nitrogen-containing secondary ions detected at the 18O-enriched regions suggest that these 18O-cholesterol-rich structures may be lipiddroplets, which have a core consisting of cholesterol esters and triacylglycerides.

Three-dimensional imaging of cholesterol and sphingolipids within a Madin-Darby canine kidney cell

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yeager, Ashley N.; Weber, Peter K.; Kraft, Mary L.

Metabolic stable isotope incorporation and secondary ion mass spectrometry(SIMS) depth profiling performed on a Cameca NanoSIMS 50 were used to image the 18O-cholesterol and 15N-sphingolipid distributions within a portion of a Madin-Darby canine kidney (MDCK) cell. Three-dimensional representations of the component-specific isotope distributions show clearly defined regions of 18O-cholesterol and 15N-sphingolipid enrichment that seem to be separate subcellular compartments. Furthermore, the low levels of nitrogen-containing secondary ions detected at the 18O-enriched regions suggest that these 18O-cholesterol-rich structures may be lipiddroplets, which have a core consisting of cholesterol esters and triacylglycerides.

Correlated optical and isotopic nanoscopy

NASA Astrophysics Data System (ADS)

Saka, Sinem K.; Vogts, Angela; Kröhnert, Katharina; Hillion, François; Rizzoli, Silvio O.; Wessels, Johannes T.

2014-04-01

The isotopic composition of different materials can be imaged by secondary ion mass spectrometry. In biology, this method is mainly used to study cellular metabolism and turnover, by pulsing the cells with marker molecules such as amino acids labelled with stable isotopes (15N, 13C). The incorporation of the markers is then imaged with a lateral resolution that can surpass 100 nm. However, secondary ion mass spectrometry cannot identify specific subcellular structures like organelles, and needs to be correlated with a second technique, such as fluorescence imaging. Here, we present a method based on stimulated emission depletion microscopy that provides correlated optical and isotopic nanoscopy (COIN) images. We use this approach to study the protein turnover in different organelles from cultured hippocampal neurons. Correlated optical and isotopic nanoscopy can be applied to a variety of biological samples, and should therefore enable the investigation of the isotopic composition of many organelles and subcellular structures.

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models.

PubMed

Li, Min; Zhang, John Z H

2017-02-14

A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models

NASA Astrophysics Data System (ADS)

Li, Min; Zhang, John Z. H.

2017-02-01

A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

Exploring Ultrafast Structural Dynamics for Energetic Enhancement or Disruption

DTIC Science & Technology

2016-03-01

it. In a pump -push/ dump probe experiment, a secondary laser pulse (push/ dump ) is used after the initial perturbation due to the pump pulse. The...increased. The pump -push/ dump probe technique is a difficult experiment that requires a highly stable laser source. Ultrafast pump -probe experiments...decomposition of solids. Journal of Applied Physics. 2001;89:4156–4166. 17. Kee TW. Femtosecond pump -push-probe and pump - dump -probe spectroscopy of

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

PubMed Central

Rutenberg-Schoenberg, Michael; Simon, Matthew D.

2015-01-01

The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. PMID:26646615

Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization.

PubMed

Zhang, Gaihua; Su, Zhen

2012-01-01

Work on protein structure prediction is very useful in biological research. To evaluate their accuracy, experimental protein structures or their derived data are used as the 'gold standard'. However, as proteins are dynamic molecular machines with structural flexibility such a standard may be unreliable. To investigate the influence of the structure flexibility, we analysed 3,652 protein structures of 137 unique sequences from 24 protein families. The results showed that (1) the three-dimensional (3D) protein structures were not rigid: the root-mean-square deviation (RMSD) of the backbone Cα of structures with identical sequences was relatively large, with the average of the maximum RMSD from each of the 137 sequences being 1.06 Å; (2) the derived data of the 3D structure was not constant, e.g. the highest ratio of the secondary structure wobble site was 60.69%, with the sequence alignments from structural comparisons of two proteins in the same family sometimes being completely different. Proteins may have several stable conformations and the data derived from resolved structures as a 'gold standard' should be optimized before being utilized as criteria to evaluate the prediction methods, e.g. sequence alignment from structural comparison. Helix/β-sheet transition exists in normal free proteins. The coil ratio of the 3D structure could affect its resolution as determined by X-ray crystallography.

Rod-shaped cavitation bubble structure in ultrasonic field.

PubMed

Bai, Lixin; Wu, Pengfei; Liu, Huiyu; Yan, Jiuchun; Su, Chang; Li, Chao

2018-06-01

Rod-shaped cavitation bubble structure in thin liquid layers in ultrasonic field is investigated experimentally. It is found that cavitation structure successively experiences several stages with the change of the thickness of the thin liquid layer. Rod-shaped structure is a stable structure of the boundary between the cavitation cloud region and the non-cavitation liquid region, which can be formed in two different ways. Cavitation bubbles in a thin liquid layer have a distribution in the thickness direction. The rod-shaped structures tend to crosslink with each other to form stable Y-branch structures. The angle of the Y-branch structure is Gauss distribution with mathematical expectation μ = 119.93. A special rod-shaped cavitation structure with source is also investigated in detail. Due to the pressure gradient in the normal direction, the primary Bjerknes force causes the bubbles in the rod-shaped structure on both sides to converge to the axis. The secondary Bjerknes forces between the bubbles also make the cluster converge, so the large bubbles which are attached to the radiating surface tend to align themselves along the central line. According to the formula deduced in this paper, the variation of curvature of curved rod-shaped structure is qualitatively analyzed. The Y-branch structure of cavitation cloud and Plateau boundary of soap bubbles are compared. Copyright © 2018 Elsevier B.V. All rights reserved.

Thermal stability and structural changes in bacterial toxins responsible for food poisoning

PubMed Central

Regenthal, Paulina; Hansen, Jesper S.; André, Ingemar

2017-01-01

The staphylococcal enterotoxins (SEs) are secreted by the bacteria Staphylococcus aureus and are the most common causative agent in staphylococcal food poisoning. The staphylococcal enterotoxin A (SEA) has been associated with large staphylococcal food poisoning outbreaks, but newer identified SEs, like staphylococcal enterotoxin H (SEH) has recently been shown to be present at similar levels as SEA in food poisoning outbreaks. Thus, we set out to investigate the thermo-stability of the three-dimensional structures of SEA, SEH and staphylococcal enterotoxin E (SEE), since heat inactivation is a common method to inactivate toxins during food processing. Interestingly, the investigated toxins behaved distinctly different upon heating. SEA and SEE were more stable at slightly acidic pH values, while SEH adopted an extremely stable structure at neutral pH, with almost no effects on secondary structural elements upon heating to 95°C, and with reversible formation of tertiary structure upon subsequent cooling to room temperature. Taken together, the data suggests that the family of staphylococcal enterotoxins have different ability to withstand heat, and thus the exact profile of heat inactivation for all SEs causing food poisoning needs to be considered to improve food safety. PMID:28207867

Improved measurements of RNA structure conservation with generalized centroid estimators.

PubMed

Okada, Yohei; Saito, Yutaka; Sato, Kengo; Sakakibara, Yasubumi

2011-01-01

Identification of non-protein-coding RNAs (ncRNAs) in genomes is a crucial task for not only molecular cell biology but also bioinformatics. Secondary structures of ncRNAs are employed as a key feature of ncRNA analysis since biological functions of ncRNAs are deeply related to their secondary structures. Although the minimum free energy (MFE) structure of an RNA sequence is regarded as the most stable structure, MFE alone could not be an appropriate measure for identifying ncRNAs since the free energy is heavily biased by the nucleotide composition. Therefore, instead of MFE itself, several alternative measures for identifying ncRNAs have been proposed such as the structure conservation index (SCI) and the base pair distance (BPD), both of which employ MFE structures. However, these measurements are unfortunately not suitable for identifying ncRNAs in some cases including the genome-wide search and incur high false discovery rate. In this study, we propose improved measurements based on SCI and BPD, applying generalized centroid estimators to incorporate the robustness against low quality multiple alignments. Our experiments show that our proposed methods achieve higher accuracy than the original SCI and BPD for not only human-curated structural alignments but also low quality alignments produced by CLUSTAL W. Furthermore, the centroid-based SCI on CLUSTAL W alignments is more accurate than or comparable with that of the original SCI on structural alignments generated with RAF, a high quality structural aligner, for which twofold expensive computational time is required on average. We conclude that our methods are more suitable for genome-wide alignments which are of low quality from the point of view on secondary structures than the original SCI and BPD.

Sum Frequency Generation Vibrational Spectroscopy Studies on ModelPeptide Adsorption at the Hydrophobic Solid-Water and HydrophilicSolid-Water Interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

York, Roger L.

2007-01-01

Sum frequency generation (SFG) vibrational spectroscopy has been used to study the interfacial structure of several polypeptides and amino acids adsorbed to hydrophobic and hydrophilic surfaces under a variety of experimental conditions. Peptide sequence, peptide chain length, peptide hydrophobicity, peptide side-chain type, surface hydrophobicity, and solution ionic strength all affect an adsorbed peptide's interfacial structure. Herein, it is demonstrated that with the choice of simple, model peptides and amino acids, surface specific SFG vibrational spectroscopy can be a powerful tool to elucidate the interfacial structure of these adsorbates. Herein, four experiments are described. In one, a series of isosequential amphiphilicmore » peptides are synthesized and studied when adsorbed to both hydrophobic and hydrophilic surfaces. On hydrophobic surfaces of deuterated polystyrene, it was determined that the hydrophobic part of the peptide is ordered at the solid-liquid interface, while the hydrophilic part of the peptide appears to have a random orientation at this interface. On a hydrophilic surface of silica, it was determined that an ordered peptide was only observed if a peptide had stable secondary structure in solution. In another experiment, the interfacial structure of a model amphiphilic peptide was studied as a function of the ionic strength of the solution, a parameter that could change the peptide's secondary structure in solution. It was determined that on a hydrophobic surface, the peptide's interfacial structure was independent of its structure in solution. This was in contrast to the adsorbed structure on a hydrophilic surface, where the peptide's interfacial structure showed a strong dependence on its solution secondary structure. In a third experiment, the SFG spectra of lysine and proline amino acids on both hydrophobic and hydrophilic surfaces were obtained by using a different experimental geometry that increases the SFG signal. Upon comparison of these spectra to the SFG spectra of interfacial polylysine and polyproline it was determined that the interfacial structure of a peptide is strongly dependent on its chain length. Lastly, SFG spectroscopy has been extended to the Amide I vibrational mode of a peptide (which is sensitive to peptide secondary structure) by building a new optical parametric amplifier based on lithium thioindate. Evidence is presented that suggests that the interfacial secondary structure of a peptide can be perturbed by a surface.« less

A global sampling approach to designing and reengineering RNA secondary structures.

PubMed

Levin, Alex; Lis, Mieszko; Ponty, Yann; O'Donnell, Charles W; Devadas, Srinivas; Berger, Bonnie; Waldispühl, Jérôme

2012-11-01

The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.e. mutated) to adopt the desired folding properties. Although computationally inexpensive, this approach raises several questions such as (i) the influence of the seed; and (ii) the efficiency of single-path directed searches that may be affected by energy barriers in the mutational landscape. In this article, we present RNA-ensign, a novel paradigm for RNA design. Instead of taking a progressive adaptive walk driven by local search criteria, we use an efficient global sampling algorithm to examine large regions of the mutational landscape under structural and thermodynamical constraints until a solution is found. When considering the influence of the seeds and the target secondary structures, our results show that, compared to single-path directed searches, our approach is more robust, succeeds more often and generates more thermodynamically stable sequences. An ensemble approach to RNA design is thus well worth pursuing as a complement to existing approaches. RNA-ensign is available at http://csb.cs.mcgill.ca/RNAensign.

A global sampling approach to designing and reengineering RNA secondary structures

PubMed Central

Levin, Alex; Lis, Mieszko; Ponty, Yann; O’Donnell, Charles W.; Devadas, Srinivas; Berger, Bonnie; Waldispühl, Jérôme

2012-01-01

The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.e. mutated) to adopt the desired folding properties. Although computationally inexpensive, this approach raises several questions such as (i) the influence of the seed; and (ii) the efficiency of single-path directed searches that may be affected by energy barriers in the mutational landscape. In this article, we present RNA-ensign, a novel paradigm for RNA design. Instead of taking a progressive adaptive walk driven by local search criteria, we use an efficient global sampling algorithm to examine large regions of the mutational landscape under structural and thermodynamical constraints until a solution is found. When considering the influence of the seeds and the target secondary structures, our results show that, compared to single-path directed searches, our approach is more robust, succeeds more often and generates more thermodynamically stable sequences. An ensemble approach to RNA design is thus well worth pursuing as a complement to existing approaches. RNA-ensign is available at http://csb.cs.mcgill.ca/RNAensign. PMID:22941632

Effect of pulsed electric field (PEF) on structures and antioxidant activity of soybean source peptides-SHCMN.

PubMed

Lin, Songyi; Liang, Rong; Li, Xingfang; Xing, Jie; Yuan, Yuan

2016-12-15

Recently, high-intensity pulsed electric field (PEF) has successfully used in improvement of antioxidant activity. Ser-His-Cys-Met-Asn (SHCMN) obtained from soybean protein was chosen to investigate the phenomenon of antioxidant activity improvement. Effects of PEF treatment on antioxidant activity of SHCMN were evaluated by DPPH radical inhibition. Nuclear magnetic resonance (NMR), mid-infrared (MIR), circular dichroism (CD) were used to analyze structures of SHCMN. Two-factor-at-a-time results show that DPPH radical inhibition of SHCMN is significantly (P<0.05) increased to 94.35±0.03% at conditions of electric field intensity of 5kV/cm, pulse frequency of 2400Hz, and retention time of 2h. In addition, MIR and NMR spectra show that the basic structure of peptides SHCMN is stable by PEF treatment. But the secondary structures (α-helix, β-turn, and random coil) can be affected and zeta potential of PEF-treated SHCNM was reduced to 0.59±0.03mV. The antioxidant activity improvement of SHCMN might result from the changes of secondary structures and zeta potential. Copyright © 2016 Elsevier Ltd. All rights reserved.

Preparation of Stable Amyloid-β Oligomers Without Perturbative Methods.

PubMed

Kotler, Samuel A; Ramamoorthy, Ayyalusamy

2018-01-01

Soluble amyloid-β (Aβ) oligomers have become a focal point in the study of Alzheimer's disease due to their ability to elicit cytotoxicity. A number of recent studies have concentrated on the structural characterization of soluble Aβ oligomers to gain insight into their mechanism of toxicity. Consequently, providing reproducible protocols for the preparation of such oligomers is of utmost importance. The method presented in this chapter details a protocol for preparing an Aβ oligomer, with a primarily disordered secondary structure, without the need for chemical modification or amino acid substitution. Due to the stability of these disordered Aβ oligomers and the reproducibility with which they form, they are amenable for biophysical and high-resolution structural characterization.

Risk prediction in stable cardiovascular disease using a high-sensitivity cardiac troponin T single biomarker strategy compared to the ESC-SCORE.

PubMed

Biener, Moritz; Giannitsis, Evangelos; Kuhner, Manuel; Zelniker, Thomas; Mueller-Hennessen, Matthias; Vafaie, Mehrshad; Stoyanov, Kiril M; Neumann, Franz-Josef; Katus, Hugo A; Hochholzer, Willibald; Valina, Christian Marc

2018-01-01

To evaluate the prognostic performance of high-sensitivity cardiac troponin T (hs-cTnT) compared with the ESC-SCORE. We included low-risk outpatients with stable cardiovascular (CV) disease categorised into need for non-secondary and secondary prevention. The prognostication of hs-cTnT at index visit was compared with the European Society of Cardiology-Systematic COronary Risk Evaluation (ESC-SCORE) with respect to all-cause mortality (ACM) and two composite endpoints (ACM, acute myocardial infarction (AMI) and stroke and ACM, AMI, stroke and rehospitalisation for acute coronary syndrome (ACS) and decompensated heart failure (DHF)). Within a median follow-up of 796 days, a total of 16 deaths, 32 composite endpoints of ACM, AMI and stroke and 83 composite endpoints of ACM, AMI, stroke, rehospitalisation for ACS and DHF were observed among 693 stable low-risk outpatients. Using C-statistics, measurement of hs-cTnT alone outperformed the ESC-SCORE for the prediction of ACM in the entire study population (Δarea under the curve (AUC) 0.221, p=0.0039) and both prevention groups (non-secondary: ΔAUC 0.164, p=0.0208; secondary: ΔAUC 0.264, p=0.0134). For the prediction of all other secondary endpoints, hs-cTnT was at least as effective as the ESC-SCORE, both in secondary and non-secondary prevention. Using continuous and categorical net reclassification improvement and integrated discrimination improvement, hs-cTnT significantly improved reclassification regarding all endpoints in the entire population and in the secondary prevention cohort. In non-secondary prevention, hs-cTnT improved reclassification only for ACM. The results were confirmed in an independent external cohort on 2046 patients. Hs-cTnT is superior to the multivariable ESC-SCORE for the prediction of ACM and a composite endpoint in stable outpatients with and without relevant CV disease. NCT01954303; Pre-results.

Understanding peptide competitive inhibition of botulinum neurotoxin A binding to SV2 protein via molecular dynamics simulations.

PubMed

Chang, Shan; He, Hong-Qiu; Shen, Lin; Wan, Hua

2015-10-01

Botulinum neurotoxins (BoNTs) are known as the most toxic natural substances. Synaptic vesicle protein 2 (SV2) has been proposed to be a protein receptor for BoNT/A. Recently, two short peptides (BoNT/A-A2 and SV2C-A3) were designed to inhibit complex formation between the BoNT/A receptor-binding domain (BoNT/A-RBD) and the synaptic vesicle protein 2C luminal domain (SV2C-LD). In this article, the two peptide complex systems are studied by molecular dynamics (MD) simulations. The structural stability analysis indicates that BoNT/A-A2 system is more stable than SV2C-A3 system. The conformational analysis implies that the β-sheet in BoNT/A-A2 system maintains its secondary structure but the two β-strands in SV2C-A3 system have remarkable conformational changes. Based on the calculation of hydrogen bonds, hydrophobic interactions and cation-π interactions, it is found that the internal hydrogen bonds play crucial roles in the structural stability of the peptides. Because of the stable secondary structure, the β-sheet in BoNT/A-A2 system establishes effective interactions at the interface and inhibits BoNT/A-RBD binding to SV2C-LD. In contrast, without other β-strands forming internal hydrogen bonds, the two isolated β-strands in SV2C-A3 system become the random coil. This conformational change breaks important hydrogen bonds and weakens cation-π interaction in the interface, so the complex formation is only partially inhibited by the two β-strands. These results are consistent with experimental studies and may be helpful in understanding the inhibition mechanisms of peptide inhibitors. © 2015 Wiley Periodicals, Inc.

Terminal sequence importance of de novo proteins from binary-patterned library: stable artificial proteins with 11- or 12-amino acid alphabet.

PubMed

Okura, Hiromichi; Takahashi, Tsuyoshi; Mihara, Hisakazu

2012-06-01

Successful approaches of de novo protein design suggest a great potential to create novel structural folds and to understand natural rules of protein folding. For these purposes, smaller and simpler de novo proteins have been developed. Here, we constructed smaller proteins by removing the terminal sequences from stable de novo vTAJ proteins and compared stabilities between mutant and original proteins. vTAJ proteins were screened from an α3β3 binary-patterned library which was designed with polar/ nonpolar periodicities of α-helix and β-sheet. vTAJ proteins have the additional terminal sequences due to the method of constructing the genetically repeated library sequences. By removing the parts of the sequences, we successfully obtained the stable smaller de novo protein mutants with fewer amino acid alphabets than the originals. However, these mutants showed the differences on ANS binding properties and stabilities against denaturant and pH change. The terminal sequences, which were designed just as flexible linkers not as secondary structure units, sufficiently affected these physicochemical details. This study showed implications for adjusting protein stabilities by designing N- and C-terminal sequences.

Comprehensive computational design of ordered peptide macrocycles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hosseinzadeh, Parisa; Bhardwaj, Gaurav; Mulligan, Vikram Khipple

Mixed chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to-date, but there is currently no way to systematically search through the structural space spanned by such compounds for new drug candidates. Natural proteins do not provide a useful guide: peptide macrocycles lack regular secondary structures and hydrophobic cores and have different backbone torsional constraints. Hence the development of new peptide macrocycles has been approached by modifying natural products or using library selection methods; the former is limited by the small number of known structures, and the latter by the limited size and diversity accessible throughmore » library-based methods. To overcome these limitations, here we enumerate the stable structures that can be adopted by macrocyclic peptides composed of L and D amino acids. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. We synthesize and characterize by NMR twelve 7-10 residue macrocycles, 9 of which have structures very close to the design models in solution. NMR structures of three 11-14 residue bicyclic designs are also very close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide based macrocycles unparalleled for other molecular systems, and vastly increase the available starting scaffolds for both rational drug design and library selection methods.« less

Transcription blockage by stable H-DNA analogs in vitro

PubMed Central

Pandey, Shristi; Ogloblina, Anna M.; Belotserkovskii, Boris P.; Dolinnaya, Nina G.; Yakubovskaya, Marianna G.; Mirkin, Sergei M.; Hanawalt, Philip C.

2015-01-01

DNA sequences that can form unusual secondary structures are implicated in regulating gene expression and causing genomic instability. H-palindromes are an important class of such DNA sequences that can form an intramolecular triplex structure, H-DNA. Within an H-palindrome, the H-DNA and canonical B-DNA are in a dynamic equilibrium that shifts toward H-DNA with increased negative supercoiling. The interplay between H- and B-DNA and the fact that the process of transcription affects supercoiling makes it difficult to elucidate the effects of H-DNA upon transcription. We constructed a stable structural analog of H-DNA that cannot flip into B-DNA, and studied the effects of this structure on transcription by T7 RNA polymerase in vitro. We found multiple transcription blockage sites adjacent to and within sequences engaged in this triplex structure. Triplex-mediated transcription blockage varied significantly with changes in ambient conditions: it was exacerbated in the presence of Mn2+ or by increased concentrations of K+ and Li+. Analysis of the detailed pattern of the blockage suggests that RNA polymerase is sterically hindered by H-DNA and has difficulties in unwinding triplex DNA. The implications of these findings for the biological roles of triple-stranded DNA structures are discussed. PMID:26101261

Principles for computational design of binding antibodies

PubMed Central

Pszolla, M. Gabriele; Lapidoth, Gideon D.; Norn, Christoffer; Dym, Orly; Unger, Tamar; Albeck, Shira; Tyka, Michael D.; Fleishman, Sarel J.

2017-01-01

Natural proteins must both fold into a stable conformation and exert their molecular function. To date, computational design has successfully produced stable and atomically accurate proteins by using so-called “ideal” folds rich in regular secondary structures and almost devoid of loops and destabilizing elements, such as cavities. Molecular function, such as binding and catalysis, however, often demands nonideal features, including large and irregular loops and buried polar interaction networks, which have remained challenging for fold design. Through five design/experiment cycles, we learned principles for designing stable and functional antibody variable fragments (Fvs). Specifically, we (i) used sequence-design constraints derived from antibody multiple-sequence alignments, and (ii) during backbone design, maintained stabilizing interactions observed in natural antibodies between the framework and loops of complementarity-determining regions (CDRs) 1 and 2. Designed Fvs bound their ligands with midnanomolar affinities and were as stable as natural antibodies, despite having >30 mutations from mammalian antibody germlines. Furthermore, crystallographic analysis demonstrated atomic accuracy throughout the framework and in four of six CDRs in one design and atomic accuracy in the entire Fv in another. The principles we learned are general, and can be implemented to design other nonideal folds, generating stable, specific, and precise antibodies and enzymes. PMID:28973872

Solution structure of dimeric Mnt repressor (1-76).

PubMed

Burgering, M J; Boelens, R; Gilbert, D E; Breg, J N; Knight, K L; Sauer, R T; Kaptein, R

1994-12-20

Wild-type Mnt repressor of Salmonella bacteriophage P22 is a tetrameric protein of 82 residues per monomer. A C-terminal deletion mutant of the repressor denoted Mnt (1-76) is a dimer in solution. The structure of this dimer has been determined using NMR. The NMR assignments of the majority of the 1H, 15N, and 13C resonances were obtained using 2D and triple-resonance 3D techniques. Elements of secondary structure were identified on the basis of characteristic sequential and medium range NOEs. For the structure determination more than 1000 NOEs per monomer were obtained, and structures were generated using distance geometry and restrained simulated annealing calculations. The discrimination of intra- vs intermonomer NOEs was based upon the observation of intersubunit NOEs in [15N,13C] double half-filtered NOESY experiments. The N-terminal part of Mnt (residues 1-44), which shows a 40% sequence homology with the Arc repressor, has a similar secondary and tertiary structure. Mnt (1-76) continues with a loop region of irregular structure, a third alpha-helix, and a random coil C-terminal peptide. Analysis of the secondary structure NOEs, the exchange rates, and the backbone chemical shifts suggests that the carboxy-terminal third helix is less stable than the remainder of the protein, but the observation of intersubunit NOEs for this part of the protein enables the positioning of this helix. The rsmd's between the backbone atoms of the N-terminal part of the Mnt repressor (residues 5-43, 5'-43') and the Arc repressor is 1.58 A, and between this region and the corresponding part of the MetJ repressor 1.43 A.

Helical self-organization and hierarchical self-assembly of an oligoheterocyclic pyridine-pyridazine strand into extended supramolecular fibers.

PubMed

Cuccia, Louis A; Ruiz, Eliseo; Lehn, Jean-Marie; Homo, Jean-Claude; Schmutz, Marc

2002-08-02

The synthesis and characterization of an alternating pyridine-pyridazine strand comprising thirteen heterocycles are described. Spontaneous folding into a helical secondary structure is based on a general molecular self-organization process enforced by the conformational information encoded within the primary structure of the molecular strand itself. Conformational control based on heterocyclic "helicity codons" illustrates a strategy for designing folding properties into synthetic oligomers (foldamers). Strong intermolecular interactions of the highly ordered lock-washer subunits of compound 3 results in hierarchical supramolecular self-assembly into protofibrils and fibrils. Compound 3 also forms mechanically stable two-dimensional Langmuir-Blodgett and cast thin films.

Synthesis and Structure of Hypervalent Iodine(III) Reagents Containing Phthalimidate and Application to Oxidative Amination Reactions.

PubMed

Kiyokawa, Kensuke; Kosaka, Tomoki; Kojima, Takumi; Minakata, Satoshi

2015-11-09

A new class of hypervalent iodine reagents containing phthalimidate was synthesized, and structurally characterized by X-ray analysis. The benziodoxole-based reagent displays satisfactory solubility in common organic solvents and is reasonably stable in solution as well as in the solid state. The reagent was used for the oxidative amination of the C(sp(3))-H bond of N,N-dimethylanilines. In addition, the reagent was also applicable to oxidative amination with rearrangement of trialkylamines as well as enamines that were prepared in situ from secondary amines and aldehydes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermal stability, storage and release of proteins with tailored fit in silica

NASA Astrophysics Data System (ADS)

Chen, Yun-Chu; Smith, Tristan; Hicks, Robert H.; Doekhie, Aswin; Koumanov, Francoise; Wells, Stephen A.; Edler, Karen J.; van den Elsen, Jean; Holman, Geoffrey D.; Marchbank, Kevin J.; Sartbaeva, Asel

2017-04-01

Biological substances based on proteins, including vaccines, antibodies, and enzymes, typically degrade at room temperature over time due to denaturation, as proteins unfold with loss of secondary and tertiary structure. Their storage and distribution therefore relies on a “cold chain” of continuous refrigeration; this is costly and not always effective, as any break in the chain leads to rapid loss of effectiveness and potency. Efforts have been made to make vaccines thermally stable using treatments including freeze-drying (lyophilisation), biomineralisation, and encapsulation in sugar glass and organic polymers. Here for the first time we show that proteins can be enclosed in a deposited silica “cage”, rendering them stable against denaturing thermal treatment and long-term ambient-temperature storage, and subsequently released into solution with their structure and function intact. This “ensilication” method produces a storable solid protein-loaded material without the need for desiccation or freeze-drying. Ensilication offers the prospect of a solution to the “cold chain” problem for biological materials, in particular for vaccines.

Thermal stability, storage and release of proteins with tailored fit in silica.

PubMed

Chen, Yun-Chu; Smith, Tristan; Hicks, Robert H; Doekhie, Aswin; Koumanov, Francoise; Wells, Stephen A; Edler, Karen J; van den Elsen, Jean; Holman, Geoffrey D; Marchbank, Kevin J; Sartbaeva, Asel

2017-04-24

Biological substances based on proteins, including vaccines, antibodies, and enzymes, typically degrade at room temperature over time due to denaturation, as proteins unfold with loss of secondary and tertiary structure. Their storage and distribution therefore relies on a "cold chain" of continuous refrigeration; this is costly and not always effective, as any break in the chain leads to rapid loss of effectiveness and potency. Efforts have been made to make vaccines thermally stable using treatments including freeze-drying (lyophilisation), biomineralisation, and encapsulation in sugar glass and organic polymers. Here for the first time we show that proteins can be enclosed in a deposited silica "cage", rendering them stable against denaturing thermal treatment and long-term ambient-temperature storage, and subsequently released into solution with their structure and function intact. This "ensilication" method produces a storable solid protein-loaded material without the need for desiccation or freeze-drying. Ensilication offers the prospect of a solution to the "cold chain" problem for biological materials, in particular for vaccines.

Symmetrical collision of multiple vortex rings

NASA Astrophysics Data System (ADS)

Hernández, R. H.; Reyes, T.

2017-10-01

In this work, we investigate the motion, interaction, and simultaneous collision between many initially stable vortex rings arranged symmetrically in two initial configurations, three and six rings making an angle of 60 and 120° between their straight path lines, respectively. We report results for laminar vortex rings in air obtained through numerical simulations of the ring velocity, pressure, and vorticity fields, both in free flight and during the entire collision. Each collision was studied for small Reynolds numbers R e <1 03 based on both the self-induced velocity and diameter of the ring. The case of three rings produces secondary vortical structures formed by laterally expanding dipolar arms with top and bottom secondary vortex rings. The case of six colliding rings produces, as secondary structures, two big rings moving in opposite directions, a process that reminds us of the head-on collision of two rings [T. T. Lim and T. B. Nickels, "Instability and reconnection in the head-on collision of two vortex rings," Nature 357, 225-227 (1992)] under a hypothetical time reversal transformation. Both collisions display a characteristic kinetic energy evolution where mean collision stages can be identified within the range of Reynolds numbers investigated here.

Structural and Functional Characterization of the Recombinant Death Domain from Death-Associated Protein Kinase

PubMed Central

Dioletis, Evangelos; Dingley, Andrew J.; Driscoll, Paul C.

2013-01-01

Death-associated protein kinase (DAPk) is a calcium/calmodulin-regulated Ser/Thr-protein kinase that functions at an important point of integration for cell death signaling pathways. DAPk has a structurally unique multi-domain architecture, including a C-terminally positioned death domain (DD) that is a positive regulator of DAPk activity. In this study, recombinant DAPk-DD was observed to aggregate readily and could not be prepared in sufficient yield for structural analysis. However, DAPk-DD could be obtained as a soluble protein in the form of a translational fusion protein with the B1 domain of streptococcal protein G. In contrast to other DDs that adopt the canonical six amphipathic α-helices arranged in a compact fold, the DAPk-DD was found to possess surprisingly low regular secondary structure content and an absence of a stable globular fold, as determined by circular dichroism (CD), NMR spectroscopy and a temperature-dependent fluorescence assay. Furthermore, we measured the in vitro interaction between extracellular-regulated kinase-2 (ERK2) and various recombinant DAPk-DD constructs. Despite the low level of structural order, the recombinant DAPk-DD retained the ability to interact with ERK2 in a 1∶1 ratio with a K d in the low micromolar range. Only the full-length DAPk-DD could bind ERK2, indicating that the apparent ‘D-motif’ located in the putative sixth helix of DAPk-DD is not sufficient for ERK2 recognition. CD analysis revealed that binding of DAPk-DD to ERK2 is not accompanied by a significant change in secondary structure. Taken together our data argue that the DAPk-DD, when expressed in isolation, does not adopt a classical DD fold, yet in this state retains the capacity to interact with at least one of its binding partners. The lack of a stable globular structure for the DAPk-DD may reflect either that its folding would be supported by interactions absent in our experimental set-up, or a limitation in the structural bioinformatics assignment of the three-dimensional structure. PMID:23922916

Structural and functional characterization of the recombinant death domain from death-associated protein kinase.

PubMed

Dioletis, Evangelos; Dingley, Andrew J; Driscoll, Paul C

2013-01-01

Death-associated protein kinase (DAPk) is a calcium/calmodulin-regulated Ser/Thr-protein kinase that functions at an important point of integration for cell death signaling pathways. DAPk has a structurally unique multi-domain architecture, including a C-terminally positioned death domain (DD) that is a positive regulator of DAPk activity. In this study, recombinant DAPk-DD was observed to aggregate readily and could not be prepared in sufficient yield for structural analysis. However, DAPk-DD could be obtained as a soluble protein in the form of a translational fusion protein with the B1 domain of streptococcal protein G. In contrast to other DDs that adopt the canonical six amphipathic α-helices arranged in a compact fold, the DAPk-DD was found to possess surprisingly low regular secondary structure content and an absence of a stable globular fold, as determined by circular dichroism (CD), NMR spectroscopy and a temperature-dependent fluorescence assay. Furthermore, we measured the in vitro interaction between extracellular-regulated kinase-2 (ERK2) and various recombinant DAPk-DD constructs. Despite the low level of structural order, the recombinant DAPk-DD retained the ability to interact with ERK2 in a 1∶1 ratio with a K d in the low micromolar range. Only the full-length DAPk-DD could bind ERK2, indicating that the apparent 'D-motif' located in the putative sixth helix of DAPk-DD is not sufficient for ERK2 recognition. CD analysis revealed that binding of DAPk-DD to ERK2 is not accompanied by a significant change in secondary structure. Taken together our data argue that the DAPk-DD, when expressed in isolation, does not adopt a classical DD fold, yet in this state retains the capacity to interact with at least one of its binding partners. The lack of a stable globular structure for the DAPk-DD may reflect either that its folding would be supported by interactions absent in our experimental set-up, or a limitation in the structural bioinformatics assignment of the three-dimensional structure.

Acetaldehyde-induced structural and conformational alterations in human immunoglobulin G: A physicochemical and multi-spectroscopic study.

PubMed

Waris, Sana; Habib, Safia; Tantry, Irfan Qadir; Khan, Rizwan Hasan; Mahmood, Riaz; Ali, Asif

2018-07-01

Acetaldehyde is a reactive aldehyde produced as an intermediate of alcohol metabolism and tobacco pyrolysis. It has the potential to interact with different biomolecules in various tissues which results in the formation of stable, unstable and covalent adducts. This causes structural and functional modifications that may lead to severe complications such as cancer. This study has probed the structural modifications in human immunoglobulin G (IgG) as a function of different concentrations of acetaldehyde in the presence of reducing agent, sodium borohydride. Acetaldehyde mediated modifications in IgG have been characterised by various physicochemical techniques. UV-spectrophotometry showed that acetaldehyde modified IgG exhibited marked increase in hyperchromicity. Fluorescence studies revealed a significant quenching of tryptophan fluorescence which resulted in loss of β-sheet secondary structure that was confirmed by circular dichroic analysis. Gross structural changes in the morphology of IgG were confirmed by increase in mass and hydrodynamic radius of this glycoprotein along with the appearance of fibrillar structures in modified IgG, when compared to the granular structure of the native form of IgG observed by scanning electron microscope. The results indicate that acetaldehyde causes alterations in the secondary and tertiary structure of the protein leading to diminution of normal function of IgG molecule. Copyright © 2018 Elsevier B.V. All rights reserved.

Purification, characterisation and salt-tolerance molecular mechanisms of aspartyl aminopeptidase from Aspergillus oryzae 3.042.

PubMed

Gao, Xianli; Yin, Yiyun; Zhou, Cunshan

2018-02-01

A salt-tolerant aspartyl aminopeptidase (approximately 57kDa) from Aspergillus oryzae 3.042 was purified and identified. Specific inhibitor experiments indicated that it was an aminopeptidase containing Zn 2+ . Its optimal and stable pH values and temperatures were 7 and 50°C, respectively. Its relative activity remained beyond 30% in 3M NaCl solution for 15d, and its K m and V max were slightly affected in 3M NaCl solution, indicating its excellent salt-tolerance. A comprehensive analysis including protein homology modelling, molecular dynamics simulation, secondary structure, acidic residues and hydrophobicity of interior residues demonstrated that aspartyl aminopeptidase had a greater stability than non-salt-tolerant protease in high salinity. Higher contents of ordered secondary structures, more salt bridges between hydrated surface acidic residues and specific basic residues and stronger hydrophobicity of interior residues were the salt-tolerance mechanisms of aspartyl aminopeptidase. Copyright © 2017. Published by Elsevier Ltd.

Kinetically trapped metastable intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.

PubMed

Sugimoto, Hayuki; Nakaura, Miho; Nishimura, Shigenori; Karita, Shuichi; Miyake, Hideo; Tanaka, Akiyoshi

2009-08-01

Refolding of a thermally unfolded disulfide-deficient mutant of the starch-binding domain of glucoamylase was investigated using differential scanning calorimetry, isothermal titration calorimetry, CD, and (1)H NMR. When the protein solution was rapidly cooled from a higher temperature, a kinetic intermediate was formed during refolding. The intermediate was unexpectedly stable compared with typical folding intermediates that have short half-lives. It was shown that this intermediate contained substantial secondary structure and tertiary packing and had the same binding ability with beta-cyclodextrin as the native state, suggesting that the intermediate is highly-ordered and native-like on the whole. These characteristics differ from those of partially folded intermediates such as molten globule states. Far-UV CD spectra showed that the secondary structure was once disrupted during the transition from the intermediate to the native state. These results suggest that the intermediate could be an off-pathway type, possibly a misfolded state, that has to undergo unfolding on its way to the native state.

Dyeing regions of oxidative hair dyes in human hair investigated by nanoscale secondary ion mass spectrometry.

PubMed

Kojima, Toru; Yamada, Hiromi; Yamamoto, Toshihiko; Matsushita, Yasuyuki; Fukushima, Kazuhiko

2013-06-01

To develop more effective oxidative hair coloring products, it is important to understand the localization of colored chromophores, which are formed from oxidative dyes, in the fine structure of hair. However, the dyeing regions of oxidative hair dyes in the fine structure of hair have not been extensively examined. In this study, we investigated the distribution and localization of colored chromophores formed by an oxidative hair coloring product in the fine structure of human hair by using a stable isotope-labeled oxidative dye with nanoscale secondary ion mass spectrometry (NanoSIMS). First, formation of the colored chromophore from a deuterium-labeled oxidative dye was examined by visible spectra similarly to a study of its formation using nonlabeled oxidative dye. Furthermore, the formation of binuclear indo dye containing deuterium in its chemical structure was confirmed using time-of-flight secondary ion mass spectrometry (TOF-SIMS) analysis. As a result of the NanoSIMS image on a cross-sectional dyed hair, although deuterium ions were detected in whole hair cross-section, quite a few of them were detected at particulate regions. These particulate regions of the dyed black hair in which deuterium ions were intensely detected were identified as melanin granules, by comparing the dyeing behaviors of black and white hair. NanoSIMS analysis revealed that melanin granules of black human hair are important dyeing regions in oxidative hair coloring. Copyright © 2013 Elsevier B.V. All rights reserved.

Electronic polarization stabilizes tertiary structure prediction of HP-36.

PubMed

Duan, Li L; Zhu, Tong; Zhang, Qing G; Tang, Bo; Zhang, John Z H

2014-04-01

Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although some intermediates were close to the native structure, the overall conformation was not stable. Further analysis revealed that the large structure fluctuation of loop and hydrophobic core regions was devoted mostly to the instability of the structure during MD simulation. The backbone root-mean-square deviation (RMSD) of the loop and hydrophobic core regions showed strong correlation with the backbone RMSD of the whole protein. The free energy landscape indicated that the distribution of main chain torsions in loop and turn regions was far away from the native state. Starting from an intermediate structure extracted from the initial AMBER simulation, HP-36 was found to generally fold to the native state under the dynamically adjusted polarized protein-specific charge (DPPC) simulation, while the peptide did not fold into the native structure when AMBER force filed was used. The two best folded structures were extracted and taken into further simulations in water employing AMBER03 charge and DPPC for 25 ns. Result showed that introducing polarization effect into interacting potential could stabilize the near-native protein structure.

Mental health trajectories among women in Australia as they age.

PubMed

Tran, Thach; Hammarberg, Karin; Ryan, Joanne; Lowthian, Judy; Freak-Poli, Rosanne; Owen, Alice; Kirkman, Maggie; Curtis, Andrea; Rowe, Heather; Brown, Helen; Ward, Stephanie; Britt, Carlene; Fisher, Jane

2018-05-23

To ascertain the trajectories of mental health among women in Australia assessed in repeat waves from their early 70 s to the end of their lives or their mid 80 s. Secondary analysis of data contributed by the 1921-26 cohort of the Australian Longitudinal Study of Women's Health Waves 1-6. Primary outcome was the 4-item SF-36 Vitality Subscale, which assesses mental health as life satisfaction, social participation, energy and enthusiasm. Structural, individual and intermediary factors were assessed using study-specific and standardised measures. Trajectories were identified using Growth Mixture Modelling and associations with baseline characteristics with Structural Equation Modelling. 12,432 women completed Survey One. Three mental health trajectories: stable high (77%); stable low (18.2%) and declining from high to low (4.8%) were identified. Compared to the stable high group, women in the stable low group were significantly less physically active, had more nutritional risks, more recent adverse life events, fewer social interactions and less social support, reported more stress and were more likely to have a serious illness or disability at Survey One. The declining group had similar characteristics to the stable high group, but were significantly more likely to report at baseline that they had experienced recent financial, physical and emotional elder abuse. These interact, but not directly with socioeconomic position and marital status. Mental health among older women is related to social relationships, general health, access to physical activity and healthy nutrition, coincidental adverse life events and experiences of interpersonal violence, in particular elder abuse.

Static voltage distribution between turns of secondary winding of air-core spiral strip transformer and its application

NASA Astrophysics Data System (ADS)

Zhang, Hong-bo; Liu, Jin-liang; Cheng, Xin-bing; Zhang, Yu

2011-09-01

The static voltage distribution between winding turns has great impact on output characteristics and lifetime of the air-core spiral strip pulse transformer (ACSSPT). In this paper, winding inductance was calculated by electromagnetic theory, so that the static voltage distribution between turns of secondary winding of ACSSPT was analyzed conveniently. According to theoretical analysis, a voltage gradient because of the turn-to-turn capacitance was clearly noticeable across the ground turns. Simulation results of Pspice and CST EM Studio codes showed that the voltage distribution between turns of secondary winding had linear increments from the output turn to the ground turn. In experiment, the difference in increased voltage between the ground turns and the output turns of a 20-turns secondary winding is almost 50%, which is believed to be responsible for premature breakdown of the insulation, particularly between the ground turns. The experimental results demonstrated the theoretical analysis and simulation results, which had important value for stable and long lifetime ACSSPT design. A new ACSSPT with improved structure has been used successfully in intense electron beam accelerators steadily.

Intermediate introns in nuclear genes of euglenids - are they a distinct type?

PubMed

Milanowski, Rafał; Gumińska, Natalia; Karnkowska, Anna; Ishikawa, Takao; Zakryś, Bożena

2016-02-29

Nuclear genes of euglenids contain two major types of introns: conventional spliceosomal and nonconventional introns. The latter are characterized by variable non-canonical borders, RNA secondary structure that brings intron ends together, and an unknown mechanism of removal. Some researchers also distinguish intermediate introns, which combine features of both types. They form a stable RNA secondary structure and are classified into two subtypes depending on whether they contain one (intermediate/nonconventional subtype) or both (conventional/intermediate subtype) canonical spliceosomal borders. However, it has been also postulated that most introns classified as intermediate could simply be special cases of conventional or nonconventional introns. Sequences of tubB, hsp90 and gapC genes from six strains of Euglena agilis were obtained. They contain four, six, and two or three introns, respectively (the third intron in the gapC gene is unique for just one strain). Conventional introns were present at three positions: two in the tubB gene (at one position conventional/intermediate introns were also found) and one in the gapC gene. Nonconventional introns are present at ten positions: two in the tubB gene (at one position intermediate/nonconventional introns were also found), six in hsp90 (at four positions intermediate/nonconventional introns were also found), and two in the gapC gene. Sequence and RNA secondary structure analyses of nonconventional introns confirmed that their most strongly conserved elements are base pairing nucleotides at positions +4, +5 and +6/ -8, -7 and -6 (in most introns CAG/CTG nucleotides were observed). It was also confirmed that the presence of the 5' GT/C end in intermediate/nonconventional introns is not the result of kinship with conventional introns, but is due to evolutionary pressure to preserve the purine at the 5' end. However, an example of a nonconventional intron with GC-AG ends was shown, suggesting the possibility of intron type conversion between nonconventional and conventional. Furthermore, an analysis of conventional introns revealed that the ability to form a stable RNA secondary structure by some introns is probably not a result of their relationship with nonconventional introns. It was also shown that acquisition of new nonconventional introns is an ongoing process and can be observed at the level of a single species. In the recently acquired intron in the gapC gene an extended direct repeats at the intron-exon junctions are present, suggesting that double-strand break repair process could be the source of new nonconventional introns.

Transcription blockage by stable H-DNA analogs in vitro.

PubMed

Pandey, Shristi; Ogloblina, Anna M; Belotserkovskii, Boris P; Dolinnaya, Nina G; Yakubovskaya, Marianna G; Mirkin, Sergei M; Hanawalt, Philip C

2015-08-18

DNA sequences that can form unusual secondary structures are implicated in regulating gene expression and causing genomic instability. H-palindromes are an important class of such DNA sequences that can form an intramolecular triplex structure, H-DNA. Within an H-palindrome, the H-DNA and canonical B-DNA are in a dynamic equilibrium that shifts toward H-DNA with increased negative supercoiling. The interplay between H- and B-DNA and the fact that the process of transcription affects supercoiling makes it difficult to elucidate the effects of H-DNA upon transcription. We constructed a stable structural analog of H-DNA that cannot flip into B-DNA, and studied the effects of this structure on transcription by T7 RNA polymerase in vitro. We found multiple transcription blockage sites adjacent to and within sequences engaged in this triplex structure. Triplex-mediated transcription blockage varied significantly with changes in ambient conditions: it was exacerbated in the presence of Mn(2+) or by increased concentrations of K(+) and Li(+). Analysis of the detailed pattern of the blockage suggests that RNA polymerase is sterically hindered by H-DNA and has difficulties in unwinding triplex DNA. The implications of these findings for the biological roles of triple-stranded DNA structures are discussed. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Bistable intrinsic charge fluctuations of a dust grain subject to secondary electron emission in a plasma.

PubMed

Shotorban, B

2015-10-01

A master equation was formulated to study intrinsic charge fluctuations of a grain in a plasma as ions and primary electrons are attached to the grain through collisional collection, and secondary electrons are emitted from the grain. Two different plasmas with Maxwellian and non-Maxwellian distributions were considered. The fluctuations could be bistable in either plasma when the secondary electron emission is present, as two stable macrostates, associated with two stable roots of the charge net current, may exist. Metastablity of fluctuations, manifested by the passage of the grain charge between two macrostates, was shown to be possible.

Study of the thermal stability of studtite by in situ Raman spectroscopy and DFT calculations

NASA Astrophysics Data System (ADS)

Colmenero, Francisco; Bonales, Laura J.; Cobos, Joaquín; Timón, Vicente

2017-03-01

The design of a safe spent nuclear fuel repository requires the knowledge of the stability of the secondary phases which precipitate when water reaches the fuel surface. Studtite is recognized as one of the secondary phases that play a key-role in the mobilization of the radionuclides contained in the spent fuel. Thereby, it has been identified as a product formed under oxidation conditions at the surface of the fuel, and recently found as a corrosion product in the Fukushima-Daiichi nuclear plant accident. Thermal stability is one of the properties that should be determined due to the high temperature of the fuel. In this work we report a detailed analysis of the structure and thermal stability of studtite. The structure has been studied both by experimental techniques (SEM, TGA, XRD and Raman spectroscopy) and theoretical DFT electronic structure and spectroscopic calculations. The comparison of the results allows us to perform for the first time the Raman bands assignment of the whole spectrum. The thermal stability of studtite has been analyzed by in situ Raman spectroscopy, with the aim of studying the effect of the heating rate and the presence of water. For this purpose, a new cell has been designed. The results show that studtite is stable under dry conditions only at temperatures below 30 °C, in contrast with the higher temperatures published up to date ( 130 °C). Opposite behaviour has been found when studtite is in contact with water; under these conditions studtite is stable up to 90 °C, what is consistent with the encounter of this phase after the Fukushima-Daiichi accident.

Study of the thermal stability of studtite by in situ Raman spectroscopy and DFT calculations.

PubMed

Colmenero, Francisco; Bonales, Laura J; Cobos, Joaquín; Timón, Vicente

2017-03-05

The design of a safe spent nuclear fuel repository requires the knowledge of the stability of the secondary phases which precipitate when water reaches the fuel surface. Studtite is recognized as one of the secondary phases that play a key-role in the mobilization of the radionuclides contained in the spent fuel. Thereby, it has been identified as a product formed under oxidation conditions at the surface of the fuel, and recently found as a corrosion product in the Fukushima-Daiichi nuclear plant accident. Thermal stability is one of the properties that should be determined due to the high temperature of the fuel. In this work we report a detailed analysis of the structure and thermal stability of studtite. The structure has been studied both by experimental techniques (SEM, TGA, XRD and Raman spectroscopy) and theoretical DFT electronic structure and spectroscopic calculations. The comparison of the results allows us to perform for the first time the Raman bands assignment of the whole spectrum. The thermal stability of studtite has been analyzed by in situ Raman spectroscopy, with the aim of studying the effect of the heating rate and the presence of water. For this purpose, a new cell has been designed. The results show that studtite is stable under dry conditions only at temperatures below 30°C, in contrast with the higher temperatures published up to date (~130°C). Opposite behaviour has been found when studtite is in contact with water; under these conditions studtite is stable up to 90°C, what is consistent with the encounter of this phase after the Fukushima-Daiichi accident. Copyright © 2016 Elsevier B.V. All rights reserved.

Chemoselective Installation of Amine Bonds on Proteins through Aza-Michael Ligation.

PubMed

Freedy, Allyson M; Matos, Maria J; Boutureira, Omar; Corzana, Francisco; Guerreiro, Ana; Akkapeddi, Padma; Somovilla, Víctor J; Rodrigues, Tiago; Nicholls, Karl; Xie, Bangwen; Jiménez-Osés, Gonzalo; Brindle, Kevin M; Neves, André A; Bernardes, Gonçalo J L

2017-12-20

Chemical modification of proteins is essential for a variety of important diagnostic and therapeutic applications. Many strategies developed to date lack chemo- and regioselectivity as well as result in non-native linkages that may suffer from instability in vivo and adversely affect the protein's structure and function. We describe here the reaction of N-nucleophiles with the amino acid dehydroalanine (Dha) in a protein context. When Dha is chemically installed in proteins, the addition of a wide-range N-nucleophiles enables the rapid formation of amine linkages (secondary and tertiary) in a chemoselective manner under mild, biocompatible conditions. These new linkages are stable at a wide range of pH values (pH 2.8 to 12.8), under reducing conditions (biological thiols such as glutathione) and in human plasma. This method is demonstrated for three proteins and is shown to be fully compatible with disulfide bridges, as evidenced by the selective modification of recombinant albumin that displays 17 structurally relevant disulfides. The practicability and utility of our approach is further demonstrated by the construction of a chemically modified C2A domain of Synaptotagmin-I protein that retains its ability to preferentially bind to apoptotic cells at a level comparable to the native protein. Importantly, the method was useful for building a homogeneous antibody-drug conjugate with a precise drug-to-antibody ratio of 2. The kinase inhibitor crizotinib was directly conjugated to Dha through its piperidine motif, and its antibody-mediated intracellular delivery results in 10-fold improvement of its cancer cell-killing efficacy. The simplicity and exquisite site-selectivity of the aza-Michael ligation described herein allows the construction of stable secondary and tertiary amine-linked protein conjugates without affecting the structure and function of biologically relevant proteins.

NMR structural and dynamical investigation of the isolated voltage-sensing domain of the potassium channel KvAP: implications for voltage gating.

PubMed

Shenkarev, Zakhar O; Paramonov, Alexander S; Lyukmanova, Ekaterina N; Shingarova, Lyudmila N; Yakimov, Sergei A; Dubinnyi, Maxim A; Chupin, Vladimir V; Kirpichnikov, Mikhail P; Blommers, Marcel J J; Arseniev, Alexander S

2010-04-28

The structure and dynamics of the isolated voltage-sensing domain (VSD) of the archaeal potassium channel KvAP was studied by high-resolution NMR. The almost complete backbone resonance assignment and partial side-chain assignment of the (2)H,(13)C,(15)N-labeled VSD were obtained for the protein domain solubilized in DPC/LDAO (2:1) mixed micelles. Secondary and tertiary structures of the VSD were characterized using secondary chemical shifts and NOE contacts. These data indicate that the spatial structure of the VSD solubilized in micelles corresponds to the structure of the domain in an open state of the channel. NOE contacts and secondary chemical shifts of amide protons indicate the presence of tightly bound water molecule as well as hydrogen bond formation involving an interhelical salt bridge (Asp62-R133) that stabilizes the overall structure of the domain. The backbone dynamics of the VSD was studied using (15)N relaxation measurements. The loop regions S1-S2 and S2-S3 were found mobile, while the S3-S4 loop (voltage-sensor paddle) was found stable at the ps-ns time scale. The moieties of S1, S2, S3, and S4 helices sharing interhelical contacts (at the level of the Asp62-R133 salt bridge) were observed in conformational exchange on the micros-ms time scale. Similar exchange-induced broadening of characteristic resonances was observed for the VSD solubilized in the membrane of lipid-protein nanodiscs composed of DMPC, DMPG, and POPC/DOPG lipids. Apparently, the observed interhelical motions represent an inherent property of the VSD of the KvAP channel and can play an important role in the voltage gating.

From Aβ Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations.

PubMed

Schwierz, Nadine; Frost, Christina V; Geissler, Phillip L; Zacharias, Martin

2017-02-02

Secondary nucleation pathways in which existing amyloid fibrils catalyze the formation of new aggregates and neurotoxic oligomers are of immediate importance for the onset and progression of Alzheimer's disease. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to study surface-activated secondary nucleation pathways at the extended lateral β-sheet surface of a preformed Aβ 9-40 filament. Calculation of free-energy profiles allows us to determine binding free energies and conformational intermediates for nucleation complexes consisting of 1-4 Aβ peptides. In addition, we combine the free-energy profiles with position-dependent diffusion profiles to extract complementary kinetic information and macroscopic growth rates. Single monomers bind to the β-sheet surface in a disordered, hydrophobically collapsed conformation, whereas dimers and larger oligomers can retain a cross-β conformation resembling a more ordered fibril structure. The association processes during secondary nucleation follow a dock/lock mechanism consisting of a fast initial encounter phase (docking) and a slow structural rearrangement phase (locking). The major driving forces for surface-activated secondary nucleation are the release of a large number of hydration water molecules and the formation of hydrophobic interface contacts, the latter being in contrast to the elongation process at filament tips, which is dominated by the formation of stable and highly specific interface hydrogen bonds. The calculated binding free energies and the association rates for the attachment of Aβ monomers and oligomers to the extended lateral β-sheet surface of the filament seed are higher compared to those for elongation at the filament tips, indicating that secondary nucleation pathways can become important once a critical concentration of filaments has formed.

Interaction of sucralose with whey protein: Experimental and molecular modeling studies

NASA Astrophysics Data System (ADS)

Zhang, Hongmei; Sun, Shixin; Wang, Yanqing; Cao, Jian

2017-12-01

The objective of this research was to study the interactions of sucralose with whey protein isolate (WPI) by using the three-dimensional fluorescence spectroscopy, circular dichroism spectroscopy and molecular modeling. The results showed that the peptide strands structure of WPI had been changed by sucralose. Sucralose binding induced the secondary structural changes and increased content of aperiodic structure of WPI. Sucralose decreased the thermal stability of WPI and acted as a structure destabilizer during the thermal unfolding process of protein. In addition, the existence of sucralose decreased the reversibility of the unfolding of WPI. Nonetheless, sucralose-WPI complex was less stable than protein alone. The molecular modeling result showed that van der Waals and hydrogen bonding interactions contribute to the complexation free binding energy. There are more than one possible binding sites of WPI with sucralose by surface binding mode.

Early Life on Earth and the Search for Extraterrestrial Biosignatures

NASA Technical Reports Server (NTRS)

Oehler, Dorothy Z.; House, Christopher

2014-01-01

In the last 2 years, scientists within the ARES Directorate at JSC have applied the technology of Secondary Ion Mass Spectrometry (SIMS) to individual organic structures preserved in Archean (approximately 3 billion years old) sediments on Earth. These organic structures are among the oldest on Earth that may be microfossils - structurally preserved remnants of ancient microbes. The SIMS work was done to determine the microfossils' stable carbon isotopic composition (delta C-13 values). This is the first time that such ancient, potential microfossils have been successfully analyzed for their individual delta C-13 values. The results support the interpretation that these structures are remnants of early life on Earth and that they may represent planktonic organisms that were widely distributed in the Earth's earliest oceans. This study has been accepted for publication in the journal Geology.

Subunit association as the stabilizing determinant for archaeal methionine adenosyltransferases.

PubMed

Garrido, Francisco; Alfonso, Carlos; Taylor, John C; Markham, George D; Pajares, María A

2009-07-01

Archaea contain a class of methionine adenosyltransferases (MATs) that exhibit substantially higher stability than their mesophilic counterparts. Their sequences are highly divergent, but preserve the essential active site motifs of the family. We have investigated the origin of this increased stability using chemical denaturation experiments on Methanococcus jannaschii MAT (Mj-MAT) and mutants containing single tryptophans in place of tyrosine residues. The results from fluorescence, circular dichroism, hydrodynamic, and enzyme activity measurements showed that the higher stability of Mj-MAT derives largely from a tighter association of its subunits in the dimer. Local fluorescence changes, interpreted using secondary structure predictions, further identify the least stable structural elements as the C-terminal ends of beta-strands E2 and E6, and the N-terminus of E3. Dimer dissociation however requires a wider perturbation of the molecule. Additional analysis was initially hindered by the lack of crystal structures for archaeal MATs, a limitation that we overcame by construction of a 3D-homology model of Mj-MAT. This model predicts preservation of the chain topology and three-domain organization typical of this family, locates the least stable structural elements at the flat contact surface between monomers, and shows that alterations in all three domains are required for dimer dissociation.

Quantitation of Oxidative Modifications of Commercial Human Albumin for Clinical Use.

PubMed

Takahashi, Teppei; Terada, Tomoyoshi; Arikawa, Hajime; Kizaki, Kazuha; Terawaki, Hiroyuki; Imai, Hajime; Itoh, Yoshinori; Era, Seiichi

2016-01-01

We investigated the quantitation of oxidative chemical modifications, such as thiol oxidation and carbonylation, in medical-grade human serum albumin (HSA) preparations, in comparison with those of healthy and diseased subjects. Four kinds of HSA products were obtained from three major suppliers in Japan. Eight male collegiate students and six healthy male volunteers were recruited as the young (21.6 years) and older (57.2 years) groups, respectively. Four male stable patients (64.3 years) treated with regular hemodialysis (HD) also enrolled in this study. Quantitative analyses for thiol oxidation and carbonylation were performed using HPLC and spectroscopic methods, respectively. Structural characterization was further investigated by differential scanning calorimetry (DSC) and circular dichroism (CD) spectropolarimetry. Significantly larger amounts of thiol-oxidized and carbonylated HSA products were observed than HSA obtained from healthy subjects. In the structural characterization, the midpoint temperature of the denaturation curve (Tm) analyzed by DSC was relatively high, and may have been caused by the added albumin-specific stabilizers, and CD-resolved secondary structure showed that HSA products had a helical conformation. Commercial HSA products for clinical use have a more thermally stable state and remain in a helix-rich structure, even though their specific amino acids (mainly Cys and Lys residues) are oxidatively modified.

Structure of the Yersinia pestis type III secretion chaperone SycH in complex with a stable fragment of YscM2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phan, Jason; Tropea, Joseph E.; Waugh, David S.

2010-11-16

Pathogenic Yersinia species use a type III secretion system to inject cytotoxic effector proteins directly into the cytosol of mammalian cells, where they neutralize the innate immune response by interfering with the signal-transduction pathways that control phagocytosis and inflammation. To be exported efficiently, some effectors must transiently associate with cognate cytoplasmic secretion chaperones. SycH is the chaperone for YopH, a potent eukaryotic-like protein tyrosine phosphatase that is essential for virulence. SycH also binds two negative regulators of type III secretion, YscM1 and YscM2, both of which share significant sequence homology with the chaperone-binding domain of YopH. Here, the structure ofmore » a complex between SycH and a stable fragment of YscM2 that was designed on the basis of limited proteolysis experiments is presented. The overall fold of SycH is very similar to the structures of other homodimeric secretion chaperones that have been determined to date. YscM2 wraps around SycH in an extended fashion, with some secondary but no tertiary structure, assuming a conformation distinct from the globular fold that it is predicted to adopt in the absence of SycH.« less

Search for Length Dependent Stable Structures of Polyglutamaine Proteins with Replica Exchange Molecular Dynamic

NASA Astrophysics Data System (ADS)

Kluber, Alexander; Hayre, Robert; Cox, Daniel

2012-02-01

Motivated by the need to find beta-structure aggregation nuclei for the polyQ diseases such as Huntington's, we have undertaken a search for length dependent structure in model polyglutamine proteins. We use the Onufriev-Bashford-Case (OBC) generalized Born implicit solvent GPU based AMBER11 molecular dynamics with the parm96 force field coupled with a replica exchange method to characterize monomeric strands of polyglutamine as a function of chain length and temperature. This force field and solvation method has been shown among other methods to accurately reproduce folded metastability in certain small peptides, and to yield accurately de novo folded structures in a millisecond time-scale protein. Using GPU molecular dynamics we can sample out into the microsecond range. Additionally, explicit solvent runs will be used to verify results from the implicit solvent runs. We will assess order using measures of secondary structure and hydrogen bond content.

Structural characterization of coagulant Moringa oleifera Lectin and its effect on hemostatic parameters.

PubMed

Luz, Luciana de Andrade; Silva, Mariana Cristina Cabral; Ferreira, Rodrigo da Silva; Santana, Lucimeire Aparecida; Silva-Lucca, Rosemeire Aparecida; Mentele, Reinhard; Oliva, Maria Luiza Vilela; Paiva, Patricia Maria Guedes; Coelho, Luana Cassandra Breitenbach Barroso

2013-07-01

Lectins are carbohydrate recognition proteins. cMoL, a coagulant Moringa oleifera Lectin, was isolated from seeds of the plant. Structural studies revealed a heat-stable and pH resistant protein with 101 amino acids, 11.67 theoretical pI and 81% similarity with a M. oleifera flocculent protein. Secondary structure content was estimated as 46% α-helix, 12% β-sheets, 17% β-turns and 25% unordered structures belonging to the α/β tertiary structure class. cMoL significantly prolonged the time required for blood coagulation, activated partial thromboplastin (aPTT) and prothrombin times (PT), but was not so effective in prolonging aPTT in asialofetuin presence. cMoL acted as an anticoagulant protein on in vitro blood coagulation parameters and at least on aPTT, the lectin interacted through the carbohydrate recognition domain. Copyright © 2013 Elsevier B.V. All rights reserved.

Study of the Radiation Resistance of Endohedral Fullerenes of Rare-Earth Elements and Their Water-Soluble Derivatives

NASA Astrophysics Data System (ADS)

Dubovskii, I. M.; Lebedev, V. T.; Shilin, V. A.; Szhogina, A. A.; Suyasova, M. V.; Sedov, V. P.

2018-01-01

Endohedral metallofullerenes Me@C2 n ( n = 30-50), their hydroxylated derivatives Me@C2 n (OH)38-40 ( Me = Tm, Ho, Eu, Sm, Co), and fullerenol C60(OH)38 have been synthesized The radiation resistance of these structures under irradiation in reactor by thermal and fast neutron fluxes in the fluence range of 1018-1019 cm-2 (cadmium ratio of 10) has been analyzed. Endofullerenols are shown to be more stable in comparison with initial endohedral fullerenes; the molecules containing Eu and Sm (atoms characterized by the largest slow-neutron absorption cross section) turned out to be most stable. The mechanism of the formation of secondary Eu and Sm endofullerenols is discussed taking into account the neutron capture and emission of γ quanta by excited nuclei, which acquire the recoil energy.

Clinical presentation and management of stable coronary artery disease in Austria.

PubMed

Pichlhöfer, Otto; Maier, Manfred; Badr-Eslam, Roza; Ristl, Robin; Zebrowska, Magdalena; Lang, Irene M

2017-01-01

Cardiovascular disease is the main cause of death in Austria. However, no systematic information exists regarding characteristics and treatments of contemporary patients with stable coronary artery disease (CAD) in Austria. We assembled two retrospective physicians' databases to describe demographics, clinical profiles, and therapeutic strategies in patients with stable CAD. In addition, we compared patient profiles of secondary care internists and hospital-based cardiologists with those of general practitioners in a primary care setting outside of hospital. The study population was identified from retrospective chart review of 1020 patients from 106 primary care physicians in Austria (ProCor II registry), and was merged with a previous similar database of 1280 patients under secondary care (ProCor I registry) to yield a total patient number of 2300. Female patients with stable CAD were older, had more angina and/or heart failure symptoms, and more depression than males. Female gender, type 2 diabetes mellitus, higher CCS class and asthma/COPD were predictors of elevated heart rate, while previous coronary events/revascularization predicted a lower heart rate in multivariate analysis. There were no significant differences with regard to characteristics and management of patients of general practitioners in the primary care setting versus internists in secondary care. Characteristics and treatments of unselected patients with stable ischemic heart disease in Austria resemble the pattern of large international registries of stable ischemic heart disease, with the exception that diabetes and systemic hypertension were more prevalent.

A quantum chemical study of the structures, stability, and spectroscopy of halogen- and hydrogen-boned complexes between cyanoacetaldehyde and hypochlorous acids

NASA Astrophysics Data System (ADS)

Tang, Qingjie; Guo, Zhenfu; Li, Qingzhong

2014-03-01

The complexes of cyanoacetaldehyde and hypohalous acid (HOX, X = Cl, Br, and I) have been investigated. They can form six different structures (A, B, C, D, E, and F), the former three structures are mainly combined through a N(O)⋯X halogen bond and the latter three structures are maintained mainly by a N(O)⋯H hydrogen bond, although other weaker interactions are also present in most structures. The hydrogen-bonded structures are more stable than the respective halogen-bonded structures. The Osbnd H and Osbnd X bonds in the halogen- and hydrogen-bonded complexes are lengthened and show an observed red shift, while those in the weaker secondary interactions are contracted and display a small blue shift. The orbital interactions in NBO analysis and the electron densities in AIM analysis provide useful and reliable information for the strength of each type of interaction in different structures.

Identifying intrinsically disordered protein regions likely to undergo binding-induced helical transitions.

PubMed

Glover, Karen; Mei, Yang; Sinha, Sangita C

2016-10-01

Many proteins contain intrinsically disordered regions (IDRs) lacking stable secondary and ordered tertiary structure. IDRs are often implicated in macromolecular interactions, and may undergo structural transitions upon binding to interaction partners. However, as binding partners of many protein IDRs are unknown, these structural transitions are difficult to verify and often are poorly understood. In this study we describe a method to identify IDRs that are likely to undergo helical transitions upon binding. This method combines bioinformatics analyses followed by circular dichroism spectroscopy to monitor 2,2,2-trifluoroethanol (TFE)-induced changes in secondary structure content of these IDRs. Our results demonstrate that there is no significant change in the helicity of IDRs that are not predicted to fold upon binding. IDRs that are predicted to fold fall into two groups: one group does not become helical in the presence of TFE and includes examples of IDRs that form β-strands upon binding, while the other group becomes more helical and includes examples that are known to fold into helices upon binding. Therefore, we propose that bioinformatics analyses combined with experimental evaluation using TFE may provide a general method to identify IDRs that undergo binding-induced disorder-to-helix transitions. Copyright © 2016 Elsevier B.V. All rights reserved.

Stability of Synthetic Cathinones in Urine.

PubMed

Glicksberg, Lindsay; Kerrigan, Sarah

2018-03-01

In this report, we evaluate the concentration, pH, temperature and analyte-dependent effects on cathinone stability in preserved human urine. A total of 22 synthetic cathinones were evaluated at 100 ng/mL and 1,000 ng/mL in pH 4 and pH 8 urine over 6 months. Specimens were stored at -20°C, 4°C, 20°C and 32°C. The stability of synthetic cathinones was highly dependent on urine pH and storage temperature. Cathinones were considerably more stable in acidic urine (pH 4) at low temperature. In alkaline urine (pH 8) at 32°C, significant losses (>20%) were observed within hours for the majority of drugs. In contrast, all drugs were stable in frozen and refrigerated urine at pH 4 for the duration of the study. These results highlight the importance of sample storage and the potential for pre-analytical changes in concentration during routine shipping and handling of specimens. Significant structural influence was also observed. Cathinones bearing a tertiary amine (pyrrolidine group) were significantly more stable than their secondary amine counterparts. The methylenedioxy group also exerted a significant stabilizing effect on both the tertiary and secondary amines. In the absence of the methylenedioxy group, no significant differences in stability were observed between the unsubstituted and ring substituted secondary amines. Half-lives at ambient temperature in pH 8 urine ranged from 9 h (3-fluoromethcathinone) to 4.3 months (methylenedioxypyrovalerone and 3,4-methylenedioxy-α-pyrrolidinobutiophenone), demonstrating the importance of analyte dependence, and the dual stabilizing effect of both the pyrollidine and methylenedioxy groups. Biological evidence may be subjected to a variety of environmental conditions prior to, and during transport to the forensic laboratory. These findings demonstrate the inherent instability of certain cathinone species in biological evidence under some conditions. Moreover, this study highlights the need for quantitative drug findings in toxicological investigations to be interpreted cautiously, and within the context of specimen storage and integrity.

Direct numerical simulation of turbulent plane Couette flow under neutral and stable stratification

NASA Astrophysics Data System (ADS)

Mortikov, Evgeny

2017-11-01

Direct numerical simulation (DNS) approach was used to study turbulence dynamics in plane Couette flow under conditions ranging from neutral stability to the case of extreme stable stratification, where intermittency is observed. Simulations were performed for Reynolds numbers, based on the channel height and relative wall speed, up to 2 ×105 . Using DNS data, which covers a wide range of stability conditions, parameterizations of pressure correlation terms used in second-order closure turbulence models are discussed. Particular attention is also paid to the sustainment of intermittent turbulence under strong stratification. Intermittent regime is found to be associated with the formation of secondary large-scale structures elongated in the spanwise direction, which define spatially confined alternating regions of laminar and turbulent flow. The spanwise length of this structures increases with the increase in the bulk Richardson number and defines and additional constraint on the computational box size. In this work DNS results are presented in extended computational domains, where the intermittent turbulence is sustained for sufficiently higher Richardson numbers than previously reported.

Strontium stable isotope behaviour accompanying basalt weathering

NASA Astrophysics Data System (ADS)

Burton, K. W.; Parkinson, I. J.; Gíslason, S. G. R.

2016-12-01

The strontium (Sr) stable isotope composition of rivers is strongly controlled by the balance of carbonate to silicate weathering (Krabbenhöft et al. 2010; Pearce et al. 2015). However, rivers draining silicate catchments possess distinctly heavier Sr stable isotope values than their bedrock compositions, pointing to significant fractionation during weathering. Some have argued for preferential release of heavy Sr from primary phases during chemical weathering, others for the formation of secondary weathering minerals that incorporate light isotopes. This study presents high-precision double-spike Sr stable isotope data for soils, rivers, ground waters and estuarine waters from Iceland, reflecting both natural weathering and societal impacts on those environments. The bedrock in Iceland is dominantly basaltic, d88/86Sr ≈ +0.27, extending to lighter values for rhyolites. Geothermal waters range from basaltic Sr stable compositions to those akin to seawater. Soil pore waters reflect a balance of input from primary mineral weathering, precipitation and litter recycling and removal into secondary phases and vegetation. Rivers and ground waters possess a wide range of d88/86Sr compositions from +0.101 to +0.858. Elemental and isotope data indicate that this fractionation primarily results from the formation or dissolution of secondary zeolite (d88/86Sr ≈ +0.10), but also carbonate (d88/86Sr ≈ +0.22) and sometimes anhydrite (d88/86Sr ≈ -0.73), driving the residual waters to heavier or lighter values, respectively. Estuarine waters largely reflect mixing with seawater, but are also be affected by adsorption onto particulates, again driving water to heavy values. Overall, these data indicate that the stability and nature of secondary weathering phases, exerts a strong control on the Sr stable isotope composition of silicate rivers. [1] Krabbenhöft et al. (2010) Geochim. Cosmochim. Acta 74, 4097-4109. [2] Pearce et al. (2015) Geochim. Cosmochim. Acta 157, 125-146.

Thermodynamic study of the native and phosphorylated regulatory domain of the CFTR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marasini, Carlotta, E-mail: marasini@ge.ibf.cnr.it; Galeno, Lauretta; Moran, Oscar

2012-07-06

Highlights: Black-Right-Pointing-Pointer CFTR mutations produce cystic fibrosis. Black-Right-Pointing-Pointer Chloride transport depends on the regulatory domain phosphorylation. Black-Right-Pointing-Pointer Regulatory domain is intrinsically disordered. Black-Right-Pointing-Pointer Secondary structure and protein stability change upon phosphorylation. -- Abstract: The regulatory domain (RD) of the cystic fibrosis transmembrane conductance regulator (CFTR), the defective protein in cystic fibrosis, is the region of the channel that regulates the CFTR activity with multiple phosphorylation sites. This domain is an intrinsically disordered protein, characterized by lack of stable or unique tertiary structure. The disordered character of a protein is directly correlated with its function. The flexibility of RD may bemore » important for its regulatory role: the continuous conformational change may be necessary for the progressive phosphorylation, and thus activation, of the channel. However, the lack of a defined and stable structure results in a considerable limitation when trying to in build a unique molecular model for the RD. Moreover, several evidences indicate significant structural differences between the native, non-phosphorylated state, and the multiple phosphorylated state of the protein. The aim of our work is to provide data to describe the conformations and the thermodynamic properties in these two functional states of RD. We have done the circular dichroism (CD) spectra in samples with a different degree of phosphorylation, from the non-phosphorylated state to a bona fide completely phosphorylated state. Analysis of CD spectra showed that the random coil and {beta}-sheets secondary structure decreased with the polypeptide phosphorylation, at expenses of an increase of {alpha}-helix. This observation lead to interpret phosphorylation as a mechanism favoring a more structured state. We also studied the thermal denaturation curves of the protein in the two conditions, monitoring the changes of the mean residue ellipticity measured at 222 nm as a function of temperature, between 20 and 95 Degree-Sign C. The thermodynamic analysis of the denaturation curves shows that phosphorylation of the protein induces a state of lower stability of R domain, characterized by a lower transition temperature, and by a smaller Gibbs free energy difference between the native and the unfolded states.« less

The Inclusion of Chitosan in Poly-ε-caprolactone Nanoparticles: Impact on the Delivery System Characteristics and on the Adsorbed Ovalbumin Secondary Structure.

PubMed

Jesus, Sandra; Fragal, Elizangela H; Rubira, Adley F; Muniz, Edvani C; Valente, Artur J M; Borges, Olga

2018-01-01

This report extensively explores the benefits of including chitosan into poly-ε-caprolactone (PCL) nanoparticles (NPs) to obtain an improved protein/antigen delivery system. Blend NPs (PCL/chitosan NPs) showed improved protein adsorption efficacy (84%) in low shear stress and aqueous environment, suggesting that a synergistic effect between PCL hydrophobic nature and the positive charges of chitosan present at the particle surface was responsible for protein interaction. Additionally, thermal analysis suggested the blend NPs were more stable than the isolated polymers and cytotoxicity assays in a primary cell culture revealed chitosan inclusion in PCL NPs reduced the toxicity of the delivery system. A quantitative 6-month stability study showed that the inclusion of chitosan in PCL NPs did not induce a change in adsorbed ovalbumin (OVA) secondary structure characterized by the increase in the unordered conformation (random coil), as it was observed for OVA adsorbed to chitosan NPs. Additionally, the slight conformational changes occurred, are not expected to compromise ovalbumin secondary structure and activity, during a 6-month storage even at high temperatures (45°C). In simulated biological fluids, PCL/chitosan NPs showed an advantageous release profile for oral delivery. Overall, the combination of PCL and chitosan characteristics provide PCL/chitosan NPs valuable features particularly important to the development of vaccines for developing countries, where it is difficult to ensure cold chain transportation and non-parenteral formulations would be preferred.

Discrete Molecular Dynamics Can Predict Helical Prestructured Motifs in Disordered Proteins

PubMed Central

Han, Kyou-Hoon; Dokholyan, Nikolay V.; Tompa, Péter; Kalmár, Lajos; Hegedűs, Tamás

2014-01-01

Intrinsically disordered proteins (IDPs) lack a stable tertiary structure, but their short binding regions termed Pre-Structured Motifs (PreSMo) can form transient secondary structure elements in solution. Although disordered proteins are crucial in many biological processes and designing strategies to modulate their function is highly important, both experimental and computational tools to describe their conformational ensembles and the initial steps of folding are sparse. Here we report that discrete molecular dynamics (DMD) simulations combined with replica exchange (RX) method efficiently samples the conformational space and detects regions populating α-helical conformational states in disordered protein regions. While the available computational methods predict secondary structural propensities in IDPs based on the observation of protein-protein interactions, our ab initio method rests on physical principles of protein folding and dynamics. We show that RX-DMD predicts α-PreSMos with high confidence confirmed by comparison to experimental NMR data. Moreover, the method also can dissect α-PreSMos in close vicinity to each other and indicate helix stability. Importantly, simulations with disordered regions forming helices in X-ray structures of complexes indicate that a preformed helix is frequently the binding element itself, while in other cases it may have a role in initiating the binding process. Our results indicate that RX-DMD provides a breakthrough in the structural and dynamical characterization of disordered proteins by generating the structural ensembles of IDPs even when experimental data are not available. PMID:24763499

Occurrence State and Molecular Structure Analysis of Extracellular Proteins with Implications on the Dewaterability of Waste-Activated Sludge.

PubMed

Wu, Boran; Ni, Bing-Jie; Horvat, Kristine; Song, Liyan; Chai, Xiaoli; Dai, Xiaohu; Mahajan, Devinder

2017-08-15

The occurrence state and molecular structure of extracellular proteins were analyzed to reveal the influencing factors on the water-holding capacities of protein-like substances in waste-activated sludge (WAS). The gelation process of extracellular proteins verified that advanced oxidation processes (AOPs) for WAS dewaterability improvement eliminated the water affinity of extracellular proteins and prevented these macromolecules from forming stable colloidal aggregates. Isobaric tags for relative and absolute quantitation proteomics identified that most of the extracellular proteins were originally derived from the intracellular part and the proteins originally located in the extracellular part were mainly membrane-associated. The main mechanism of extracellular protein transformation during AOPs could be represented by the damage of the membrane or related external encapsulating structure and the release of intracellular substances. For the selected representative extracellular proteins, the strong correlation (R 2 > 0.97, p < 0.03) between the surface hydrophilicity index and α-helix percentages in the secondary structure indicated that the water affinity relied more on the spatial distribution of hydrophilic functional groups rather than the content. Destructing the secondary structure represented by the α-helix and stretching the polypeptide aggregation in the water phase through disulfide bond removal might be the key to eliminating the inhibitory effects of extracellular proteins on the interstitial water removal from WAS.

Using phylogenetic probes for quantification of stable isotope labeling and microbial community analysis

DOEpatents

Brodie, Eoin L; DeSantis, Todd Z; Karaoz, Ulas; Andersen, Gary L

2014-12-09

Herein is described methods for a high-sensitivity means to measure the incorporation of stable isotope labeled substrates into RNA following stable isotope probing experiments (SIP). RNA is hybridized to a set of probes such as phylogenetic microarrays and isotope incorporation is quantified such as by secondary ion mass spectrometer imaging (NanoSIMS).

POLYPOIDAL CHOROIDAL VASCULOPATHY SECONDARY TO A STABLE CHOROIDAL NEVUS.

PubMed

Wong, James G; Lai, Xin Jie; Sarafian, Richard Y; Wong, Hon Seng; Smith, Jeremy B

2016-01-01

Choroidal nevus is the most common ocular fundus tumor in adults. Previous studies have widely discussed the features of choroidal neovascularization secondary to nevus and its treatment options. Polypoidal choroidal vasculopathy (PCV) is an exudative chorioretinopathy that is often underdiagnosed. Clinical features, natural history, and treatment response of PCV are distinct from occult choroidal neovascularization. Polypoidal choroidal vasculopathy secondary to choroidal nevus has not been previously documented. We report a patient with a history of stable choroidal nevus who developed a polypoidal lesion at the edge of the nevus lesion. A white woman who presented with a choroidal nevus and clinical features of PCV was examined using fundoscopy, optical coherence tomography, fluorescein angiography, and indocyanine green angiography. A polypoidal lesion with an associated branching vascular network adjacent to the nevus was demonstrated by optical coherence tomography, fluorescein angiography, and indocyanine green angiography. The patient was asymptomatic and was managed conservatively. Our case showed that PCV developing in association with a stable choroidal nevus. Pathogenic mechanisms of this condition may include chronic degenerative or inflammatory changes at the level of the retinal pigment epithelium resulting in vascular changes. Unlike treatment of occult choroidal neovascularization secondary to nevus, optimal management of PCV secondary to nevus may vary. Indocyanine green angiography is the gold standard for the diagnosis of PCV and is a useful investigation in atypical choroidal neovascularization.

Ceramic Nanocomposites from Tailor-Made Preceramic Polymers

PubMed Central

Mera, Gabriela; Gallei, Markus; Bernard, Samuel; Ionescu, Emanuel

2015-01-01

The present Review addresses current developments related to polymer-derived ceramic nanocomposites (PDC-NCs). Different classes of preceramic polymers are briefly introduced and their conversion into ceramic materials with adjustable phase compositions and microstructures is presented. Emphasis is set on discussing the intimate relationship between the chemistry and structural architecture of the precursor and the structural features and properties of the resulting ceramic nanocomposites. Various structural and functional properties of silicon-containing ceramic nanocomposites as well as different preparative strategies to achieve nano-scaled PDC-NC-based ordered structures are highlighted, based on selected ceramic nanocomposite systems. Furthermore, prospective applications of the PDC-NCs such as high-temperature stable materials for thermal protection systems, membranes for hot gas separation purposes, materials for heterogeneous catalysis, nano-confinement materials for hydrogen storage applications as well as anode materials for secondary ion batteries are introduced and discussed in detail. PMID:28347023

Synthesis of New Ba Complex as Metalorganic Source for Metalorganic Chemical Vapor Deposition and Optimization of Its Molecule Structure

NASA Astrophysics Data System (ADS)

Zama, Hideaki; Morishita, Tadataka

2000-10-01

New Ba(DPM)2-amine (DPM=dipivaloylmethane) adduct compounds were attempted to be synthesized from Ba(DPM)2 and amines. Complexes obtained were evaluated based on decreases of their weight with increasing temperature by thermogravimetry. The simple vaporizing phenomenon, showing a one-step weight-reduction curve, was observed only in the case of using tetraethylenepentamine and pentaethylenehexamine (pentaen) as adduct molecules, which have a simple chain structure and five to six primary and secondary amine radicals. From the viewpoint of applicability to film growth, they have the best structure based on a survey in this study using sixteen amine molecules with distinctive structures. When we used Ba(DPM)2-pentaen as a metalorganic source for a metalorganic chemical vapor deposition method at a vaporizing temperature of 140°C, the Ba supply rate remained stable within a standard deviation of 1.6% for over 300 h.

Biomimetic Silk Scaffolds with an Amorphous Structure for Soft Tissue Engineering.

PubMed

Sang, Yonghuan; Li, Meirong; Liu, Jiejie; Yao, Yuling; Ding, Zhaozhao; Wang, Lili; Xiao, Liying; Lu, Qiang; Fu, Xiaobing; Kaplan, David L

2018-03-21

Fine tuning physical cues of silk fibroin (SF) biomaterials to match specific requirements for different soft tissues would be advantageous. Here, amorphous SF nanofibers were used to fabricate scaffolds with better hierarchical extracellular matrix (ECM) mimetic microstructures than previous silk scaffolds. Kinetic control was introduced into the scaffold forming process, resulting in the direct production of water-stable scaffolds with tunable secondary structures and thus mechanical properties. These biomaterials remained with amorphous structures, offering softer properties than prior scaffolds. The fine mechanical tunability of these systems provides a feasible way to optimize physical cues for improved cell proliferation and enhanced neovascularization in vivo. Multiple physical cues, such as partly ECM mimetic structures and optimized stiffness, provided suitable microenvironments for tissue ingrowth, suggesting the possibility of actively designing bioactive SF biomaterials. These systems suggest a promising strategy to develop novel SF biomaterials for soft tissue repair and regenerative medicine.

Structural stability of myoglobin and glycomyoglobin: a comparative molecular dynamics simulation study.

PubMed

Alizadeh-Rahrovi, Joulia; Shayesteh, Alireza; Ebrahim-Habibi, Azadeh

2015-09-01

Glycoproteins are formed as the result of enzymatic glycosylation or chemical glycation in the body, and produced in vitro in industrial processes. The covalently attached carbohydrate molecule(s) confer new properties to the protein, including modified stability. In the present study, the structural stability of a glycoprotein form of myoglobin, bearing a glucose unit in the N-terminus, has been compared with its native form by the use of molecular dynamics simulation. Both structures were subjected to temperatures of 300 and 500 K in an aqueous environment for 10 ns. Changes in secondary structures and RMSD were then assessed. An overall higher stability was detected for glycomyoglobin, for which the most stable segments/residues were highlighted and compared with the native form. The simple addition of a covalently bound glucose is suggested to exert its stabilizing effect via increased contacts with surrounding water molecules, as well as a different pattern of interactions with neighbor residues.

The effects of motif net charge and amphiphilicity on the self-assembly of functionally designer RADA16-I peptides.

PubMed

Wu, Dongni; Zhang, Shuangying; Zhao, Yuyuan; Ao, Ningjian; Ramakrishna, Seeram; He, Liumin

2018-03-16

RADA16-I (Ac-(RADA) 4 -CONH 2 ) is a widely investigated self-assembling peptide (SAP) in the biomedical field. It can undergo ordered self-assembly to form stable secondary structures, thereby further forming a nanofiber hydrogel. The modification of RADA16-I with functional peptide motifs has become a popular research topic. Researchers aim to exhibit particular biomedical signaling, and subsequently, further expand its applications. However, only a few fundamental reports are available on the influences of the peptide motifs on self-assembly mechanisms of designer functional RADA16-I SAPs. In this study, we designed RGD-modified RADA16-I SAPs with a series of net charges and amphiphilicities. The assembly/reassembly of these functionally designer SAPs was thoroughly studied using Raman spectroscopy, CD spectroscopy, and AFM. The nanofiber morphology and the secondary structure largely depended on the balance between the hydrophobic effects versus like-charge repulsions of the motifs, which should be to the focus in order to achieve a tailored nanostructure. Our study would contribute insight into considerations for sophisticated design of SAPs for biomedical applications.

On the structure of cellular solutions in Rayleigh-Benard-Marangoni flows in small-aspect-ratio containers

NASA Technical Reports Server (NTRS)

Dijkstra, Henk A.

1992-01-01

Multiple steady flow patterns occur in surface-tension/buoyancy-driven convection in a liquid layer heated from below (Rayleigh-Benard-Marangoni flows). Techniques of numerical bifurcation theory are used to study the multiplicity and stability of two-dimensional steady flow patterns (rolls) in rectangular small-aspect-ratio containers as the aspect ratio is varied. For pure Marangoni flows at moderate Biot and Prandtl number, the transitions occurring when paths of codimension 1 singularities intersect determine to a large extent the multiplicity of stable patterns. These transitions also lead, for example, to Hopf bifurcations and stable periodic flows for a small range in aspect ratio. The influence of the type of lateral walls on the multiplicity of steady states is considered. 'No-slip' lateral walls lead to hysteresis effects and typically restrict the number of stable flow patterns (with respect to 'slippery' sidewalls) through the occurrence of saddle node bifurcations. In this way 'no-slip' sidewalls induce a selection of certain patterns, which typically have the largest Nusselt number, through secondary bifurcation.

Secondary reconstruction of maxillofacial trauma.

PubMed

Castro-Núñez, Jaime; Van Sickels, Joseph E

2017-08-01

Craniomaxillofacial trauma is one of the most complex clinical conditions in contemporary maxillofacial surgery. Vital structures and possible functional and esthetic sequelae are important considerations following this type of trauma and intervention. Despite the best efforts of the primary surgery, there are a group of patients that will have poor outcomes requiring secondary reconstruction to restore form and function. The purpose of this study is to review current concepts on secondary reconstruction to the maxillofacial complex. The evaluation of a posttraumatic patient for a secondary reconstruction must include an assessment of the different subunits of the upper face, middle face, and lower face. Virtual surgical planning and surgical guides represent the most important innovations in secondary reconstruction over the past few years. Intraoperative navigational surgery/computed-assisted navigation is used in complex cases. Facial asymmetry can be corrected or significantly improved by segmentation of the computerized tomography dataset and mirroring of the unaffected side by means of virtual surgical planning. Navigational surgery/computed-assisted navigation allows for a more precise surgical correction when secondary reconstruction involves the replacement of extensive anatomical areas. The use of technology can result in custom-made replacements and prebent plates, which are more stable and resistant to fracture because of metal fatigue. Careful perioperative evaluation is the key to positive outcomes of secondary reconstruction after trauma. The advent of technological tools has played a capital role in helping the surgical team perform a given treatment plan in a more precise and predictable manner.

Photosynthesis in reproductive structures: costs and benefits

PubMed Central

Raven, John A.; Griffiths, Howard

2015-01-01

The role of photosynthesis by reproductive structures during grain-filling has important implications for cereal breeding, but the methods for assessing the contribution by reproductive structures to grain-filling are invasive and prone to compensatory changes elsewhere in the plant. A technique analysing the natural abundance of stable carbon isotopes in soluble carbohydrates has significant promise. However, it depends crucially on there being no more than two sources of organic carbon (leaf and ear/awn), with significantly different 13C:12C ratios and no secondary fractionation during grain-filling. The role of additional peduncle carbohydrate reserves represents a potential means for N remobilization, as well as for hydraulic continuity during grain-filling. The natural abundance of the stable isotopes of carbon and oxygen are also useful for exploring the influence of reproduction on whole plant carbon and water relations and have been used to examine the resource costs of reproduction in females and males of dioecious plants. Photosynthesis in reproductive structures is widespread among oxygenic photosynthetic organisms, including many clades of algae and embryophytes of different levels of complexity. The possible evolutionary benefits of photosynthesis in reproductive structures include decreasing the carbon cost of reproduction and ‘use’ of transpiratory loss of water to deliver phloem-immobile calcium Ca2+ and silicon [Si(OH)4] via the xylem. The possible costs of photosynthesis in reproductive structures are increasing damage to DNA from photosynthetically active, and hence UV-B, radiation and the production of reactive oxygen species. PMID:25871648

First Year Adjustment in the Secondary School.

ERIC Educational Resources Information Center

Loosemore, Jean Ann

1978-01-01

This study investigated the relationship between adjustment to secondary school and 17 cognitive and noncognitive variables, including intelligence (verbal and nonverbal reasoning), academic achievement, extraversion-introversion, stable/unstable, social adjustment, endeavor, age, sex, and school form. (CP)

Synthesis of plant-mediated gold nanoparticles and catalytic role of biomatrix-embedded nanomaterials

PubMed Central

Sharma, Nilesh C.; Nath, Sudip; Parsons, Jason G.; Gardea- Torresdey, Jorge L.; Pal, Tarasankar

2008-01-01

Growth of Sesbania seedlings in chloroaurate solution resulted in the accumulation of gold with the formation of stable gold nanoparticles in plant tissues. Transmission electron microscopy revealed the intracellular distribution of monodisperse nanospheres, possibly due to reduction of the metal ions by secondary metabolites present in cells. X-ray absorption near-edge structure and extended X-ray absorption fine structure demonstrated a high degree of efficiency for the biotransformation of Au(III) into Au(0) by plant tissues. The catalytic function of the nanoparticle-rich biomass was substantiated by the reduction of aqueous 4-nitrophenol (4-NP). This is the first report of gold nanoparticle-bearing biomatrix directly reducing a toxic pollutant, 4-NP. PMID:17711235

R-loops: targets for nuclease cleavage and repeat instability.

PubMed

Freudenreich, Catherine H

2018-01-11

R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias. Recently, it was found that R-loops at an expanded CAG/CTG repeat tract cause DNA breaks as well as repeat instability (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Two factors were identified as causing R-loop-dependent breaks at CAG/CTG tracts: deamination of cytosines and the MutLγ (Mlh1-Mlh3) endonuclease, defining two new mechanisms for how R-loops can generate DNA breaks (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Following R-loop-dependent nicking, base excision repair resulted in repeat instability. These results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. This perspective summarizes mechanisms of R-loop-induced fragility at G-rich repeats and new links between DNA breaks and repeat instability.

The effects of disulfide bonds on the denatured state of barnase.

PubMed Central

Clarke, J.; Hounslow, A. M.; Bond, C. J.; Fersht, A. R.; Daggett, V.

2000-01-01

The effects of engineered disulfide bonds on protein stability are poorly understood because they can influence the structure, dynamics, and energetics of both the native and denatured states. To explore the effects of two engineered disulfide bonds on the stability of barnase, we have conducted a combined molecular dynamics and NMR study of the denatured state of the two mutants. As expected, the disulfide bonds constrain the denatured state. However, specific extended beta-sheet structure can also be detected in one of the mutant proteins. This mutant is also more stable than would be predicted. Our study suggests a possible cause of the very high stability conferred by this disulfide bond: the wild-type denatured ensemble is stabilized by a nonnative hydrophobic cluster, which is constrained from occurring in the mutant due to the formation of secondary structure. PMID:11206061

Adsorption orientations and immunological recognition of antibodies on graphene

NASA Astrophysics Data System (ADS)

Vilhena, J. G.; Dumitru, A. C.; Herruzo, Elena T.; Mendieta-Moreno, Jesús I.; Garcia, Ricardo; Serena, P. A.; Pérez, Rubén

2016-07-01

Large-scale molecular dynamics (MD) simulations and atomic force microscopy (AFM) in liquid are combined to characterize the adsorption of Immunoglobulin G (IgG) antibodies over a hydrophobic surface modeled with a three-layer graphene slab. We consider explicitly the water solvent, simulating systems with massive sizes (up to 770 000 atoms), for four different adsorption orientations. Protocols based on steered MD to speed up the protein diffusion stage and to enhance the dehydration process are combined with long simulation times (>150 ns) in order to make sure that the final adsorption states correspond to actual stable configurations. Our MD results and the AFM images demonstrate that the IgG antibodies are strongly adsorbed, do not unfold, and retain their secondary and tertiary structures upon deposition. Statistical analysis of the AFM images shows that many of the antibodies adopt vertical orientations, even at very small coverages, which expose at least one Fab binding site for recognition events. Single molecule force spectroscopy experiments demonstrate the immunological response of the deposited antibodies by recognizing its specific antigens. The above properties together with the strong anchoring and preservation of the secondary structure, make graphene an excellent candidate for the development of immunosensors.Large-scale molecular dynamics (MD) simulations and atomic force microscopy (AFM) in liquid are combined to characterize the adsorption of Immunoglobulin G (IgG) antibodies over a hydrophobic surface modeled with a three-layer graphene slab. We consider explicitly the water solvent, simulating systems with massive sizes (up to 770 000 atoms), for four different adsorption orientations. Protocols based on steered MD to speed up the protein diffusion stage and to enhance the dehydration process are combined with long simulation times (>150 ns) in order to make sure that the final adsorption states correspond to actual stable configurations. Our MD results and the AFM images demonstrate that the IgG antibodies are strongly adsorbed, do not unfold, and retain their secondary and tertiary structures upon deposition. Statistical analysis of the AFM images shows that many of the antibodies adopt vertical orientations, even at very small coverages, which expose at least one Fab binding site for recognition events. Single molecule force spectroscopy experiments demonstrate the immunological response of the deposited antibodies by recognizing its specific antigens. The above properties together with the strong anchoring and preservation of the secondary structure, make graphene an excellent candidate for the development of immunosensors. Electronic supplementary information (ESI) available: Further details concerning the experimental methods, the MD simulation protocols, and the characterization and stability of the different adsorption configurations. See DOI: 10.1039/C5NR07612A

Stabilization of neurotoxic Alzheimer amyloid-β oligomers by protein engineering

PubMed Central

Sandberg, Anders; Luheshi, Leila M.; Söllvander, Sofia; Pereira de Barros, Teresa; Macao, Bertil; Knowles, Tuomas P. J.; Biverstål, Henrik; Lendel, Christofer; Ekholm-Petterson, Frida; Dubnovitsky, Anatoly; Lannfelt, Lars; Dobson, Christopher M.; Härd, Torleif

2010-01-01

Soluble oligomeric aggregates of the amyloid-β peptide (Aβ) have been implicated in the pathogenesis of Alzheimer’s disease (AD). Although the conformation adopted by Aβ within these aggregates is not known, a β-hairpin conformation is known to be accessible to monomeric Aβ. Here we show that this β-hairpin is a building block of toxic Aβ oligomers by engineering a double-cysteine mutant (called Aβcc) in which the β-hairpin is stabilized by an intramolecular disulfide bond. Aβ40cc and Aβ42cc both spontaneously form stable oligomeric species with distinct molecular weights and secondary-structure content, but both are unable to convert into amyloid fibrils. Biochemical and biophysical experiments and assays with conformation-specific antibodies used to detect Aβ aggregates in vivo indicate that the wild-type oligomer structure is preserved and stabilized in Aβcc oligomers. Stable oligomers are expected to become highly toxic and, accordingly, we find that β-sheet-containing Aβ42cc oligomers or protofibrillar species formed by these oligomers are 50 times more potent inducers of neuronal apoptosis than amyloid fibrils or samples of monomeric wild-type Aβ42, in which toxic aggregates are only transiently formed. The possibility of obtaining completely stable and physiologically relevant neurotoxic Aβ oligomer preparations will facilitate studies of their structure and role in the pathogenesis of AD. For example, here we show how kinetic partitioning into different aggregation pathways can explain why Aβ42 is more toxic than the shorter Aβ40, and why certain inherited mutations are linked to protofibril formation and early-onset AD. PMID:20713699

Crystallographic and theoretical studies of an inclusion complex of β-cyclodextrin with fentanyl.

PubMed

Ogawa, Noriko; Nagase, Hiromasa; Loftsson, Thorsteinn; Endo, Tomohiro; Takahashi, Chisato; Kawashima, Yoshiaki; Ueda, Haruhisa; Yamamoto, Hiromitsu

2017-10-15

The crystal structure of an inclusion complex of β-cyclodextrin (β-CD) with fentanyl was determined by single crystal X-ray diffraction analysis. The crystal belongs to the triclinic space group P1 and the complex comprises one fentanyl, two β-CD, and several water molecules. β-CD and fentanyl form a host-guest inclusion complex at a ratio of 2:1 and the asymmetric unit of the complex contains two host molecules (β-CDs) in a head-to-head arrangement that form dimers through hydrogen bonds between the secondary hydroxyl groups of β-CD and one guest molecule. Fentanyl is totally contained within the β-CD cavity and the structure of the phenylethyl part of fentanyl inside the dimeric cavity of the complex is disordered. Furthermore, theoretical molecular conformational calculations were conducted to clarify the mobility of the guest molecule in the β-CD cavity using CONFLEX software. Crystal optimization and crystal energy calculations were also conducted. The results of the theoretical calculations confirmed that the conformation of disorder part 1, which was high in occupancy by crystal structure analysis, was more stable. The phenylethyl part of fentanyl existed in several stable conformations. Copyright © 2017 Elsevier B.V. All rights reserved.

Understanding catalyst behavior during in situ heating through simultaneous secondary and transmitted electron imaging.

PubMed

Howe, Jane Y; Allard, Lawrence F; Bigelow, Wilbur C; Demers, Hendrix; Overbury, Steven H

2014-01-01

By coupling techniques of simultaneous secondary (SE) and transmitted electron (TE) imaging at high resolution in a modern scanning transmission electron microscope (STEM), with the ability to heat specimens using a highly stable MEMS-based heating platform, we obtained synergistic information to clarify the behavior of catalysts during in situ thermal treatments. Au/iron oxide catalyst 'leached' to remove surface Au was heated to temperatures as high as 700°C. The Fe2O3 support particle structure tended to reduce to Fe3O4 and formed surface terraces; the formation, coalescence, and mobility of 1- to 2-nm particles on the terraces were characterized in SE, STEM-ADF, and TEM-BF modes. If combined with simultaneous nanoprobe spectroscopy, this approach will open the door to a new way of studying the kinetics of nano-scaled phenomena.

Understanding catalyst behavior during in situ heating through simultaneous secondary and transmitted electron imaging

NASA Astrophysics Data System (ADS)

Howe, Jane Y.; Allard, Lawrence F.; Bigelow, Wilbur C.; Demers, Hendrix; Overbury, Steven H.

2014-11-01

By coupling techniques of simultaneous secondary (SE) and transmitted electron (TE) imaging at high resolution in a modern scanning transmission electron microscope (STEM), with the ability to heat specimens using a highly stable MEMS-based heating platform, we obtained synergistic information to clarify the behavior of catalysts during in situ thermal treatments. Au/iron oxide catalyst 'leached' to remove surface Au was heated to temperatures as high as 700°C. The Fe2O3 support particle structure tended to reduce to Fe3O4 and formed surface terraces; the formation, coalescence, and mobility of 1- to 2-nm particles on the terraces were characterized in SE, STEM-ADF, and TEM-BF modes. If combined with simultaneous nanoprobe spectroscopy, this approach will open the door to a new way of studying the kinetics of nano-scaled phenomena.

Topographically induced internal solitary waves in a pycnocline: Ultrasonic probes and stereo-correlation measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dossmann, Yvan, E-mail: yvan.dossmann@anu.edu.au; CNRM-GAME, UMR3589 METEO-FRANCE and CNRS, 42 avenue Gaspard Coriolis, 31057 Toulouse Cedex 01; Laboratoire d’Aérologie, 14 avenue Edouard Belin, 31400 Toulouse

Internal solitary waves (ISWs) are large amplitude stable waves propagating in regions of high density gradients such as the ocean pycnocline. Their dynamics has often been investigated in two-dimensional approaches, however, their three-dimensional evolution is still poorly known. Experiments have been conducted in the large stratified water tank of CNRM-GAME to study the generation of ISWs in two academic configurations inspired by oceanic regimes. First, ultrasonic probes are used to measure the interfacial displacement in the two configurations. In the primary generation case for which the two layers are of constant density, the generation of ISWs is investigated in twomore » series of experiments with varying amplitude and forcing frequency. In the secondary generation case for which the lower layer is stratified, the generation of ISWs from the impact of an internal wave beam on the pycnocline and their subsequent dynamics is studied. The dynamics of ISWs in these two regimes accords well with analytical approaches and numerical simulations performed in analogous configurations. Then, recent developments of a stereo correlation technique are used to describe the three-dimensional structure of propagating ISWs. In the primary generation configuration, small transverse effects are observed in the course of the ISW propagation. In the secondary generation configuration, larger transverse structures are observed in the interfacial waves dynamics. The interaction between interfacial troughs and internal waves propagating in the lower stratified layer are a possible cause for the generation of these structures. The magnitude of these transverse structures is quantified with a nondimensional parameter in the two configurations. They are twice as large in the secondary generation case as in the primary generation case.« less

Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain

PubMed Central

2012-01-01

Background Post-transcriptional control of gene expression is mostly conducted by specific elements in untranslated regions (UTRs) of mRNAs, in collaboration with specific binding proteins and RNAs. In several well characterized cases, these RNA elements are known to form stable secondary structures. RNA secondary structures also may have major functional implications for long noncoding RNAs (lncRNAs). Recent transcriptional data has indicated the importance of lncRNAs in brain development and function. However, no methodical efforts to investigate this have been undertaken. Here, we aim to systematically analyze the potential for RNA structure in brain-expressed transcripts. Results By comprehensive spatial expression analysis of the adult mouse in situ hybridization data of the Allen Mouse Brain Atlas, we show that transcripts (coding as well as non-coding) associated with in silico predicted structured probes are highly and significantly enriched in almost all analyzed brain regions. Functional implications of these RNA structures and their role in the brain are discussed in detail along with specific examples. We observe that mRNAs with a structure prediction in their UTRs are enriched for binding, transport and localization gene ontology categories. In addition, after manual examination we observe agreement between RNA binding protein interaction sites near the 3’ UTR structures and correlated expression patterns. Conclusions Our results show a potential use for RNA structures in expressed coding as well as noncoding transcripts in the adult mouse brain, and describe the role of structured RNAs in the context of intracellular signaling pathways and regulatory networks. Based on this data we hypothesize that RNA structure is widely involved in transcriptional and translational regulatory mechanisms in the brain and ultimately plays a role in brain function. PMID:22651826

Investigation of mRNA quadruplex formation in Escherichia coli.

PubMed

Wieland, Markus; Hartig, Jörg S

2009-01-01

The protocol presented here allows for the investigation of the formation of unusual nucleic acid structures in the 5'-untranslated region (UTR) of bacteria by correlating gene expression levels to the in vitro stability of the respective structure. In particular, we describe the introduction of G-quadruplex forming sequences close to the ribosome-binding site (RBS) on the mRNA of a reporter gene and the subsequent read-out of the expression levels. Insertion of a stable secondary structure results in the cloaking of RBS and eventually reduced gene expression levels. The structures and stability of the introduced sequences are further characterized by circular dichroism (CD) spectroscopy and thermal melting experiments. The extent of inhibition is then correlated to the stability of the respective quadruplex structure, allowing judgement of whether factors other than thermodynamic stability affect the formation of a given quadruplex sequence in vivo. Measuring gene expression levels takes 2 d including cloning; CD experiments take 5 hours per experiment.

Equalizing secondary path effects using the periodicity of fMRI acoustic noise.

PubMed

Kannan, Govind; Milani, Ali A; Panahi, Issa; Briggs, Richard

2008-01-01

Non-minimum phase secondary path has a direct effect on achieving a desired noise attenuation level in active noise control (ANC) systems. The adaptive noise canceling filter is often a causal FIR filter which may not be able to sufficiently equalize the effect of a non-minimum phase secondary path, since in theory only a non-causal filter can equalize it. However a non-causal stable filter can be found to equalize the non-minimum phase effect of secondary path. Realization of non-causal stable filters requires knowledge of future values of input signal. In this paper we develop methods for equalizing the non-minimum phase property of the secondary path and improving the performance of an ANC system by exploiting the periodicity of fMRI acoustic noise. It has been shown that the scanner noise component is highly periodic and hence predictable which enables easy realization of non-causal filtering. Improvement in performance due to the proposed methods (with and without the equalizer) is shown for periodic fMRI acoustic noise.

Ribozyme-catalysed RNA synthesis using triplet building blocks.

PubMed

Attwater, James; Raguram, Aditya; Morgunov, Alexey S; Gianni, Edoardo; Holliger, Philipp

2018-05-15

RNA-catalyzed RNA replication is widely believed to have supported a primordial biology. However, RNA catalysis is dependent upon RNA folding, and this yields structures that can block replication of such RNAs. To address this apparent paradox we have re-examined the building blocks used for RNA replication. We report RNA-catalysed RNA synthesis on structured templates when using trinucleotide triphosphates (triplets) as substrates, catalysed by a general and accurate triplet polymerase ribozyme that emerged from in vitro evolution as a mutualistic RNA heterodimer. The triplets cooperatively invaded and unraveled even highly stable RNA secondary structures, and support non-canonical primer-free and bidirectional modes of RNA synthesis and replication. Triplet substrates thus resolve a central incongruity of RNA replication, and here allow the ribozyme to synthesise its own catalytic subunit '+' and '-' strands in segments and assemble them into a new active ribozyme. © 2018, Attwater et al.

Structural changes evaluation with Raman spectroscopy in meat batters prepared by different processes.

PubMed

Kang, Zhuang-Li; Li, Xiang; He, Hong-Ju; Ma, Han-Jun; Song, Zhao-Jun

2017-08-01

A comprehensive study was conducted to evaluate the structural changes of meat and protein of pork batters produced by chopping or beating process through the phase-contrast micrograph, laser light scattering analyzer, scanning electronic microscopy and Raman spectrometer. The results showed that the shattered myofibrilla fragments were shorter and particle-sizes were smaller in the raw batter produced by beating process than those in the chopping process. Compared with the raw and cooked batters produced by chopping process, modifications in amide I and amide III bands revealed a significant decrease of α -helix content and an increase of β -sheet, β -turn and random coils content in the beating process. The changes in secondary structure of protein in the batter produced by beating process was thermally stable. Moreover, more tyrosine residues were buried, and more gauche-gauche-trans disulfide bonds conformations and hydrophobic interactions were formed in the batter produced by beating process.

Trophic network models explain instability of Early Triassic terrestrial communities

PubMed Central

Roopnarine, Peter D; Angielczyk, Kenneth D; Wang, Steve C; Hertog, Rachel

2007-01-01

Studies of the end-Permian mass extinction have emphasized potential abiotic causes and their direct biotic effects. Less attention has been devoted to secondary extinctions resulting from ecological crises and the effect of community structure on such extinctions. Here we use a trophic network model that combines topological and dynamic approaches to simulate disruptions of primary productivity in palaeocommunities. We apply the model to Permian and Triassic communities of the Karoo Basin, South Africa, and show that while Permian communities bear no evidence of being especially susceptible to extinction, Early Triassic communities appear to have been inherently less stable. Much of the instability results from the faster post-extinction diversification of amphibian guilds relative to amniotes. The resulting communities differed fundamentally in structure from their Permian predecessors. Additionally, our results imply that changing community structures over time may explain long-term trends like declining rates of Phanerozoic background extinction PMID:17609191

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rantalainen, Kimmo I.; Christensen, Peter A.; Hafren, Anders

The viral genome-linked protein (VPg) of Potato virus A (PVA) is a multifunctional protein that belongs to a class of intrinsically disordered proteins. Typically, this type of protein gains a more stable structure upon interactions or posttranslational modifications. In a membrane lipid strip overlay binding assay, PVA VPg was found to bind phosphatidylserine (PS), but not phosphatidylcholine (PC). According to circular dichroism spectroscopy, the secondary structure of PVA VPg was stabilized upon interactions with PS and phosphatidylglycerol (PG), but not with PC vesicles. It is possible that this stabilization favored the formation of alpha-helical structures. Limited tryptic digestion showed thatmore » the interaction with anionic vesicles protected certain, otherwise accessible, trypsin cleavage sites. An electron microscopy study revealed that interaction with VPg substantially increased the vesicle diameter and caused the formation of pore or plaque-like electron dense spots on the vesicle surface, which gradually led to disruption of the vesicles.« less

Testing comparison models of DASS-12 and its reliability among adolescents in Malaysia.

PubMed

Osman, Zubaidah Jamil; Mukhtar, Firdaus; Hashim, Hairul Anuar; Abdul Latiff, Latiffah; Mohd Sidik, Sherina; Awang, Hamidin; Ibrahim, Normala; Abdul Rahman, Hejar; Ismail, Siti Irma Fadhilah; Ibrahim, Faisal; Tajik, Esra; Othman, Norlijah

2014-10-01

The 21-item Depression, Anxiety and Stress Scale (DASS-21) is frequently used in non-clinical research to measure mental health factors among adults. However, previous studies have concluded that the 21 items are not stable for utilization among the adolescent population. Thus, the aims of this study are to examine the structure of the factors and to report on the reliability of the refined version of the DASS that consists of 12 items. A total of 2850 students (aged 13 to 17 years old) from three major ethnic in Malaysia completed the DASS-21. The study was conducted at 10 randomly selected secondary schools in the northern state of Peninsular Malaysia. The study population comprised secondary school students (Forms 1, 2 and 4) from the selected schools. Based on the results of the EFA stage, 12 items were included in a final CFA to test the fit of the model. Using maximum likelihood procedures to estimate the model, the selected fit indices indicated a close model fit (χ(2)=132.94, df=57, p=.000; CFI=.96; RMR=.02; RMSEA=.04). Moreover, significant loadings of all the unstandardized regression weights implied an acceptable convergent validity. Besides the convergent validity of the item, a discriminant validity of the subscales was also evident from the moderate latent factor inter-correlations, which ranged from .62 to .75. The subscale reliability was further estimated using Cronbach's alpha and the adequate reliability of the subscales was obtained (Total=76; Depression=.68; Anxiety=.53; Stress=.52). The new version of the 12-item DASS for adolescents in Malaysia (DASS-12) is reliable and has a stable factor structure, and thus it is a useful instrument for distinguishing between depression, anxiety and stress. Copyright © 2014 Elsevier Inc. All rights reserved.

Shape memory polymers

DOEpatents

Wilson, Thomas S.; Bearinger, Jane P.

2017-08-29

New shape memory polymer compositions, methods for synthesizing new shape memory polymers, and apparatus comprising an actuator and a shape memory polymer wherein the shape memory polymer comprises at least a portion of the actuator. A shape memory polymer comprising a polymer composition which physically forms a network structure wherein the polymer composition has shape-memory behavior and can be formed into a permanent primary shape, re-formed into a stable secondary shape, and controllably actuated to recover the permanent primary shape. Polymers have optimal aliphatic network structures due to minimization of dangling chains by using monomers that are symmetrical and that have matching amine and hydroxl groups providing polymers and polymer foams with clarity, tight (narrow temperature range) single transitions, and high shape recovery and recovery force that are especially useful for implanting in the human body.

Shape memory polymers

DOEpatents

Wilson, Thomas S.; Bearinger, Jane P.

2015-06-09

New shape memory polymer compositions, methods for synthesizing new shape memory polymers, and apparatus comprising an actuator and a shape memory polymer wherein the shape memory polymer comprises at least a portion of the actuator. A shape memory polymer comprising a polymer composition which physically forms a network structure wherein the polymer composition has shape-memory behavior and can be formed into a permanent primary shape, re-formed into a stable secondary shape, and controllably actuated to recover the permanent primary shape. Polymers have optimal aliphatic network structures due to minimization of dangling chains by using monomers that are symmetrical and that have matching amine and hydroxyl groups providing polymers and polymer foams with clarity, tight (narrow temperature range) single transitions, and high shape recovery and recovery force that are especially useful for implanting in the human body.

The Stable Pairing Problem

ERIC Educational Resources Information Center

Greenwell, Raymond N.; Seabold, Daniel E.

2014-01-01

The Gale-Shapley stable marriage theorem is a fascinating piece of twentieth-century mathematics that has many practical applications--from labor markets to school admissions--yet is accessible to secondary school mathematics students. David Gale and Lloyd Shapley were both mathematicians and economists who published their work on the Stable…

A semi-supervised learning approach for RNA secondary structure prediction.

PubMed

Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki

2015-08-01

RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited. Copyright © 2015 Elsevier Ltd. All rights reserved.

Near-surface geophysical methods for investigating the Buyukcekmece landslide in Istanbul, Turkey

NASA Astrophysics Data System (ADS)

Yalcinkaya, Esref; Alp, Hakan; Ozel, Oguz; Gorgun, Ethem; Martino, Salvatore; Lenti, Luca; Bourdeau, Celine; Bigarre, Pascal; Coccia, Stella

2016-11-01

In this study, near-surface geophysical techniques are used to investigate the physical characteristics of the Buyukcekmece landslide (Istanbul, Turkey). The Buyukcekmece landslide has continuous activity at a low velocity and is classified as a complex mechanism. It includes rototranslational parts, several secondary scarps, several landslide terraces, and evidence of two earth flows. It mainly develops in the clayey layers of the Danismen Formation. According to our findings, P-wave velocities ranging from 300 m/s to 2400 m/s do not provide notable discrimination between sliding mass and stable soil. They show variations in blocks reflecting a complex structure. We obtained the S-wave velocity structure of the landslide up to 80 m by combining the analysis of MASW and ReMi. It is clear that S-wave velocities are lower in the landslide compared to those of the stable area. Identical S-wave velocities for the entire area at depths higher than 60 m may point out the maximum thickness of the landslide mass. Resonance frequencies obtained from the H/V analysis of the landslide area are generally higher than those of the stable area. The depths computed by using an empirical relationship between the resonance frequency and the soil thickness point out the failure surfaces from 10 to 50 m moving downslope from the landslide crown area. The resistivity values within the landslide are generally lower than 30 Ω m, i.e., a typical value for remolded clayey debris. The geophysical results reflect an overview of the geological model, but the complexity of the landslide makes it difficult to map the landslide structure in detail.

An Experimentally Robust Model of Monomeric Apolipoprotein A-I Created from a Chimera of Two X-ray Structures and Molecular Dynamics Simulations

PubMed Central

2015-01-01

High-density lipoprotein (HDL) retards atherosclerosis by accepting cholesterol from the artery wall. However, the structure of the proposed acceptor, monomeric apolipoprotein A-I (apoA-I), the major protein of HDL, is poorly understood. Two published models for monomeric apoA-I used cross-linking distance constraints to derive best fit conformations. This approach has limitations. (i) Cross-linked peptides provide no information about secondary structure. (ii) A protein chain can be folded in multiple ways to create a best fit. (iii) Ad hoc folding of a secondary structure is unlikely to produce a stable orientation of hydrophobic and hydrophilic residues. To address these limitations, we used a different approach. We first noted that the dimeric apoA-I crystal structure, (Δ185–243)apoA-I, is topologically identical to a monomer in which helix 5 forms a helical hairpin, a monomer with a hydrophobic cleft running the length of the molecule. We then realized that a second crystal structure, (Δ1–43)apoA-I, contains a C-terminal structure that fits snuggly via aromatic and hydrophobic interactions into the hydrophobic cleft. Consequently, we combined these crystal structures into an initial model that was subjected to molecular dynamics simulations. We tested the initial and simulated models and the two previously published models in three ways: against two published data sets (domains predicted to be helical by H/D exchange and six spin-coupled residues) and against our own experimentally determined cross-linking distance constraints. We note that the best fit simulation model, superior by all tests to previously published models, has dynamic features of a molten globule with interesting implications for the functions of apoA-I. PMID:25423138

Aggregation of gluten proteins in model dough after fibre polysaccharide addition.

PubMed

Nawrocka, Agnieszka; Szymańska-Chargot, Monika; Miś, Antoni; Wilczewska, Agnieszka Z; Markiewicz, Karolina H

2017-09-15

FT-Raman spectroscopy, thermogravimetry and differential scanning calorimetry were used to study changes in structure of gluten proteins and their thermal properties influenced by four dietary fibre polysaccharides (microcrystalline cellulose, inulin, apple pectin and citrus pectin) during development of a model dough. The flour reconstituted from wheat starch and wheat gluten was mixed with the polysaccharides in five concentrations: 3%, 6%, 9%, 12% and 18%. The obtained results showed that all polysaccharides induced similar changes in secondary structure of gluten proteins concerning formation of aggregates (1604cm -1 ), H-bonded parallel- and antiparallel-β-sheets (1690cm -1 ) and H-bonded β-turns (1664cm -1 ). These changes concerned mainly glutenins since β-structures are characteristic for them. The observed structural changes confirmed hypothesis about partial dehydration of gluten network after polysaccharides addition. The gluten aggregation and dehydration processes were also reflected in the DSC results, while the TGA ones showed that gluten network remained thermally stable after polysaccharides addition. Copyright © 2017 Elsevier Ltd. All rights reserved.

High performance EUV multilayer structures insensitive to capping layer optical parameters.

PubMed

Pelizzo, Maria Guglielmina; Suman, Michele; Monaco, Gianni; Nicolosi, Piergiorgio; Windt, David L

2008-09-15

We have designed and tested a-periodic multilayer structures containing protective capping layers in order to obtain improved stability with respect to any possible changes of the capping layer optical properties (due to oxidation and contamination, for example)-while simultaneously maximizing the EUV reflection efficiency for specific applications, and in particular for EUV lithography. Such coatings may be particularly useful in EUV lithographic apparatus, because they provide both high integrated photon flux and higher stability to the harsh operating environment, which can affect seriously the performance of the multilayer-coated projector system optics. In this work, an evolutive algorithm has been developed in order to design these a-periodic structures, which have been proven to have also the property of stable performance with respect to random layer thickness errors that might occur during coating deposition. Prototypes have been fabricated, and tested with EUV and X-ray reflectometry, and secondary electron spectroscopy. The experimental results clearly show improved performance of our new a-periodic coatings design compared with standard periodic multilayer structures.

Rapid acquisition of beta-sheet structure in the prion protein prior to multimer formation.

PubMed

Post, K; Pitschke, M; Schäfer, O; Wille, H; Appel, T R; Kirsch, D; Mehlhorn, I; Serban, H; Prusiner, S B; Riesner, D

1998-11-01

The N-terminally truncated form of the prion protein, PrP 27-30, and the corresponding recombinant protein, rPrP, were solubilized in 0.2% SDS, and the transitions induced by changing the conditions from 0.2% SDS to physiological conditions, i.e. removing SDS, were characterized with respect to solubility, resistance to proteolysis, secondary structure and multimerization. Circular dichroism, electron microscopy and fluorescence correlation spectroscopy were used to study the structural transitions of PrP. Within one minute the alpha-helical structure of PrP was transformed into one that was enriched in beta-sheets and consisted mainly of dimers. Larger oligomers were found after 20 minutes and larger multimers exhibiting resistance to proteolysis were found after several hours. It was concluded that the monomeric alpha-helical conformation was stable in SDS or when attached to the membrane; however, the state of lowest free energy in aqueous solution at neutral pH seems to be the multimeric, beta-sheet enriched conformation.

Toward shared care for people with cancer: developing the model with patients and GPs.

PubMed

Hall, Susan J; Samuel, Leslie M; Murchie, Peter

2011-10-01

The number of people surviving cancer for extended periods is increasing. Consequently, due to workload and quality issues, there is considerable interest in alternatives to traditional secondary care-led cancer follow-up. To explore the views of potential recipients of shared follow-up of cancer. To conduct a modelling exercise for shared follow-up and to explore the opinions and experiences of both the patients and GPs involved. Semi-structured audio-taped telephone or face-to-face interviews were conducted with 18 patients with a range of cancers currently attending for structured follow-up in secondary care. Six GPs and five patients (four with melanoma and one with stable metastatic colorectal cancer) took part in a shared follow-up modelling exercise. During the modelling exercise, the GPs attended 4 review meetings, which included brief training seminars, and at the conclusion 10 individuals took part in semi-structured audio-taped telephone or face-to-face interviews. Many rural patients, and some urban patients, would appreciate follow-up being available nearer to home with the associated benefits of time saved and easier parking and continuity of care. Patients have concerns related to the level of extra training received by the GP and loss of contact with their consultant. GPs have concerns about gaining and maintaining the clinical skills needed to conduct follow-up, especially if the numbers of patients seen are small. They also have concerns about lack of support from other GPs, and some administrative and organizational issues. Many patients would be willing to have GPs share their cancer follow-up with the caveat that they had received extra training and were appropriately supported by secondary care specialists. Patients attending shared care clinics appreciated a local service and longer appointment times. GPs stress the importance of maintaining their own clinical skills and reliable clinical and administrative support from secondary care.

Secondary Students' Stable and Unstable Optics Conceptions Using Contextualized Questions

ERIC Educational Resources Information Center

Chu, Hye-Eun; Treagust, David F.

2014-01-01

This study focuses on elucidating and explaining reasons for the stability of and interrelationships between students' conceptions about "Light Propagation" and "Visibility of Objects" using contextualized questions across 3 years of secondary schooling from Years 7 to 9. In a large-scale quantitative study involving 1,233…

A multi-state coarse grained modeling approach for an intrinsically disordered peptide

NASA Astrophysics Data System (ADS)

Ramezanghorbani, Farhad; Dalgicdir, Cahit; Sayar, Mehmet

2017-09-01

Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LKα 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LKα 14 is disordered in dilute solutions; however, it strictly adopts the α -helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an α -helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.

A multi-state coarse grained modeling approach for an intrinsically disordered peptide.

PubMed

Ramezanghorbani, Farhad; Dalgicdir, Cahit; Sayar, Mehmet

2017-09-07

Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LKα14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LKα14 is disordered in dilute solutions; however, it strictly adopts the α-helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an α-helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.

Correlating Polymer Crystals via Self-Induced Nucleation

NASA Astrophysics Data System (ADS)

Reiter, Günter

Crystallizable polymers often form multiple stacks of uniquely oriented lamellae, which have good registry despite being separated by amorphous fold surfaces. These correlations require multiple synchronized, yet unidentified, nucleation events. Here, we demonstrate that in thin films of isotactic polystyrene, the probability of generating correlated lamellae is controlled by the branched morphology of a single primary lamella. The nucleation density ns of secondary lamellae is found to be dependent on the width of the branches of the primary lamella. This relation is independent of molecular weight, crystallization temperature, and film thickness. We propose a nucleation mechanism based on the insertion of polymers into a branched primary lamellar crystal. Even in single crystals, characterized by faceted structures with a well-defined envelope reflecting the underlying crystal unit cell, polymers are folded and thus in a meta-stable state. Annealing such meta-stable single crystals allowed to unveil the initial morphological framework of a dendritic single crystal, i.e. the initial stages of growth.

Beating the Heat - Fast Scanning Melts Silk Beta Sheet Crystals

NASA Astrophysics Data System (ADS)

Cebe, Peggy; Hu, Xiao; Kaplan, David L.; Zhuravlev, Evgeny; Wurm, Andreas; Arbeiter, Daniela; Schick, Christoph

2013-01-01

Beta-pleated-sheet crystals are among the most stable of protein secondary structures, and are responsible for the remarkable physical properties of many fibrous proteins, such as silk, or proteins forming plaques as in Alzheimer's disease. Previous thinking, and the accepted paradigm, was that beta-pleated-sheet crystals in the dry solid state were so stable they would not melt upon input of heat energy alone. Here we overturn that assumption and demonstrate that beta-pleated-sheet crystals melt directly from the solid state to become random coils, helices, and turns. We use fast scanning chip calorimetry at 2,000 K/s and report the first reversible thermal melting of protein beta-pleated-sheet crystals, exemplified by silk fibroin. The similarity between thermal melting behavior of lamellar crystals of synthetic polymers and beta-pleated-sheet crystals is confirmed. Significance for controlling beta-pleated-sheet content during thermal processing of biomaterials, as well as towards disease therapies, is envisioned based on these new findings.

RNA-SSPT: RNA Secondary Structure Prediction Tools.

PubMed

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

RNA-SSPT: RNA Secondary Structure Prediction Tools

PubMed Central

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes. PMID:24250115

Chemical and surface analysis during evolution of arsenopyrite oxidation by Acidithiobacillus thiooxidans in the presence and absence of supplementary arsenic.

PubMed

Ramírez-Aldaba, Hugo; Valles, O Paola; Vazquez-Arenas, Jorge; Rojas-Contreras, J Antonio; Valdez-Pérez, Donato; Ruiz-Baca, Estela; Meraz-Rodríguez, Mónica; Sosa-Rodríguez, Fabiola S; Rodríguez, Ángel G; Lara, René H

2016-10-01

Bioleaching of arsenopyrite presents a great interest due to recovery of valuable metals and environmental issues. The current study aims to evaluate the arsenopyrite oxidation by Acidithiobacillus thiooxidans during 240h at different time intervals, in the presence and absence of supplementary arsenic. Chemical and electrochemical characterizations are carried out using Raman, AFM, SEM-EDS, Cyclic Voltammetry, EIS, electrophoretic and adhesion forces to comprehensively assess the surface behavior and biooxidation mechanism of this mineral. These analyses evidence the formation of pyrite-like secondary phase on abiotic control surfaces, which contrast with the formation of pyrite (FeS2)-like, orpiment (As2S3)-like and elementary sulfur and polysulfide (Sn(2-)/S(0)) phases found on biooxidized surfaces. Voltammetric results indicate a significant alteration of arsenopyrite due to (bio)oxidation. Resistive processes determined with EIS are associated with chemical and electrochemical reactions mediated by (bio)oxidation, resulting in the transformation of arsenopyrite surface and biofilm direct attachment. Charge transfer resistance is increased when (bio)oxidation is performed in the presence of supplementary arsenic, in comparison with lowered abiotic control resistances obtained in its absence; reinforcing the idea that more stable surface products are generated when As(V) is in the system. Biofilm structure is mainly comprised of micro-colonies, progressively enclosed in secondary compounds. A more compact biofilm structure with enhanced formation of secondary compounds is identified in the presence of supplementary arsenic, whereby variable arsenopyrite reactivity is linked and attributed to these secondary compounds, including Sn(2-)/S(0), pyrite-like and orpiment-like phases. Copyright © 2016 Elsevier B.V. All rights reserved.

Identifying Stable Variants of Callous-Unemotional Traits: A Longitudinal Study of At-Risk Girls

ERIC Educational Resources Information Center

Goulter, Natalie; Kimonis, Eva R.; Hawes, Samuel W.; Stepp, Stephanie; Hipwell, Alison E.

2017-01-01

Callous-unemotional (CU) traits have proven important for designating children and adolescents showing a pattern of particularly severe, stable, and aggressive antisocial behaviors (Frick, Ray, Thornton, & Kahn, 2014). Individuals with secondary CU traits represent a subpopulation that are distinguished from those with primary CU traits by…

The G-quadruplex augments translation in the 5' untranslated region of transforming growth factor β2.

PubMed

Agarwala, Prachi; Pandey, Satyaprakash; Mapa, Koyeli; Maiti, Souvik

2013-03-05

Transforming growth factor β2 (TGFβ2) is a versatile cytokine with a prominent role in cell migration, invasion, cellular development, and immunomodulation. TGFβ2 promotes the malignancy of tumors by inducing epithelial-mesenchymal transition, angiogenesis, and immunosuppression. As it is well-documented that nucleic acid secondary structure can regulate gene expression, we assessed whether any secondary motif regulates its expression at the post-transcriptional level. Bioinformatics analysis predicts an existence of a 23-nucleotide putative G-quadruplex sequence (PG4) in the 5' untranslated region (UTR) of TGFβ2 mRNA. The ability of this stretch of sequence to form a highly stable, intramolecular parallel quadruplex was demonstrated using ultraviolet and circular dichroism spectroscopy. Footprinting studies further validated its existence in the presence of a neighboring nucleotide sequence. Following structural characterization, we evaluated the biological relevance of this secondary motif using a dual luciferase assay. Although PG4 inhibits the expression of the reporter gene, its presence in the context of the entire 5' UTR sequence interestingly enhances gene expression. Mutation or removal of the G-quadruplex sequence from the 5' UTR of the gene diminished the level of expression of this gene at the translational level. Thus, here we highlight an activating role of the G-quadruplex in modulating gene expression of TGFβ2 at the translational level and its potential to be used as a target for the development of therapeutics against cancer.

Ligand Based-Pharmacophore Modeling and Extended Bi oactivity Prediction for Salinosporamide A, B and C from Marine Actino mycetes Salinispora tropica.

PubMed

Dineshkumar, Kesavan; Vasudevan, Aparna; Hopper, Waheeta

2017-01-01

Actinomycetes produce structurally unique secondary metabolites with pharmaceutically essential bioactivities. Salinispora, an obligate marine actinomycete, produces structurally varied and unique secondary metabolites. There is plenty of scope for development of drugs from the novel compounds isolated from Salinispora. Anticancer, antibacterial and anti-protozoa activities have been shown for Salinosporamides A, B and C, the secondary metabolites identified from Salinispora, which make them interesting subjects for further extended biological activity prediction. An in silico ligand based-pharmacophore approach was used for the prediction of extended biological targets for salinosporamide A, B and C. Pharmacophore models of salinosporamide A, B and C were generated individually and screened against known drug databases. The drugs with best fitness score were shortlisted, and their respective targets pertaining to their bioactivity were retrieved. The predicted biological drug targets were docked with salinosporamide A, B and C for validation. The glucocorticoid receptor and methionine aminopeptidase 2 showed good docking score and binding energy with salinosporamide A, B and C. Molecular dynamics studies of the protein-ligand complexes showed stable interactions suggesting that the predicted new targets for salinosporamides might be promising. The glucocorticoid receptor and methionine aminopeptidase 2 could be possible new drug targets of bioactivity of salinosporamides. These proteins could be the druggable targets for antiinflammatory and anticancer activity of salinosporamides. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Molecular Evolution of the Non-Coding Eosinophil Granule Ontogeny Transcript

PubMed Central

Rose, Dominic; Stadler, Peter F.

2011-01-01

Eukaryotic genomes are pervasively transcribed. A large fraction of the transcriptional output consists of long, mRNA-like, non-protein-coding transcripts (mlncRNAs). The evolutionary history of mlncRNAs is still largely uncharted territory. In this contribution, we explore in detail the evolutionary traces of the eosinophil granule ontogeny transcript (EGOT), an experimentally confirmed representative of an abundant class of totally intronic non-coding transcripts (TINs). EGOT is located antisense to an intron of the ITPR1 gene. We computationally identify putative EGOT orthologs in the genomes of 32 different amniotes, including orthologs from primates, rodents, ungulates, carnivores, afrotherians, and xenarthrans, as well as putative candidates from basal amniotes, such as opossum or platypus. We investigate the EGOT gene phylogeny, analyze patterns of sequence conservation, and the evolutionary conservation of the EGOT gene structure. We show that EGO-B, the spliced isoform, may be present throughout the placental mammals, but most likely dates back even further. We demonstrate here for the first time that the whole EGOT locus is highly structured, containing several evolutionary conserved, and thermodynamic stable secondary structures. Our analyses allow us to postulate novel functional roles of a hitherto poorly understood region at the intron of EGO-B which is highly conserved at the sequence level. The region contains a novel ITPR1 exon and also conserved RNA secondary structures together with a conserved TATA-like element, which putatively acts as a promoter of an independent regulatory element. PMID:22303364

The complete mitochondrial genome of the pink stem borer, Sesamia inferens, in comparison with four other Noctuid moths.

PubMed

Chai, Huan-Na; Du, Yu-Zhou

2012-01-01

The complete 15,413-bp mitochondrial genome (mitogenome) of Sesamia inferens (Walker) (Lepidoptera: Noctuidae) was sequenced and compared with those of four other noctuid moths. All of the mitogenomes analyzed displayed similar characteristics with respect to gene content, genome organization, nucleotide comparison, and codon usages. Twelve-one protein-coding genes (PCGs) utilized the standard ATN, but the cox1 gene used CGA as the initiation codon; cox1, cox2, and nad4 genes had the truncated termination codon T in the S. inferens mitogenome. All of the tRNA genes had typical cloverleaf secondary structures except for trnS1(AGN), in which the dihydrouridine (DHU) arm did not form a stable stem-loop structure. Both the secondary structures of rrnL and rrnS genes inferred from the S. inferens mitogenome closely resembled those of other noctuid moths. In the A+T-rich region, the conserved motif "ATAGA" followed by a long T-stretch was observed in all noctuid moths, but other specific tandem-repeat elements were more variable. Additionally, the S. inferens mitogenome contained a potential stem-loop structure, a duplicated 17-bp repeat element, a decuplicated segment, and a microsatellite "(AT)(7)", without a poly-A element upstream of the trnM in the A+T-rich region. Finally, the phylogenetic relationships were reconstructed based on amino acid sequences of mitochondrial 13 PCGs, which support the traditional morphologically based view of relationships within the Noctuidae.

The Complete Mitochondrial Genome of the Pink Stem Borer, Sesamia inferens, in Comparison with Four Other Noctuid Moths

PubMed Central

Chai, Huan-Na; Du, Yu-Zhou

2012-01-01

The complete 15,413-bp mitochondrial genome (mitogenome) of Sesamia inferens (Walker) (Lepidoptera: Noctuidae) was sequenced and compared with those of four other noctuid moths. All of the mitogenomes analyzed displayed similar characteristics with respect to gene content, genome organization, nucleotide comparison, and codon usages. Twelve-one protein-coding genes (PCGs) utilized the standard ATN, but the cox1 gene used CGA as the initiation codon; cox1, cox2, and nad4 genes had the truncated termination codon T in the S. inferens mitogenome. All of the tRNA genes had typical cloverleaf secondary structures except for trnS1(AGN), in which the dihydrouridine (DHU) arm did not form a stable stem-loop structure. Both the secondary structures of rrnL and rrnS genes inferred from the S. inferens mitogenome closely resembled those of other noctuid moths. In the A+T-rich region, the conserved motif “ATAGA” followed by a long T-stretch was observed in all noctuid moths, but other specific tandem-repeat elements were more variable. Additionally, the S. inferens mitogenome contained a potential stem-loop structure, a duplicated 17-bp repeat element, a decuplicated segment, and a microsatellite “(AT)7”, without a poly-A element upstream of the trnM in the A+T-rich region. Finally, the phylogenetic relationships were reconstructed based on amino acid sequences of mitochondrial 13 PCGs, which support the traditional morphologically based view of relationships within the Noctuidae. PMID:22949858

Enzyme stability, thermodynamics and secondary structures of α-amylase as probed by the CD spectroscopy.

PubMed

Kikani, B A; Singh, S P

2015-11-01

An amylase of a thermophilic bacterium, Bacillus sp. TSSC-3 (GenBank Number, EU710557) isolated from the Tulsi Shyam hot spring reservoir (Gujarat, India) was purified to the homogeneity in a single step on phenyl sepharose 6FF. The molecular weight of the enzyme was 25kD, while the temperature and pH optima for the enzyme catalysis were 80°C and 7, respectively. The purified enzyme was highly thermostable with broad pH stability and displayed remarkable resistance against surfactants, chelators, urea, guanidine HCl and various solvents as well. The stability and changes in the secondary structure of the enzyme under various extreme conditions were determined by the circular dichroism (CD) spectroscopy. The stability trends and the changes in the α-helices and β-sheets were analyzed by Mean Residual Ellipticity (MRE) and K2D3. The CD data confirmed the structural stability of the enzyme under various harsh conditions, yet it indicated reduced α-helix content and increased β-sheets upon denaturation. The thermodynamic parameters; deactivation rate constant, half-life, changes in entropy, enthalpy, activation energy and Gibb's free energy indicated that the enzyme-substrate reactions were highly stable. The overall profile of the enzyme: high thermostability, alkalitolerance, calcium independent nature, dextrose equivalent values and resistance against chemical denaturants, solvents and surfactants suggest its commercial applications. Copyright © 2015 Elsevier B.V. All rights reserved.

K-Partite RNA Secondary Structures

NASA Astrophysics Data System (ADS)

Jiang, Minghui; Tejada, Pedro J.; Lasisi, Ramoni O.; Cheng, Shanhong; Fechser, D. Scott

RNA secondary structure prediction is a fundamental problem in structural bioinformatics. The prediction problem is difficult because RNA secondary structures may contain pseudoknots formed by crossing base pairs. We introduce k-partite secondary structures as a simple classification of RNA secondary structures with pseudoknots. An RNA secondary structure is k-partite if it is the union of k pseudoknot-free sub-structures. Most known RNA secondary structures are either bipartite or tripartite. We show that there exists a constant number k such that any secondary structure can be modified into a k-partite secondary structure with approximately the same free energy. This offers a partial explanation of the prevalence of k-partite secondary structures with small k. We give a complete characterization of the computational complexities of recognizing k-partite secondary structures for all k ≥ 2, and show that this recognition problem is essentially the same as the k-colorability problem on circle graphs. We present two simple heuristics, iterated peeling and first-fit packing, for finding k-partite RNA secondary structures. For maximizing the number of base pair stackings, our iterated peeling heuristic achieves a constant approximation ratio of at most k for 2 ≤ k ≤ 5, and at most frac6{1-(1-6/k)^k} le frac6{1-e^{-6}} < 6.01491 for k ≥ 6. Experiment on sequences from PseudoBase shows that our first-fit packing heuristic outperforms the leading method HotKnots in predicting RNA secondary structures with pseudoknots. Source code, data set, and experimental results are available at http://www.cs.usu.edu/ mjiang/rna/kpartite/.

Engineering Aromatic-Aromatic Interactions To Nucleate Folding in Intrinsically Disordered Regions of Proteins.

PubMed

Balakrishnan, Swati; Sarma, Siddhartha P

2017-08-22

Aromatic interactions are an important force in protein folding as they combine the stability of a hydrophobic interaction with the selectivity of a hydrogen bond. Much of our understanding of aromatic interactions comes from "bioinformatics" based analyses of protein structures and from the contribution of these interactions to stabilizing secondary structure motifs in model peptides. In this study, the structural consequences of aromatic interactions on protein folding have been explored in engineered mutants of the molten globule protein apo-cytochrome b 5 . Structural changes from disorder to order due to aromatic interactions in two variants of the protein, viz., WF-cytb5 and FF-cytb5, result in significant long-range secondary and tertiary structure. The results show that 54 and 52% of the residues in WF-cytb5 and FF-cytb5, respectively, occupy ordered regions versus 26% in apo-cytochrome b 5 . The interactions between the aromatic groups are offset-stacked and edge-to-face for the Trp-Phe and Phe-Phe mutants, respectively. Urea denaturation studies indicate that both mutants have a C m higher than that of apo-cytochrome b 5 and are more stable to chaotropic agents than apo-cytochrome b 5 . The introduction of these aromatic residues also results in "trimer" interactions with existing aromatic groups, reaffirming the selectivity of the aromatic interactions. These studies provide insights into the aromatic interactions that drive disorder-to-order transitions in intrinsically disordered regions of proteins and will aid in de novo protein design beyond small peptide scaffolds.

A structural model for apolipoprotein C-II amyloid fibrils: experimental characterization and molecular dynamics simulations.

PubMed

Teoh, Chai Lean; Pham, Chi L L; Todorova, Nevena; Hung, Andrew; Lincoln, Craig N; Lees, Emma; Lam, Yuen Han; Binger, Katrina J; Thomson, Neil H; Radford, Sheena E; Smith, Trevor A; Müller, Shirley A; Engel, Andreas; Griffin, Michael D W; Yarovsky, Irene; Gooley, Paul R; Howlett, Geoffrey J

2011-02-04

The self-assembly of specific proteins to form insoluble amyloid fibrils is a characteristic feature of a number of age-related and debilitating diseases. Lipid-free human apolipoprotein C-II (apoC-II) forms characteristic amyloid fibrils and is one of several apolipoproteins that accumulate in amyloid deposits located within atherosclerotic plaques. X-ray diffraction analysis of aligned apoC-II fibrils indicated a simple cross-β-structure composed of two parallel β-sheets. Examination of apoC-II fibrils using transmission electron microscopy, scanning transmission electron microscopy, and atomic force microscopy indicated that the fibrils are flat ribbons composed of one apoC-II molecule per 4.7-Å rise of the cross-β-structure. Cross-linking results using single-cysteine substitution mutants are consistent with a parallel in-register structural model for apoC-II fibrils. Fluorescence resonance energy transfer analysis of apoC-II fibrils labeled with specific fluorophores provided distance constraints for selected donor-acceptor pairs located within the fibrils. These findings were used to develop a simple 'letter-G-like' β-strand-loop-β-strand model for apoC-II fibrils. Fully solvated all-atom molecular dynamics (MD) simulations showed that the model contained a stable cross-β-core with a flexible connecting loop devoid of persistent secondary structure. The time course of the MD simulations revealed that charge clusters in the fibril rearrange to minimize the effects of same-charge interactions inherent in parallel in-register models. Our structural model for apoC-II fibrils suggests that apoC-II monomers fold and self-assemble to form a stable cross-β-scaffold containing relatively unstructured connecting loops. Copyright © 2010 Elsevier Ltd. All rights reserved.

Structural Transformation Detection Contributes to Screening of Behaviorally Active Compounds: Dynamic Binding Process Analysis of DhelOBP21 from Dastarcus helophoroides.

PubMed

Yang, Rui-Nan; Li, Dong-Zhen; Yu, Guangqiang; Yi, Shan-Cheng; Zhang, Yinan; Kong, De-Xin; Wang, Man-Qun

2017-12-01

In light of reverse chemical ecology, the fluorescence competitive binding assays of functional odorant binding proteins (OBPs) is a recent advanced approach for screening behaviorally active compounds of insects. Previous research on Dastareus helophoroides identified a minus-C OBP, DhelOBP21, which preferably binds to several ligands. In this study, only (+)-β-pinene proved attractive to unmated adult beetles. To obtain a more in-depth explanation of the lack of behavioral activity of other ligands we selected compounds with high (camphor) and low (β-caryophyllene) binding affinities. The structural transformation of OBPs was investigated using well-established approaches for studying binding processes, such as fluorescent quenching assays, circular dichroism, and molecular dynamics. The dynamic binding process revealed that the flexibility of DhelOBP21 seems conducive to binding specific ligands, as opposed to broad substrate binding. The compound (+)-β-pinene and DhelOBP21 formed a stable complex through a secondary structural transformation of DhelOBP21, in which its amino-terminus transformed from random coil to an α-helix to cover the binding pocket. On the other hand, camphor could not efficiently induce a stable structural transformation, and its high binding affinities were due to strong hydrogen-bonding, compromising the structure of the protein. The other compound, β-caryophyllene, only collided with DhelOBP21 and could not be positioned in the binding pocket. Studying structural transformation of these proteins through examining the dynamic binding process rather than using approaches that just measure binding affinities such as fluorescence competitive binding assays can provide a more efficient and reliable approach for screening behaviorally active compounds.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaur, Sandeep, E-mail: sipusukhn@gmail.com; Sharma, Amrish; Mudahar, Isha, E-mail: isha@pbi.ac.in

First principle calculations based on density functional theory were performed to calculate the structural and electronic properties of C{sub 20}-N{sub m}@C{sub n} dimer complexes. The calculated binding energies of the complexes formed are comparable to C{sub 60} dimer which ensures their stability. The bond lengths of these dimer complexes were found to be nearly same as pure complexes C{sub 20}-C{sub n}. Further, nitrogen (N) atoms were encapsulated inside the secondary cage (C{sub n}) of dimer complexes and the number of N atoms depends on diameter of the cage. The HOMO-LUMO gaps of new proposed complexes indicate the increase in gapmore » as compared to pure complexes. Mulliken charge analysis of these complexes has been studied which shows the significant charge transfer from the N atoms to the secondary cage of these complexes. The study propose the formation of the new dimer complexes which are stable and are able to encapsulate atoms which are otherwise reactive in free space.« less

Effects of Surface Treatments on Secondary Electron Emission from CVD Diamond Films

NASA Technical Reports Server (NTRS)

Mearini, G. T.; Krainsky, I. L.; Dayton, J. A., Jr.; Zorman, Christian; Wang, Yaxin; Lamouri, A.

1995-01-01

Secondary electron emission (SEE) properties of polycrystalline diamond films grown by chemical vapor deposition (CVD) were measured. The total secondary yield (sigma) from as-grown samples was observed to be as high as 20 at room temperature and 48 while heating at 700 K in vacuum. Electron-beam-activated, alkali-terminated diamond films have shown stable values of sigma as high as 60 when coated with CsI and similarly high values when coated with other alkali halides. Diamond coated with BaF2 had a stable sigma of 6, but no enhancement of the SEE properties was observed with coatings of Ti or Au. Hydrogen was identified to give rise to this effect in as-grown films. However, electron beam exposure led to a reduction in sigma values as low as 2. Exposure to a molecular hydrogen environment restored sigma to its original value after degradation, and enabled stable secondary emission during electron beam exposure. Atomic hydrogen and hydrogen plasma treatments were performed on diamond/Mo samples in an attempt to increase the near-surface hydrogen concentration which might lead to increased stability in the secondary emission. Raman scattering analysis, scanning electron microscopy, and Auger electron spectroscopy (AES) confirmed that hydrogen plasma and atomic hydrogen treatments improved the quality of the CVD diamond significantly. Elastic recoil detection (ERD) showed that heating as-grown diamond targets to 7OO K, which was correlated with an increase in sigma, removed contaminants from the surface but did not drive hydrogen from the diamond bulk. ERD showed that the hydrogen plasma treatment produced an increase in the hydrogen concentration in the near-surface region which did not decrease while heating in vacuum at 700 K, but no improvement in the SEE properties was observed.

RSRE: RNA structural robustness evaluator

PubMed Central

Shu, Wenjie; Zheng, Zhiqiang; Wang, Shengqi

2007-01-01

Biological robustness, defined as the ability to maintain stable functioning in the face of various perturbations, is an important and fundamental topic in current biology, and has become a focus of numerous studies in recent years. Although structural robustness has been explored in several types of RNA molecules, the origins of robustness are still controversial. Computational analysis results are needed to make up for the lack of evidence of robustness in natural biological systems. The RNA structural robustness evaluator (RSRE) web server presented here provides a freely available online tool to quantitatively evaluate the structural robustness of RNA based on the widely accepted definition of neutrality. Several classical structure comparison methods are employed; five randomization methods are implemented to generate control sequences; sub-optimal predicted structures can be optionally utilized to mitigate the uncertainty of secondary structure prediction. With a user-friendly interface, the web application is easy to use. Intuitive illustrations are provided along with the original computational results to facilitate analysis. The RSRE will be helpful in the wide exploration of RNA structural robustness and will catalyze our understanding of RNA evolution. The RSRE web server is freely available at http://biosrv1.bmi.ac.cn/RSRE/ or http://biotech.bmi.ac.cn/RSRE/. PMID:17567615

FANCJ promotes DNA synthesis through G-quadruplex structures

PubMed Central

Castillo Bosch, Pau; Segura-Bayona, Sandra; Koole, Wouter; van Heteren, Jane T; Dewar, James M; Tijsterman, Marcel; Knipscheer, Puck

2014-01-01

Our genome contains many G-rich sequences, which have the propensity to fold into stable secondary DNA structures called G4 or G-quadruplex structures. These structures have been implicated in cellular processes such as gene regulation and telomere maintenance. However, G4 sequences are prone to mutations particularly upon replication stress or in the absence of specific helicases. To investigate how G-quadruplex structures are resolved during DNA replication, we developed a model system using ssDNA templates and Xenopus egg extracts that recapitulates eukaryotic G4 replication. Here, we show that G-quadruplex structures form a barrier for DNA replication. Nascent strand synthesis is blocked at one or two nucleotides from the G4. After transient stalling, G-quadruplexes are efficiently unwound and replicated. In contrast, depletion of the FANCJ/BRIP1 helicase causes persistent replication stalling at G-quadruplex structures, demonstrating a vital role for this helicase in resolving these structures. FANCJ performs this function independently of the classical Fanconi anemia pathway. These data provide evidence that the G4 sequence instability in FANCJ−/− cells and Fancj/dog1 deficient C. elegans is caused by replication stalling at G-quadruplexes. PMID:25193968

Effect of pH shifts on IgE-binding capacity and conformational structure of tropomyosin from short-neck clam (Ruditapes philippinarum).

PubMed

Lin, Haixin; Li, Zhenxing; Lin, Hong; Song, Yongna; Lv, Liangtao; Hao, Zina

2015-12-01

The aim of the present study was to assess pH-induced changes in conformational structures and potential allergenicity of tropomyosin from short-neck clams. As defined with circular dichroism (CD), an unfolded structure was found at pH values ranging from 2.0 to 5.0, followed by the loss of secondary structure at pH of 1.0. Correspondingly, surface hydrophobicity was reduced by 97.7% when pH was reduced from 7.0 to 1.0. Further indirect ELISA and dot-blot results of pH shifted tropomyosin showed that potential allergenicity correlated well with structural changes, as well as with SGF digestibility. Allergenicity decreased significantly with unfolding of the protein and was stable when surface hydrophobicity recovered back to neutral conditions. These results showed that conformational changes in tropomyosin induced by pH shifting significantly influenced the allergenicity of tropomyosin, and that the resulting changes occurred predominately in the acidic pH range. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evaluation of a pilot service to facilitate discharge of patients with stable long-term mental health needs from secondary to primary care: the role of Primary Care Mental Health Specialists.

PubMed

Hamilton-West, Kate; Hotham, Sarah; Yang, Wei; Hedayioglu, Julie; Brigden, Charlotte

2017-07-01

Aim We aimed to evaluate a pilot service to facilitate discharge of patients with stable long-term mental health needs from secondary to primary care. Patients with stable long-term mental health conditions are often not discharged from secondary mental health services when no longer needed due to insufficient systems and processes to enable safe, effective, recovery-focussed treatment and support. The Primary Care Mental Health Specialist (PCMHS) Service was developed to address this gap; new PCMHS posts were introduced to act as a conduit for patients being discharged from secondary care and a single point of referral back into secondary care, should it be required. The two-year pilot, across six Clinical Commissioning Groups in South East England, began in March 2013. Interviews were conducted with all PCMHS employed in the pilot service (n=13) and a sample of service users (n=12). The views of professionals working alongside the service, including GPs, Psychiatrists and Mental Health Nurses, were captured using a brief online questionnaire (n=50). Time and Activity Recording Sheets were used to capture data required for economic analysis. Findings Our findings indicate that the service is working well from the perspective of patients; staff employed within the service and professionals working alongside the service. Patients described the service as a 'safety net' they could fall back on in case of difficulties, whereas staff used the analogy of a 'bridge' to describe the way the service improved communication and collaboration between the various professionals and organisations involved in the patient's care. Improvements in well-being were seen to result from increased support for those transitioning from secondary to primary care, a more pro-active approach to relapse prevention and increased engagement in daily activities. Each PCMHS covered 36 patients in a one-month period, with a unit cost of £73.01 per patient.

Chitosan nanoparticles-trypsin interactions: Bio-physicochemical and molecular dynamics simulation studies.

PubMed

Salar, Safoura; Mehrnejad, Faramarz; Sajedi, Reza H; Arough, Javad Mohammadnejad

2017-10-01

Herein, we investigated the effect of the chitosan nanoparticles (CsNP) on the structure, dynamics, and activity of trypsin. The enzyme activity in complex with the nanoparticles slightly increased, which represents the interactions between the nanoparticles and the enzyme. The kinetic parameters of the enzyme, K m and k cat , increased after adding the nanoparticles, resulting in a slight increase in the catalytic efficiency (k cat /K m ). However, the effect of the nanoparticles on the kinetic stability of trypsin has not exhibited significant variations. Fluorescence spectroscopy did not show remarkable changes in the trypsin conformation in the presence of the nanoparticles. The circular dichroism (CD) spectroscopy results also revealed the secondary structure of trypsin attached to the nanoparticles slightly changed. Furthermore, we used molecular dynamics (MD) simulation to find more information about the interaction mechanisms between the nanoparticles and trypsin. The root mean square deviation (RMSD) of Cα atoms results have shown that in the presence of the nanoparticles, trypsin was stable. The simulation and the calculation of the binding free energy demonstrate that the nonpolar interactions are the most important forces for the formation of stable nanoparticle-trypsin complex. This study has explicitly elucidated that the nanoparticles have not considerable effect on the trypsin. Copyright © 2017. Published by Elsevier B.V.

Structural changes in halophilic and non-halophilic proteases in response to chaotropic reagents.

PubMed

Sinha, Rajeshwari; Khare, S K

2014-08-01

Halophilic enzymes have been established for their stability and catalytic abilities under harsh operational conditions. These have been documented to withstand denaturation at high temperature, pH, organic solvents, and chaotropic agents. However, this stability is modulated by salt. The present study targets an important aspect in understanding protein-urea/GdmCl interactions using proteases from halophilic Bacillus sp. EMB9 and non-halophilic subtilisin (Carlsberg) from Bacillus licheniformis as model systems. While, halophilic protease containing 1 % (w/v) NaCl (0.17 M) retained full activity towards urea (8 M), non-halophilic protease lost about 90 % activity under similar conditions. The secondary and tertiary structure were lost in non-halophilic but preserved for halophilic protein. This effect could be due to the possible charge screening and shielding of the protein surface by Ca(2+) and Na(+) ions rendering it stable against denaturation. The dialyzed halophilic protease almost behaved like the non-halophilic counterpart. Incorporation of NaCl (up to 5 %, w/v or 0.85 M) in dialyzed EMB9 protease containing urea/GdmCl, not only helped regain of proteolytic activity but also evaded denaturing action. Deciphering the basis of this salt modulated stability amidst a denaturing milieu will provide guidelines and templates for engineering stable proteins/enzymes for biotechnological applications.

Dynamic binding of replication protein a is required for DNA repair

PubMed Central

Chen, Ran; Subramanyam, Shyamal; Elcock, Adrian H.; Spies, Maria; Wold, Marc S.

2016-01-01

Replication protein A (RPA), the major eukaryotic single-stranded DNA (ssDNA) binding protein, is essential for replication, repair and recombination. High-affinity ssDNA-binding by RPA depends on two DNA binding domains in the large subunit of RPA. Mutation of the evolutionarily conserved aromatic residues in these two domains results in a separation-of-function phenotype: aromatic residue mutants support DNA replication but are defective in DNA repair. We used biochemical and single-molecule analyses, and Brownian Dynamics simulations to determine the molecular basis of this phenotype. Our studies demonstrated that RPA binds to ssDNA in at least two modes characterized by different dissociation kinetics. We also showed that the aromatic residues contribute to the formation of the longer-lived state, are required for stable binding to short ssDNA regions and are needed for RPA melting of partially duplex DNA structures. We conclude that stable binding and/or the melting of secondary DNA structures by RPA is required for DNA repair, including RAD51 mediated DNA strand exchange, but is dispensable for DNA replication. It is likely that the binding modes are in equilibrium and reflect dynamics in the RPA–DNA complex. This suggests that dynamic binding of RPA to DNA is necessary for different cellular functions. PMID:27131385

Structural elucidation and molecular characterization of Marinobacter sp. α-amylase.

PubMed

Kumar, Sumit; Khan, Rizwan Hasan; Khare, S K

2016-01-01

Halophiles have been perceived as potential source of novel enzymes in recent years. The interest emanates from their ability to catalyze efficiently under high salt and organic solvents. Marinobacter sp. EMB8 α-amylase was found to be active and stable in salt and organic solvents. A study was carried out using circular dichroism (CD), fluorescence spectroscopy, and bioinformatics analysis of similar protein sequence to ascertain molecular basis of salt and solvent adaptability of α-amylase. Structural changes recorded in the presence of varying amounts of NaCl exhibited an increase in negative ellipticity as a function of salt, confirming that salt stabilizes the protein and increases the secondary structure, making it catalytically functional. The data of intrinsic and extrinsic fluorescence (using 1-anilinonaphthalene 8-sulfonate [ANS] as probe) further confirmed the role of salt. The α-amylase was active in the presence of nonpolar solvents, namely, hexane and decane, but inactivated by ethanol. The decrease in the activity was correlated with the loss of tertiary structure in the presence of ethanol. Guanidine hydrochloride and pH denaturation indicated the molten globule state at pH 4.0. Partial N-terminal amino acid sequence of the purified α-amylase revealed the relatedness to Pseudoalteromonas sp. α-amylase. "FVHLFEW" was found as the N-terminal signature sequence. Bioinformatics analysis was done using M. algicola α-amylase protein having the same N-terminal signature sequence. The three-dimensional structure of Marinobacter α-amylase was deduced using the I-TASSER server, which reflected the enrichment of acidic amino acids on the surface, imparting the stability in the presence of salt. Our study clearly indicate that salt is necessary for maintaining the secondary and tertiary structure of halophilic protein, which is a necessary prerequisite for catalysis.

High-throughput density functional calculations to optimize properties and interfacial chemistry of piezoelectric materials

NASA Astrophysics Data System (ADS)

Barr, Jordan A.; Lin, Fang-Yin; Ashton, Michael; Hennig, Richard G.; Sinnott, Susan B.

2018-02-01

High-throughput density functional theory calculations are conducted to search through 1572 A B O3 compounds to find a potential replacement material for lead zirconate titanate (PZT) that exhibits the same excellent piezoelectric properties as PZT and lacks both its use of the toxic element lead (Pb) and the formation of secondary alloy phases with platinum (Pt) electrodes. The first screening criterion employed a search through the Materials Project database to find A -B combinations that do not form ternary compounds with Pt. The second screening criterion aimed to eliminate potential candidates through first-principles calculations of their electronic structure, in which compounds with a band gap of 0.25 eV or higher were retained. Third, thermodynamic stability calculations were used to compare the candidates in a Pt environment to compounds already calculated to be stable within the Materials Project. Formation energies below or equal to 100 meV/atom were considered to be thermodynamically stable. The fourth screening criterion employed lattice misfit to identify those candidate perovskites that have low misfit with the Pt electrode and high misfit of potential secondary phases that can be formed when Pt alloys with the different A and B components. To aid in the final analysis, dynamic stability calculations were used to determine those perovskites that have dynamic instabilities that favor the ferroelectric distortion. Analysis of the data finds three perovskites warranting further investigation: CsNb O3 , RbNb O3 , and CsTa O3 .

Plant secondary metabolite-induced shifts in bacterial community structure and degradative ability in contaminated soil.

PubMed

Uhlik, Ondrej; Musilova, Lucie; Ridl, Jakub; Hroudova, Miluse; Vlcek, Cestmir; Koubek, Jiri; Holeckova, Marcela; Mackova, Martina; Macek, Tomas

2013-10-01

The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and degradative activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with changes in chlorobiphenyl degradation capacity. In order to address this issue, we have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons and DNA-stable isotope probing (SIP). Our model system was set in laboratory microcosms with PCB-contaminated soil, which was enriched for 8 weeks with the suspensions of flavonoid naringin, terpene limonene, and phenolic caffeic acid. Our results show that application of selected plant secondary metabolites resulted in bacterial community structure far different from the control one (no natural compound amendment). The community in soil treated with caffeic acid is almost solely represented by Proteobacteria, Acidobacteria, and Verrucomicrobia (together over 99 %). Treatment with naringin resulted in an enrichment of Firmicutes to the exclusion of Acidobacteria and Verrucomicrobia. SIP was applied in order to identify populations actively participating in 4-chlorobiphenyl catabolism. We observed that naringin and limonene in soil foster mainly populations of Hydrogenophaga spp., caffeic acid Burkholderia spp. and Pseudoxanthomonas spp. None of these populations were detected among 4-chlorobiphenyl utilizers in non-amended soil. Similarly, the degradation of individual PCB congeners was influenced by the addition of different plant compounds. Residual content of PCBs was lowest after treating the soil with naringin. Addition of caffeic acid resulted in comparable decrease of total PCBs with non-amended soil; however, higher substituted congeners were more degraded after caffeic acid treatment compared to all other treatments. Finally, it appears that plant secondary metabolites have a strong effect on the bacterial community structure, activity, and associated degradative ability.

Triangular prism-shaped β-peptoid helices as unique biomimetic scaffolds

NASA Astrophysics Data System (ADS)

Laursen, Jonas S.; Harris, Pernille; Fristrup, Peter; Olsen, Christian A.

2015-05-01

β-Peptoids are peptidomimetics based on N-alkylated β-aminopropionic acid residues (or N-alkyl-β-alanines). This type of peptide mimic has previously been incorporated in biologically active ligands and has been hypothesized to be able to exhibit foldamer properties. Here we show, for the first time, that β-peptoids can be tuned to fold into stable helical structures. We provide high-resolution X-ray crystal structures of homomeric β-peptoid hexamers, which reveal right-handed helical conformations with exactly three residues per turn and a helical pitch of 9.6-9.8 Å between turns. The presence of folded conformations in solution is supported by circular dichroism spectroscopy showing length- and solvent dependency, and molecular dynamics simulations provide further support for a stabilized helical secondary structure in organic solvent. We thus outline a framework for future design of novel biomimetics that display functional groups with high accuracy in three dimensions, which has potential for development of new functional materials.

High Efficient Photo-Fenton Catalyst of α-Fe2O3/MoS2 Hierarchical Nanoheterostructures: Reutilization for Supercapacitors

NASA Astrophysics Data System (ADS)

Yang, Xijia; Sun, Haiming; Zhang, Lishu; Zhao, Lijun; Lian, Jianshe; Jiang, Qing

2016-08-01

A novel three-dimensional (3D) α-Fe2O3/MoS2 hierarchical nanoheterostructure is effectively synthesized via a facile hydrothermal method. The zero-dimensional (0D) Fe2O3 nanoparticles guide the growth of two-dimensional (2D) MoS2 nanosheets and formed 3D flower-like structures, while MoS2 facilitates the good dispersion of porous Fe2O3 with abundant oxygen vacancies. This charming 3D-structure with perfect match of non-equal dimension exhibits high recyclable photo-Fenton catalytic activity for Methyl orange pollutant and nice specific capacity in reusing as supercapacitor after catalysis. The synergistic effect between Fe2O3 and MoS2, the intermediate nanointerfaces, the 3D porous structures, and the abundant oxygen vacancies both contribute to highly active catalysis, nice electrochemical performance and stable cycling. This strategy is simple, cheap, and feasible for maximizing the value of the materials, as well as eliminating the secondary pollution.

High Efficient Photo-Fenton Catalyst of α-Fe2O3/MoS2 Hierarchical Nanoheterostructures: Reutilization for Supercapacitors.

PubMed

Yang, Xijia; Sun, Haiming; Zhang, Lishu; Zhao, Lijun; Lian, Jianshe; Jiang, Qing

2016-08-16

A novel three-dimensional (3D) α-Fe2O3/MoS2 hierarchical nanoheterostructure is effectively synthesized via a facile hydrothermal method. The zero-dimensional (0D) Fe2O3 nanoparticles guide the growth of two-dimensional (2D) MoS2 nanosheets and formed 3D flower-like structures, while MoS2 facilitates the good dispersion of porous Fe2O3 with abundant oxygen vacancies. This charming 3D-structure with perfect match of non-equal dimension exhibits high recyclable photo-Fenton catalytic activity for Methyl orange pollutant and nice specific capacity in reusing as supercapacitor after catalysis. The synergistic effect between Fe2O3 and MoS2, the intermediate nanointerfaces, the 3D porous structures, and the abundant oxygen vacancies both contribute to highly active catalysis, nice electrochemical performance and stable cycling. This strategy is simple, cheap, and feasible for maximizing the value of the materials, as well as eliminating the secondary pollution.

Effect of calcium ions on structure and stability of the C1q-like domain of otolin-1 from human and zebrafish.

PubMed

Hołubowicz, Rafał; Wojtas, Magdalena; Taube, Michał; Kozak, Maciej; Ożyhar, Andrzej; Dobryszycki, Piotr

2017-12-01

Otolin-1 is a collagen-like protein expressed in the inner ear of vertebrates. It provides an organic scaffold for otoliths in fish and otoconia in land vertebrates. In this study, the expression and purification procedure of C1q-like domain of otolin-1 from human and zebrafish was developed. The structure and stability of the proteins were investigated. The results of sedimentation velocity analytical ultracentrifugation and small-angle X-ray scattering indicated that the C1q-like domain of otolin-1 forms stable trimers in solution in the presence of calcium ions. It was also observed that calcium ions influenced the secondary structure of the proteins. C1q-like domains were stabilized by the calcium ions. The human variant was especially affected by the calcium ions. The results indicate the importance of the C1q-like domain for the assembly of the organic matrix of otoliths and otoconia. © 2017 Federation of European Biochemical Societies.

Effects of high hydrostatic pressure on the structure and potential allergenicity of the major allergen bovine β-lactoglobulin.

PubMed

Meng, Xuanyi; Bai, Yuxin; Gao, Jinyan; Li, Xin; Chen, Hongbing

2017-03-15

Bovine β-lactoglobulin (β-Lg) is recognized as a significant milk allergen in several countries. In this study, β-Lg was isolated and treated with high hydrostatic pressure (HHP) at 100, 200, 300, 400, and 500MPa. The allergenic properties of the HHP-treated β-Lg were characterized by indirect competitive enzyme-linked immunosorbent assay with anti-β-Lg rabbit antibody and the sera of patients allergic to cows' milk. The conformation of the HHP-treated β-Lg was examined with ultraviolet absorption spectroscopy, endogenous fluorescence spectroscopy, exogenous fluorescence spectroscopy, and circular dichroism spectroscopy analyses. The results indicated that IgG binding increased with treatment pressure, and IgE binding was lowest at 200MPa and highest at 400MPa. The tertiary structure of β-Lg changed significantly after HHP, whereas the primary and secondary structures remained stable. Overall, this study suggests that the conformational changes in HHP-treated β-Lg contribute to its altered allergenicity. Copyright © 2016 Elsevier Ltd. All rights reserved.

Silicon nitride ceramic development in Thales Alenia Space : qualification achievement and further developments for future applications

NASA Astrophysics Data System (ADS)

Cornillon, L.; Devilliers, C.; Behar-Lafenetre, S.; Ait-Zaid, S.; Berroth, K.; Bravo, A. C.

2017-11-01

Dealing with ceramic materials for more than two decades, Thales Alenia Space - France has identified Silicon Nitride Si3N4 as a high potential material for the manufacturing of stiff, stable and lightweight truss structure for future large telescopes. Indeed, for earth observation or astronomic observation, space mission requires more and more telescopes with high spatial resolution, which leads to the use of large primary mirrors, and a long distance between primary and secondary mirrors. Therefore current and future large space telescopes require a huge truss structure to hold and locate precisely the mirrors. Such large structure requires very strong materials with high specific stiffness and a low coefficient of thermal expansion (CTE). Based on the silicon nitride performances and on the know how of FCT Ingenieurkeramik to manufacture complex parts, Thales Alenia Space (TAS) has engaged, in cooperation with FCT, activities to develop and qualify silicon nitride parts for other applications for space projects.

Silicon nitride ceramic development in Thales Alenia Space: qualification achiement and further developments for future applications

NASA Astrophysics Data System (ADS)

Cornillon, L.; Devilliers, C.; Behar-Lafenetre, S.; Ait-Zaid, S.; Berroth, K.; Bravo, A. C.

2017-11-01

Dealing with ceramic materials for more than two decades, Thales Alenia Space - France has identified Silicon Nitride Si3N4 as a high potential material for the manufacturing of stiff, stable and lightweight truss structure for future large telescopes. Indeed, for earth observation or astronomic observation, space mission requires more and more telescopes with high spatial resolution, which leads to the use of large primary mirrors, and a long distance between primary and secondary mirrors. Therefore current and future large space telescopes require a huge truss structure to hold and locate precisely the mirrors. Such large structure requires very strong materials with high specific stiffness and a low coefficient of thermal expansion (CTE). Based on the silicon nitride performances and on the know how of FCT Ingenieurkeramik to manufacture complex parts, Thales Alenia Space (TAS) has engaged, in cooperation with FCT, activities to develop and qualify silicon nitride parts for other applications for space projects.

Cyclic trimer of human cystatin C, an amyloidogenic protein - molecular dynamics and experimental studies

NASA Astrophysics Data System (ADS)

Chrabåszczewska, Magdalena; Maszota-Zieleniak, Martyna; Pietralik, Zuzanna; Taube, Michał; Rodziewicz-Motowidło, Sylwia; Szymańska, Aneta; Szutkowski, Kosma; Clemens, Daniel; Grubb, Anders; Kozak, Maciej

2018-05-01

Human cystatin C (HCC) is a cysteine protease inhibitor that takes a series of oligomeric forms in solution (e.g., dimers, trimers, tetramers, decamers, dodecamers, and other higher oligomers). The best-known form of cystatin C is the dimer, which arises as a result of a domain swapping mechanism. The formation of the HCC oligomeric forms, which is most likely due to this domain swapping mechanism, is associated with the aggregation of HCC into amyloid fibrils and deposits. To investigate the structure of a specific HCC oligomer, we developed a covalently stabilized trimer of HCC. An atomic model of this HCC trimer was proposed on the basis of molecular docking and molecular dynamics simulations. The most stable model of the HCC trimer obtained from the molecular dynamics simulations is characterized by a well-preserved secondary structure. The molecular size and structural parameters of the HCC trimer in solution were also confirmed by Small Angle Neutron Scattering and Nuclear Magnetic Resonance Diffusometry.

Aminophenoxycyclotriphosphazene cured epoxy resins and the composites, laminates, adhesives and structures thereof

NASA Technical Reports Server (NTRS)

Kumar, Devendra (Inventor); Fohlen, George M. (Inventor); Parker, John A. (Inventor)

1977-01-01

Aminophenoxy cyclotriphosphazenes such as hexakis (4-aminophenoxy) cyclotriphosphazene and tris (4-aminophenoxy)-tris phenoxy cyclotriphosphazene are used as curing agents for epoxy resins. These 1,2-epoxy resins are selected from di- or polyepoxide containing organic moieties of the formula (CH2-CHO-CH2) m-W-R-W- (CH2CH-CH2O)m where R is diphenyl dimethylmethane, diphenylmethane; W is a nitrogen or oxygen atom; and m is 1 when W is oxygen and 2 when W is nitrogen. The resins are cured thermally in stages at between about 110 to 135 C for between about 1 and 10 min, then at between about 175 to 185 C for between 0.5 to 10 hr and post cured at between about 215 and 235 C for between 0.1 and 2 hr. These resins are useful for making fire resistant elevated temperature stable composites, laminates, molded parts, and adhesives and structures, usually for aircraft secondary structures and for spacecraft construction.

Guano-Derived Nutrient Subsidies Drive Food Web Structure in Coastal Ponds.

PubMed

Vizzini, Salvatrice; Signa, Geraldina; Mazzola, Antonio

2016-01-01

A stable isotope study was carried out seasonally in three coastal ponds (Marinello system, Italy) affected by different gull guano input to investigate the effect of nutrient subsidies on food web structure and dynamics. A marked 15N enrichment occurred in the pond receiving the highest guano input, indicating that gull-derived fertilization (guanotrophication) had a strong localised effect and flowed across trophic levels. The main food web response to guanotrophication was an overall erosion of the benthic pathway in favour of the planktonic. Subsidized primary consumers, mostly deposit feeders, switched their diet according to organic matter source availability. Secondary consumers and, in particular, fish from the guanotrophic pond, acted as couplers of planktonic and benthic pathways and showed an omnivorous trophic behaviour. Food web structure showed substantial variability among ponds and a marked seasonality in the subsidized one: an overall simplification was evident only in summer when guano input maximises its trophic effects, while higher trophic diversity and complexity resulted when guano input was low to moderate.

Guano-Derived Nutrient Subsidies Drive Food Web Structure in Coastal Ponds

PubMed Central

Vizzini, Salvatrice; Signa, Geraldina; Mazzola, Antonio

2016-01-01

A stable isotope study was carried out seasonally in three coastal ponds (Marinello system, Italy) affected by different gull guano input to investigate the effect of nutrient subsidies on food web structure and dynamics. A marked 15N enrichment occurred in the pond receiving the highest guano input, indicating that gull-derived fertilization (guanotrophication) had a strong localised effect and flowed across trophic levels. The main food web response to guanotrophication was an overall erosion of the benthic pathway in favour of the planktonic. Subsidized primary consumers, mostly deposit feeders, switched their diet according to organic matter source availability. Secondary consumers and, in particular, fish from the guanotrophic pond, acted as couplers of planktonic and benthic pathways and showed an omnivorous trophic behaviour. Food web structure showed substantial variability among ponds and a marked seasonality in the subsidized one: an overall simplification was evident only in summer when guano input maximises its trophic effects, while higher trophic diversity and complexity resulted when guano input was low to moderate. PMID:26953794

Plasma membrane aquaporins mediates vesicle stability in broccoli

PubMed Central

Martínez-Ballesta, Maria del Carmen; García-Gomez, Pablo; Yepes-Molina, Lucía; Guarnizo, Angel L.; Teruel, José A.

2018-01-01

The use of in vitro membrane vesicles is attractive because of possible applications in therapies. Here we aimed to compare the stability and functionality of plasma membrane vesicles extracted from control and salt-treated broccoli. The impact of the amount of aquaporins was related to plasma membrane osmotic water permeability and the stability of protein secondary structure. Here, we describe for first time an increase in plant aquaporins acetylation under high salinity. Higher osmotic water permeability in NaCl vesicles has been related to higher acetylation, upregulation of aquaporins, and a more stable environment to thermal denaturation. Based on our findings, we propose that aquaporins play an important role in vesicle stability. PMID:29420651

Dissecting protein function: an efficient protocol for identifying separation-of-function mutations that encode structurally stable proteins.

PubMed

Lubin, Johnathan W; Rao, Timsi; Mandell, Edward K; Wuttke, Deborah S; Lundblad, Victoria

2013-03-01

Mutations that confer the loss of a single biochemical property (separation-of-function mutations) can often uncover a previously unknown role for a protein in a particular biological process. However, most mutations are identified based on loss-of-function phenotypes, which cannot differentiate between separation-of-function alleles vs. mutations that encode unstable/unfolded proteins. An alternative approach is to use overexpression dominant-negative (ODN) phenotypes to identify mutant proteins that disrupt function in an otherwise wild-type strain when overexpressed. This is based on the assumption that such mutant proteins retain an overall structure that is comparable to that of the wild-type protein and are able to compete with the endogenous protein (Herskowitz 1987). To test this, the in vivo phenotypes of mutations in the Est3 telomerase subunit from Saccharomyces cerevisiae were compared with the in vitro secondary structure of these mutant proteins as analyzed by circular-dichroism spectroscopy, which demonstrates that ODN is a more sensitive assessment of protein stability than the commonly used method of monitoring protein levels from extracts. Reverse mutagenesis of EST3, which targeted different categories of amino acids, also showed that mutating highly conserved charged residues to the oppositely charged amino acid had an increased likelihood of generating a severely defective est3(-) mutation, which nevertheless encoded a structurally stable protein. These results suggest that charge-swap mutagenesis directed at a limited subset of highly conserved charged residues, combined with ODN screening to eliminate partially unfolded proteins, may provide a widely applicable and efficient strategy for generating separation-of-function mutations.

Photodynamic therapy for polypoidal choroidal vasculopathy secondary to choroidal nevus.

PubMed

Wong, James G; Lai, Xin Jie; Sarafian, Richard Y; Wong, Hon Seng; Smith, Jeremy B

2017-01-01

We report a case of a Caucasian female who developed active polypoidal choroidal vasculopathy (PCV) at the edge of a stable choroidal nevus and was successfully treated with verteporfin photodynamic therapy. No active polyp was detectable on indocyanine green angiography 2 years after treatment, and good vision was maintained. Indocyanine green angiography is a useful investigation to diagnose PCV and may be underutilized. Unlike treatment of choroidal neovascularization secondary to choroidal nevus, management of PCV secondary to nevus may not require intravitreal anti-vascular endothelial growth factor therapy. Photodynamic monotherapy may be an effective treatment of secondary PCV.

Exploring the Molecular Design of Protein Interaction Sites with Molecular Dynamics Simulations and Free Energy Calculations†

PubMed Central

Liang, Shide; Li, Liwei; Hsu, Wei-Lun; Pilcher, Meaghan N.; Uversky, Vladimir; Zhou, Yaoqi; Dunker, A. Keith; Meroueh, Samy O.

2009-01-01

The significant work that has been invested toward understanding protein–protein interaction has not translated into significant advances in structure-based predictions. In particular redesigning protein surfaces to bind to unrelated receptors remains a challenge, partly due to receptor flexibility, which is often neglected in these efforts. In this work, we computationally graft the binding epitope of various small proteins obtained from the RCSB database to bind to barnase, lysozyme, and trypsin using a previously derived and validated algorithm. In an effort to probe the protein complexes in a realistic environment, all native and designer complexes were subjected to a total of nearly 400 ns of explicit-solvent molecular dynamics (MD) simulation. The MD data led to an unexpected observation: some of the designer complexes were highly unstable and decomposed during the trajectories. In contrast, the native and a number of designer complexes remained consistently stable. The unstable conformers provided us with a unique opportunity to define the structural and energetic factors that lead to unproductive protein–protein complexes. To that end we used free energy calculations following the MM-PBSA approach to determine the role of nonpolar effects, electrostatics and entropy in binding. Remarkably, we found that a majority of unstable complexes exhibited more favorable electrostatics than native or stable designer complexes, suggesting that favorable electrostatic interactions are not prerequisite for complex formation between proteins. However, nonpolar effects remained consistently more favorable in native and stable designer complexes reinforcing the importance of hydrophobic effects in protein–protein binding. While entropy systematically opposed binding in all cases, there was no observed trend in the entropy difference between native and designer complexes. A series of alanine scanning mutations of hot-spot residues at the interface of native and designer complexes showed less than optimal contacts of hot-spot residues with their surroundings in the unstable conformers, resulting in more favorable entropy for these complexes. Finally, disorder predictions revealed that secondary structures at the interface of unstable complexes exhibited greater disorder than the stable complexes. PMID:19113835

Thermal stability and magnetic properties of MgFe2O4@ZnO nanoparticles

NASA Astrophysics Data System (ADS)

Mallesh, S.; Prabu, D.; Srinivas, V.

2017-05-01

Magnesium ferrite, MgFe2O4, (MgFO) nanoparticles (NPs) have been synthesized through sol-gel process. Subsequently, as prepared particles were coated with Zinc-oxide (ZnO) layer(s) through ultrasonication process. Thermal stability, structure and magnetic properties of as-prepared (AP) and annealed samples in the temperature range of 350 °C-1200 °C have been investigated. Structural data suggests that AP MgFO NPs and samples annealed below 500 °C in air exhibit stable ferrite phase. However, α-Fe2O3 and a small fraction of MgO secondary phases appear along with ferrite phase on annealing in the temperatures range 500 °C- 1000 °C. This results in significant changes in magnetic moment for AP NPs 0.77 μB increases to 0.92 μB for 1200 °C air annealed sample. The magnetic properties decreased at intermediate temperatures due to the presence of secondary phases. On the other hand, pure ferrite phase could be stabilized with an optimum amount of ZnO coated MgFO NPs for samples annealed in the temperature range 500 °C-1000 °C with improvement in magnetic behavior compared to that of MgFO samples.

The effect of steam sterilization on recombinant spider silk particles.

PubMed

Lucke, Matthias; Winter, Gerhard; Engert, Julia

2015-03-15

In this work, the recombinant spider silk protein eADF4(C16) was used to fabricate particles in the submicron range using a micromixing method. Furthermore, particles in the micrometer range were produced using an ultrasonic atomizer system. Both particle species were manufactured by an all-aqueous process. The submicroparticles were 332 nm in average diameter, whereas 6.70 μm was the median size of the microparticles. Both particle groups showed a spherical shape and exhibited high β-sheet content in secondary structure. Submicro- and microparticles were subsequently steam sterilized and investigated with respect to particle size, secondary structure and thermal stability. Sterilization temperature and time were increased to assess the thermal stability of eADF4(C16) particles. Actually, particles remained stable and their properties did not change even after autoclaving at 134°C. Both, the untreated and the autoclaved submicroparticles showed no overt cytotoxicity on human dermal fibroblasts after incubation for 72 h. The eADF4(C16) particles were already loaded with proteins and small molecules in previous studies. With that, we can provide a highly promising parenteral drug delivery system based on a defined polypeptide carrier, manufactured with an all-aqueous process and being fully sterilizable. Copyright © 2015 Elsevier B.V. All rights reserved.

Ultrastable α phase nickel hydroxide as energy storage materials for alkaline secondary batteries

NASA Astrophysics Data System (ADS)

Huang, Haili; Guo, Yinjian; Cheng, Yuanhui

2018-03-01

α Phase nickel hydroxide (α-Ni(OH)2) has higher theoretical capacity than that of commercial β phase Ni(OH)2. But the low stability inhibits its wide application in alkaline rechargeable batteries. Here, we propose a totally new idea to stabilize α phase Ni(OH)2 by introducing large organic molecule into the interlayer spacing together with doping multivalent cobalt into the layered Ni(OH)2 host. Ethylene glycol is served as neutral stabilizer in the interlayer spacing. Nickel is substituted by cobalt to increase the electrostatic attraction between layered Ni(OH)2 host and anion ions in the interlayer spacing. Polyethylene glycol (PEG-200) is utilized to design a three-dimensional network structure. This prepared α-Ni(OH)2-20 exhibits specific capacity as high as 334 mAh g-1and good structural stability even after immersing into strong alkaline zincate solution for 20 days. Ni(OH)2 electrode with a specific capacity of 35 mAh cm-2 is fabricated and used as positive electrode in zinc-nickel single flow batteries, which also shows good cycling stability. This result can provide an important guideline for the rational design and preparation of highly active and stable α phase Ni(OH)2 for alkaline secondary battery.

De novo design and structure-activity relationships of peptide emulsifiers and foaming agents.

PubMed

Enser, M; Bloomberg, G B; Brock, C; Clark, D C

1990-04-01

A series of eight amphipathic peptides (8, 11, 15, 2 x 18, 22, 26, 29 amino acids in length) were designed to investigate the effects of amino acid composition, peptide length and secondary structure on surface activity assessed as emulsification and foaming activity. The potential for alpha-helix formation at the hydrophobic/hydrophilic interface was maximized through the use of helix-forming amino acids, a relatively large hydrophobic surface of 200 degrees of arc and ion pairs between basic and acidic amino acids on the hydrophilic surface. Emulsification activity increased rapidly between 11 and 22 residues as alpha-helicity in aqueous solution increased. Despite their small size, the peptides produced exceptionally stable emulsions, compared with proteins. Foaming activity was enhanced by the presence of aromatic amino acids and the activity of the best peptide examined was superior to that of bovine serum albumin and beta-lactoglobulin.

Intrinsic folding of small peptide chains: spectroscopic evidence for the formation of beta-turns in the gas phase.

PubMed

Chin, Wutharath; Dognon, Jean-Pierre; Piuzzi, François; Tardivel, Benjamin; Dimicoli, Iliana; Mons, Michel

2005-01-19

Laser desorption of model peptides coupled to laser spectroscopic techniques enables the gas-phase observation of genuine secondary structures of biology. Spectroscopic evidence for the formation of beta-turns in gas-phase peptide chains containing glycine and phenylalanine residues establishes the intrinsic stability of these forms and their ability to compete with other stable structures. The precise characterization of local minima on the potential energy surface from IR spectroscopy constitutes an acute assessment for the state-of-the-art quantum mechanical calculations also presented. The observation of different types of beta-turns depending upon the residue order within the sequence is found to be consistent with the residue propensities in beta-turns of proteins, which suggests that the prevalence of glycine in type II and II' turns stems essentially from an energetic origin, already at play under isolated conditions.

Energetic rationale for an unexpected and abrupt reversal of guanidinium chloride-induced unfolding of peptide deformylase.

PubMed

Berg, Alexander K; Manokaran, Sumathra; Eiler, Daniel; Kooren, Joel; Mallik, Sanku; Srivastava, D K

2008-01-01

Peptide deformylase (PDF) catalyzes the removal of formyl group from the N-terminal methionine residues of nascent proteins in prokaryotes, and this enzyme is a high priority target for antibiotic design. In pursuit of delineating the structural-functional features of Escherichia coli PDF (EcPDF), we investigated the mechanistic pathway for the guanidinium chloride (GdmCl)-induced unfolding of the enzyme by monitoring the secondary structural changes via CD spectroscopy. The experimental data revealed that EcPDF is a highly stable enzyme, and it undergoes slow denaturation in the presence of varying concentrations of GdmCl. The most interesting aspect of these studies has been the abrupt reversal of the unfolding pathway at low to moderate concentrations of the denaturant, but not at high concentration. An energetic rationale for such an unprecedented feature in protein chemistry is offered.

Biophysical evaluation of hybrid Fc fusion protein of hGH to achieve basal buffer system.

PubMed

Kim, Nam Ah; An, In Bok; Lim, Hye Seong; Yang, Sang In; Jeong, Seong Hoon

2016-11-20

A newly developed hybrid Fc (hyFc) is a non-immunogenic and non-cytolytic Fc with intact Ig structure derived from human IgD and IgG4. It is fused with the human growth hormone (GXD-9) and was evaluated by various biophysical techniques. Two thermal transitions were evident by DSC, reflecting the unfolding of IgG4 and the conjugated protein. The highest T m of the initial GXD-9 was 68.17°C and the T m of the two domains were around 66°C and 70°C. Although T m increased with decreasing concentration, which reflects increasing conformational stability, aggregation issues were still observed by DLS. This might be caused by decreasing or low zeta potential due to a highly complex structure. The protein was dialyzed to various pH (6.2-8.2) values to enhance conformational stability and to overcome aggregation issues. The results of CD spectroscopy were correlated with DSC measurements to evaluate its conformational stability. Changes in secondary structural contents were similar as determined by DSC and DLS. In conclusion, GXD-9 was found to be most stable at pH 7.0. The investigation of the biophysical stability of a hyFc-fusion protein has demonstrated a positive feasibility of developing more stable formulations to facilitate the initial drug development process for further clinical trials. Copyright © 2016 Elsevier B.V. All rights reserved.

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts

PubMed Central

Hafsa, Noor E.; Arndt, David; Wishart, David S.

2015-01-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains.

PubMed

Wang, Zhiming; Qiao, Zhu; Ye, Sheng; Zhang, Rongguang

2015-04-01

Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.

Molecular modeling of the human sperm associated antigen 11 B (SPAG11B) proteins.

PubMed

Narmadha, Ganapathy; Yenugu, Suresh

2015-04-01

Antimicrobial proteins and peptides are ubiquitous in nature with diverse structural and biological properties. Among them, the human beta-defensins are known to contribute to the innate immune response. Besides the defensins, a number of defensin-like proteins and peptides are expressed in many organ systems including the male reproductive system. Some of the protein isoforms encoded by the sperm associated antigen 11B (SPAG11) gene in humans are beta-defensin-like and exhibit structure dependent and salt tolerant antimicrobial activity, besides contributing to sperm maturation. Though some of the functional roles of these proteins are reported, the structural and molecular features that contribute to their antimicrobial activity is not yet reported. In this study, using in silico tools, we report the three dimensional structure of the human SPAG11B proteins and their C-terminal peptides. web-based hydropathy, amphipathicity, and topology (WHAT) analyses and grand average of hydropathy (GRAVY) indices show that these proteins and peptides are amphipathic and highly hydrophilic. Self-optimized prediction method with alignment (SOPMA) analyses and circular dichroism data suggest that the secondary structure of these proteins and peptides primarily contain beta-sheet and random coil structure and alpha-helix to a lesser extent. Ramachandran plots show that majority of the amino acids in these proteins and peptides fall in the permissible regions, thus indicating stable structures. The secondary structure of SPAG11B isoforms and their peptides were not perturbed with increasing NaCl concentration (0-300 mM) and at different pH (3, 7, and 10), thus reinforcing our previously reported observation that their antimicrobial activity is salt tolerant. To the best of our knowledge, for the first time, results of our study provide vital information on the structural features of SPAG11B protein isoforms and their contribution to antimicrobial activity.

SL1 revisited: functional analysis of the structure and conformation of HIV-1 genome RNA.

PubMed

Sakuragi, Sayuri; Yokoyama, Masaru; Shioda, Tatsuo; Sato, Hironori; Sakuragi, Jun-Ichi

2016-11-11

The dimer initiation site/dimer linkage sequence (DIS/DLS) region of HIV is located on the 5' end of the viral genome and suggested to form complex secondary/tertiary structures. Within this structure, stem-loop 1 (SL1) is believed to be most important and an essential key to dimerization, since the sequence and predicted secondary structure of SL1 are highly stable and conserved among various virus subtypes. In particular, a six-base palindromic sequence is always present at the hairpin loop of SL1 and the formation of kissing-loop structure at this position between the two strands of genomic RNA is suggested to trigger dimerization. Although the higher-order structure model of SL1 is well accepted and perhaps even undoubted lately, there could be stillroom for consideration to depict the functional SL1 structure while in vivo (in virion or cell). In this study, we performed several analyses to identify the nucleotides and/or basepairing within SL1 which are necessary for HIV-1 genome dimerization, encapsidation, recombination and infectivity. We unexpectedly found that some nucleotides that are believed to contribute the formation of the stem do not impact dimerization or infectivity. On the other hand, we found that one G-C basepair involved in stem formation may serve as an alternative dimer interactive site. We also report on our further investigation of the roles of the palindromic sequences on viral replication. Collectively, we aim to assemble a more-comprehensive functional map of SL1 on the HIV-1 viral life cycle. We discovered several possibilities for a novel structure of SL1 in HIV-1 DLS. The newly proposed structure model suggested that the hairpin loop of SL1 appeared larger, and genome dimerization process might consist of more complicated mechanism than previously understood. Further investigations would be still required to fully understand the genome packaging and dimerization of HIV.

Experimental study on cesium immobilization in struvite structures.

PubMed

Wagh, Arun S; Sayenko, S Y; Shkuropatenko, V A; Tarasov, R V; Dykiy, M P; Svitlychniy, Y O; Virych, V D; Ulybkina, Е А

2016-01-25

Ceramicrete, a chemically bonded phosphate ceramic, was developed for nuclear waste immobilization and nuclear radiation shielding. Ceramicrete products are fabricated by an acid-base reaction between magnesium oxide and mono potassium phosphate that has a struvite-K mineral structure. In this study, we demonstrate that this crystalline structure is ideal for incorporating radioactive Cs into a Ceramicrete matrix. This is accomplished by partially replacing K by Cs in the struvite-K structure, thus forming struvite-(K, Cs) mineral. X-ray diffraction and thermo-gravimetric analyses are used to confirm such a replacement. The resulting product is non-leachable and stable at high temperatures, and hence it is an ideal matrix for immobilizing Cs found in high-activity nuclear waste streams. The product can also be used for immobilizing secondary waste streams generated during glass vitrification of spent fuel, or the method described in this article can be used as a pretreatment method during glass vitrification of high level radioactive waste streams. Furthermore, it suggests a method of producing safe commercial radioactive Cs sources. Copyright © 2015 Elsevier B.V. All rights reserved.

Early stage structural development of prototypical zeolitic imidazolate framework (ZIF) in solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Terban, Maxwell W.; Banerjee, Debasis; Ghose, Sanjit

Given the wide-ranging potential applications of metal organic frameworks (MOFs), an emerging imperative is to understand their formation with atomic scale precision. This will aid in designing syntheses for next-generation MOFs with enhanced properties and functionalities. Major challenges are to characterize the early-stage seeds, and the pathways to framework growth, which require synthesis coupled with in situ structural characterization sensitive to nanoscale structures in solution. Here we report measurements of an in situ synthesis of a prototypical MOF, ZIF-8, utilizing synchrotron X-ray atomic pair distribution function (PDF) analysis optimized for sensitivity to dilute species, complemented by mass spectrometry, electron microscopy,more » and density functional theory calculations. We observe that despite rapid formation of the crystalline product, a high concentration of Zn(2-MeIm) 4(2-MeIm=2-methylimidazolate) initially forms and persists as stable clusters over long times. A secondary, amorphous phase also pervades during the synthesis, which has a structural similarity to the final ZIF-8 and may act as an intermediate to the final product.« less

Computational design of RNAs with complex energy landscapes.

PubMed

Höner zu Siederdissen, Christian; Hammer, Stefan; Abfalter, Ingrid; Hofacker, Ivo L; Flamm, Christoph; Stadler, Peter F

2013-12-01

RNA has become an integral building material in synthetic biology. Dominated by their secondary structures, which can be computed efficiently, RNA molecules are amenable not only to in vitro and in vivo selection, but also to rational, computation-based design. While the inverse folding problem of constructing an RNA sequence with a prescribed ground-state structure has received considerable attention for nearly two decades, there have been few efforts to design RNAs that can switch between distinct prescribed conformations. We introduce a user-friendly tool for designing RNA sequences that fold into multiple target structures. The underlying algorithm makes use of a combination of graph coloring and heuristic local optimization to find sequences whose energy landscapes are dominated by the prescribed conformations. A flexible interface allows the specification of a wide range of design goals. We demonstrate that bi- and tri-stable "switches" can be designed easily with moderate computational effort for the vast majority of compatible combinations of desired target structures. RNAdesign is freely available under the GPL-v3 license. Copyright © 2013 Wiley Periodicals, Inc.

Early stage structural development of prototypical zeolitic imidazolate framework (ZIF) in solution

DOE PAGES

Terban, Maxwell W.; Banerjee, Debasis; Ghose, Sanjit; ...

2018-02-05

Given the wide-ranging potential applications of metal organic frameworks (MOFs), an emerging imperative is to understand their formation with atomic scale precision. This will aid in designing syntheses for next-generation MOFs with enhanced properties and functionalities. Major challenges are to characterize the early-stage seeds, and the pathways to framework growth, which require synthesis coupled with in situ structural characterization sensitive to nanoscale structures in solution. Here we report measurements of an in situ synthesis of a prototypical MOF, ZIF-8, utilizing synchrotron X-ray atomic pair distribution function (PDF) analysis optimized for sensitivity to dilute species, complemented by mass spectrometry, electron microscopy,more » and density functional theory calculations. We observe that despite rapid formation of the crystalline product, a high concentration of Zn(2-MeIm) 4(2-MeIm=2-methylimidazolate) initially forms and persists as stable clusters over long times. A secondary, amorphous phase also pervades during the synthesis, which has a structural similarity to the final ZIF-8 and may act as an intermediate to the final product.« less

Hyperactive antifreeze proteins from longhorn beetles: some structural insights.

PubMed

Kristiansen, Erlend; Wilkens, Casper; Vincents, Bjarne; Friis, Dennis; Lorentzen, Anders Blomkild; Jenssen, Håvard; Løbner-Olesen, Anders; Ramløv, Hans

2012-11-01

This study reports on structural characteristics of hyperactive antifreeze proteins (AFPs) from two species of longhorn beetles. In Rhagium mordax, eight unique mRNAs coding for five different mature AFPs were identified from cold-hardy individuals. These AFPs are apparently homologues to a previously characterized AFP from the closely related species Rhagium inquisitor, and consist of six identifiable repeats of a putative ice binding motif TxTxTxT spaced irregularly apart by segments varying in length from 13 to 20 residues. Circular dichroism spectra show that the AFPs from both species have a high content of β-sheet and low levels of α-helix and random coil. Theoretical predictions of residue-specific secondary structure locate these β-sheets within the putative ice-binding motifs and the central parts of the segments separating them, consistent with an overall β-helical structure with the ice-binding motifs stacked in a β-sheet on one side of the coil. Molecular dynamics models based on these findings show that these AFPs would be energetically stable in a β-helical conformation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Expansion method in secondary total ear reconstruction for undesirable reconstructed ear.

PubMed

Liu, Tun; Hu, Jintian; Zhou, Xu; Zhang, Qingguo

2014-09-01

Ear reconstruction by autologous costal cartilage grafting is the most widely applied technique with fewer complications. However, undesirable ear reconstruction brings more problems to plastic surgeons. Some authors resort to free flap or osseointegration technique with prosthetic ear. In this article, we introduce a secondary total ear reconstruction with expanded skin flap method. From July 2010 to April 2012, 7 cases of undesirable ear reconstruction were repaired by tissue expansion method. Procedures including removal of previous cartilage framework, soft tissue expander insertion, and second stage of cartilage framework insertion were performed to each case regarding their local conditions. The follow-up time ranged from 6 months to 2.5 years. All of the cases recovered well with good 3-dimensional forms, symmetrical auriculocephalic angle, and stable fixation. All these evidence showed that this novel expansion method is safe, stable, and less traumatic for secondary total ear reconstruction. With sufficient expanded skin flap and refabricated cartilage framework, lifelike appearance of reconstructed ear could be acquired without causing additional injury.

Hydrogen /Hydride/-air secondary battery

NASA Technical Reports Server (NTRS)

Sarradin, J.; Bronoel, G.; Percheron-Guegan, A.; Achard, J. C.

1979-01-01

The use of metal hydrides as negative electrodes in a hydrogen-air secondary battery seems promising. However, in an unpressurized cell, more stable hydrides that LaNi5H6 must be selected. Partial substitutions of nickel by aluminium or manganese increase the stability of hydrides. Combined with an air reversible electrode, a specific energy close to 100 Wh/kg can be expected.

Variation of the stable isotopes of water with altitiude in the Saint Elias Mountains of Canada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holdsworth, G.; Fogarasi, S.; Krouse, H.R.

1991-04-20

The stable isotopes of water, measured in melt samples taken from snow pits and cores at locations between 1,750- and 5,930-m altitude on Mount Logan and between 2,900 and 4,900 m on Mount Steele, in the Saint Elias Mountains, Yukon, show a distinctive altitudinal distribution. Several {delta}{sup 18}O and {delta}D versus altitude profiles indicate the general persistence of a nearly iso-{delta} step, or staircase structure, separating a lower region of altitude dependent isotopic fractionation between 1,750 and 3,350 m from another apparent frictionation sequence appearing above about 5,300 m. On the one hand, postdepositional changes to isotope ratios in snowmore » at different altitudes may cause distortions to an otherwise nearly monotonic isotope fractionation sequence, but the main anomaly appears to be far too large to be explained this way. On the other hand, an explanation linked to processes occuring in the lower and midtroposphere is based on established meteorological principles as well as on upper air data. This hypothesis is proposed as the primary one to explain the gross features of the observed isotope profiles. It is compatible with the concept of secondary-source moisture arriving via the upper troposphere, and it does not exclude the effects of postdepositional stratigraphic and stable isotope ratio changes. Over interannual time scales, any vertical modulation of the observed isotope-altitude structure, from, for example, changes in wind regime, would give rise to an additional signal in any ice core {delta} time series. These findings identify a potential difficulty in the interpretation of stable isotope records obtained from high mountain ice core sites. It is possible that the results may have application to atmospheric circulation modeling, where the effects of extreme topography are being studied.« less

Binary asteroid population. 3. Secondary rotations and elongations

NASA Astrophysics Data System (ADS)

Pravec, P.; Scheirich, P.; Kušnirák, P.; Hornoch, K.; Galád, A.; Naidu, S. P.; Pray, D. P.; Világi, J.; Gajdoš, Š.; Kornoš, L.; Krugly, Yu. N.; Cooney, W. R.; Gross, J.; Terrell, D.; Gaftonyuk, N.; Pollock, J.; Husárik, M.; Chiorny, V.; Stephens, R. D.; Durkee, R.; Reddy, V.; Dyvig, R.; Vraštil, J.; Žižka, J.; Mottola, S.; Hellmich, S.; Oey, J.; Benishek, V.; Kryszczyńska, A.; Higgins, D.; Ries, J.; Marchis, F.; Baek, M.; Macomber, B.; Inasaridze, R.; Kvaratskhelia, O.; Ayvazian, V.; Rumyantsev, V.; Masi, G.; Colas, F.; Lecacheux, J.; Montaigut, R.; Leroy, A.; Brown, P.; Krzeminski, Z.; Molotov, I.; Reichart, D.; Haislip, J.; LaCluyze, A.

2016-03-01

We collected data on rotations and elongations of 46 secondaries of binary and triple systems among near-Earth, Mars-crossing and small main belt asteroids. 24 were found or are strongly suspected to be synchronous (in 1:1 spin-orbit resonance), and the other 22, generally on more distant and/or eccentric orbits, were found or are suggested to have asynchronous rotations. For 18 of the synchronous secondaries, we constrained their librational angles, finding that their long axes pointed to within 20° of the primary on most epochs. The observed anti-correlation of secondary synchroneity with orbital eccentricity and the limited librational angles agree with the theories by Ćuk and Nesvorný (Ćuk, M., Nesvorný, D. [2010]. Icarus 207, 732-743) and Naidu and Margot (Naidu, S.P., Margot, J.-L. [2015]. Astron. J. 149, 80). A reason for the asynchronous secondaries being on wider orbits than synchronous ones may be longer tidal circularization time scales at larger semi-major axes. The asynchronous secondaries show relatively fast spins; their rotation periods are typically < 10 h. An intriguing observation is a paucity of chaotic secondary rotations; with an exception of (35107) 1991 VH, the secondary rotations are single-periodic with no signs of chaotic rotation and their periods are constant on timescales from weeks to years. The secondary equatorial elongations show an upper limit of a2 /b2 ∼ 1.5 . The lack of synchronous secondaries with greater elongations appears consistent, considering uncertainties of the axis ratio estimates, with the theory by Ćuk and Nesvorný that predicts large regions of chaotic rotation in the phase space for a2 /b2 ≳√{ 2 } . Alternatively, secondaries may not form or stay very elongated in gravitational (tidal) field of the primary. It could be due to the secondary fission mechanism suggested by Jacobson and Scheeres (Jacobson, S.A., Scheeres, D.J. [2011]. Icarus 214, 161-178), as its efficiency is correlated with the secondary elongation. Sharma (Sharma, I. [2014]. Icarus 229, 278-294) found that rubble-pile satellites with a2 /b2 ≲ 1.5 are more stable to finite structural perturbations than more elongated ones. It appears that more elongated secondaries, if they originally formed in spin fission of parent asteroid, are less likely to survive intact and they more frequently fail or fission.

Free Energy and Structure of Helix-forming Peptides: A Theoretical Investigation

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim

This thesis focuses on the structure and free energy of helical secondary structures of short peptides in a variety of experimental settings. Specifically, the formation of alpha-, pi- and 310-helices was investigated using large-scale classical molecular dynamics simulations with state-of-the-art force fields. In addition, the recently developed Adaptively Biased Molecular Dynamics (ABMD) and Steered Molecular Dynamics (SMD) methods were used to calculate the corresponding free energies. The most important results are as follows. For the examined peptide homopolymers, the observed minima on the free energy landscapes (based on suitable collective variables such as the radius of gyration, number of hydrogen bonds, and handedness) were associated with alpha-helices and "globular" or "knot-like" configurations only. No evidence was found to indicate that 310- or pi-helices represent equilibrium structures for these systems. In addition, the free energy landscape of short peptide chains formed by mixing two different amino acids were also examined. These results too indicate that the alpha-helix is only equilibrium helical secondary structure, and that the mixing of different amino acids does not result in the introduction of any significant new minima into the free energy landscapes. These results are in agreement with experimental observations insofar as these indicate that helical structural motifs are primary based on alpha-helices, with 310- and pi-helices being observed only rarely. Although pi- and 310-helices represent nonequilibrium structures, we were still able to estimate their free energies by means of SMD simulations. The helical secondary structure of the examined polypeptide chains is due to the formation of hydrogen bonds. However, there are other mechanisms that may allow for the additional stabilization of these structures. Specifically, in the so-called AK-(4,7) protein, the possible presence of disulfide bonds connecting cysteine residues may significantly alter the free energy landscapes and therefore the stability of different helical structures. We therefore examined this issue with ABMD simulations. However, our results show that while the free energy landscapes are indeed significantly altered only the formation of alpha-helices is favored as a secondary structural motif. Since all the results indicate that alpha-helix formation dominates, it is natural to think in terms of an alpha-helix forming propensity for different amino acids. To address this question, we carried out an extensive residue-by-residue population analysis of different amino acid guests in an alanine-based host setting. Such an analysis allows us to rank the different amino acid guests based on whether they increased or decreased the population in the alpha-helix region of the corresponding Ramachandran plots. Our ranking of the different guest amino acids is in reasonable correspondence with the experimental results, although some differences are observed. Finally, using a four-beads coarse-grained model were have investigated the stability of GA88 and GB88 proteins, which are quite similar in terms of their amino acid sequence, by means of 10mus simulations. The results indicate that while the three alpha-helix bundle of the GA88 protein remains stable, the 2beta--alpha--2beta configuration of the GB88 protein does not: the latter rapidly converts to a structure consisting mostly of helices similar to the GA88 protein design. These results indicate that this particular four-bead coarse-grained model is not able to properly grasp the dynamics of the beta-sheet secondary structure and overstabilizes the corresponding helical content.

Development of a general non-noble metal catalyst for the benign amination of alcohols with amines and ammonia.

PubMed

Cui, Xinjiang; Dai, Xingchao; Deng, Youquan; Shi, Feng

2013-03-11

The N-alkylation of amines or ammonia with alcohols is a valuable route for the synthesis of N-alkyl amines. However, as a potentially clean and economic choice for N-alkyl amine synthesis, non-noble metal catalysts with high activity and good selectivity are rarely reported. Normally, they are severely limited due to low activity and poor generality. Herein, a simple NiCuFeOx catalyst was designed and prepared for the N-alkylation of ammonia or amines with alcohol or primary amines. N-alkyl amines with various structures were successfully synthesized in moderate to excellent yields in the absence of organic ligands and bases. Typically, primary amines could be efficiently transformed into secondary amines and N-heterocyclic compounds, and secondary amines could be N-alkylated to synthesize tertiary amines. Note that primary and secondary amines could be produced through a one-pot reaction of ammonia and alcohols. In addition to excellent catalytic performance, the catalyst itself possesses outstanding superiority, that is, it is air and moisture stable. Moreover, the magnetic property of this catalyst makes it easily separable from the reaction mixture and it could be recovered and reused for several runs without obvious deactivation. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polyhydroxyester films obtained by non-catalyzed melt-polycondensation of natural occurring fatty polyhydroxyacids.

NASA Astrophysics Data System (ADS)

Benitez, Jose; Heredia-Guerrero, José; Guzman-Puyol, Susana; Barthel, Markus; Dominguez, Eva; Heredia, Antonio

2015-08-01

Free-standing polyesters films from mono and polyhydroxylated fatty acids (C16 and C18) have been obtained by non-catalyzed melt-condensation polymerization in air at 150°C. Chemical characterization by Fourier Transform Infrared Spectroscopy (FTIR) and 13C Magic Angle Spinning Nuclear Magnetic Resonance (13C MAS-NMR) has confirmed the formation of the corresponding esters and the occurrence of hydroxyl partial oxidation which extent depends on the type of hydroxylation of the monomer (primary or secondary). Generally, polyester films obtained are hydrophobic, insoluble in common solvents, amorphous and infusible as revealed by X-ray Diffraction (XRD) and Differential Scanning Calorimetry (DSC). In ?-polyhydroxy acids, esterification reaction with primary hydroxyls is preferential and, therefore, the structure can be defined as linear with variable branching depending on the amount of esterified secondary hydroxyls. The occurrence side oxidative reactions like the diol cleavage are responsible for chain cross-linking. Films are thermally stable up to 200-250°C though this limit can be extended up to 300°C in the absence of ester bonds involving secondary hydroxyls. By analogy with natural occurring fatty polyesters (i.e. cutin in higher plants) these polymers are proposed as biodegradable and non-toxic barrier films or coatings to be used, for instance, in food packing

Plasticity in variation of xylem and phloem cell characteristics of Norway spruce under different local conditions

PubMed Central

Gričar, Jožica; Prislan, Peter; de Luis, Martin; Gryc, Vladimír; Hacurová, Jana; Vavrčík, Hanuš; Čufar, Katarina

2015-01-01

There is limited information on intra-annual plasticity of secondary tissues of tree species growing under different environmental conditions. To increase the knowledge about the plasticity of secondary growth, which allows trees to adapt to specific local climatic regimes, we examined climate–radial growth relationships of Norway spruce [Picea abies (L.) H. Karst.] from three contrasting locations in the temperate climatic zone by analyzing tree-ring widths for the period 1932–2010, and cell characteristics in xylem and phloem increments formed in the years 2009–2011. Variation in the structure of xylem and phloem increments clearly shows that plasticity in seasonal dynamics of cambial cell production and cell differentiation exists on xylem and phloem sides. Anatomical characteristics of xylem and phloem cells are predominantly site-specific characteristics, because they varied among sites but were fairly uniform among years in trees from the same site. Xylem and phloem tissues formed in the first part of the growing season seemed to be more stable in structure, indicating their priority over latewood and late phloem for tree performance. Long-term climate and radial growth analyses revealed that growth was in general less dependent on precipitation than on temperature; however, growth sensitivity to local conditions differed among the sites. Only partial dependence of radial growth of spruce on climatic factors on the selected sites confirms its strategy to adapt the structure of wood and phloem increments to function optimally in local conditions. PMID:26442044

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

PubMed

Hafsa, Noor E; Arndt, David; Wishart, David S

2015-07-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Housing and sexual health among street-involved youth.

PubMed

Kumar, Maya M; Nisenbaum, Rosane; Barozzino, Tony; Sgro, Michael; Bonifacio, Herbert J; Maguire, Jonathon L

2015-10-01

Street-involved youth (SIY) carry a disproportionate burden of sexually transmitted diseases (STD). Studies among adults suggest that improving housing stability may be an effective primary prevention strategy for improving sexual health. Housing options available to SIY offer varying degrees of stability and adult supervision. This study investigated whether housing options offering more stability and adult supervision are associated with fewer STD and related risk behaviors among SIY. A cross-sectional study was performed using public health survey and laboratory data collected from Toronto SIY in 2010. Three exposure categories were defined a priori based on housing situation: (1) stable and supervised housing, (2) stable and unsupervised housing, and (3) unstable and unsupervised housing. Multivariate logistic regression was used to test the association between housing category and current or recent STD. Secondary analyses were performed using the following secondary outcomes: blood-borne infection, recent binge-drinking, and recent high-risk sexual behavior. The final analysis included 184 SIY. Of these, 28.8 % had a current or recent STD. Housing situation was stable and supervised for 12.5 %, stable and unsupervised for 46.2 %, and unstable and unsupervised for 41.3 %. Compared to stable and supervised housing, there was no significant association between current or recent STD among stable and unsupervised housing or unstable and unsupervised housing. There was no significant association between housing category and risk of blood-borne infection, binge-drinking, or high-risk sexual behavior. Although we did not demonstrate a significant association between stable and supervised housing and lower STD risk, our incorporation of both housing stability and adult supervision into a priori defined exposure groups may inform future studies of housing-related prevention strategies among SIY. Multi-modal interventions beyond housing alone may also be required to prevent sexual morbidity among these vulnerable youth.

The conservation and function of RNA secondary structure in plants

PubMed Central

Vandivier, Lee E.; Anderson, Stephen J.; Foley, Shawn W.; Gregory, Brian D.

2016-01-01

RNA transcripts fold into secondary structures via intricate patterns of base pairing. These secondary structures impart catalytic, ligand binding, and scaffolding functions to a wide array of RNAs, forming a critical node of biological regulation. Among their many functions, RNA structural elements modulate epigenetic marks, alter mRNA stability and translation, regulate alternative splicing, transduce signals, and scaffold large macromolecular complexes. Thus, the study of RNA secondary structure is critical to understanding the function and regulation of RNA transcripts. Here, we review the origins, form, and function of RNA secondary structure, focusing on plants. We then provide an overview of methods for probing secondary structure, from physical methods such as X-ray crystallography and nuclear magnetic resonance imaging (NMR) to chemical and nuclease probing methods. Marriage with high-throughput sequencing has enabled these latter methods to scale across whole transcriptomes, yielding tremendous new insights into the form and function of RNA secondary structure. PMID:26865341

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

PubMed Central

Dong, Min; Graham, Mitchell; Yadav, Nehul

2017-01-01

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

Structure of poly(ethylene glycol)-modified horseradish peroxidase in organic solvents: infrared amide I spectral changes upon protein dehydration are largely caused by protein structural changes and not by water removal per se.

PubMed Central

Al-Azzam, Wasfi; Pastrana, Emil A; Ferrer, Yancy; Huang, Qing; Schweitzer-Stenner, Reinhard; Griebenow, Kai

2002-01-01

Fourier transform infrared (FTIR) spectroscopy has emerged as a powerful tool to guide the development of stable lyophilized protein formulations by providing information on the structure of proteins in amorphous solids. The underlying assumption is that IR spectral changes in the amide I and III region upon protein dehydration are caused by protein structural changes. However, it has been claimed that amide I IR spectral changes could be the result of water removal per se. Here, we investigated whether such claims hold true. The structure of horseradish peroxidase (HRP) and poly(ethylene glycol)-modified HRP (HRP-PEG) has been investigated under various conditions (in aqueous solution, the amorphous dehydrated state, and dissolved/suspended in toluene and benzene) by UV-visible (UV-Vis), FTIR, and resonance Raman spectroscopy. The resonance Raman and UV-Vis spectra of dehydrated HRP-PEG dissolved in neat toluene or benzene were very similar to that of HRP in aqueous buffer, and thus the heme environment (heme iron spin, coordination, and redox state) was essentially the same under both conditions. Therefore, the three-dimensional structure of HRP-PEG dissolved in benzene and toluene was similar to that in aqueous solution. The amide I IR spectra of HRP-PEG in aqueous buffer and of dehydrated HRP-PEG dissolved in neat benzene and toluene were also very similar, and the secondary structure compositions (percentages of alpha-helices and beta-sheets) were within the standard error the same. These results are irreconcilable with recent claims that water removal per se could cause substantial amide I IR spectral changes (M. van de Weert, P.I. Haris, W.E. Hennink, and D.J. Crommelin. 2001. Anal. Biochem. 297:160-169). On the contrary, amide I IR spectral changes upon protein dehydration are caused by perturbations in the secondary structure. PMID:12496131

Stability of Secondary and Tertiary Structures of Virus-Like Particles Representing Noroviruses: Effects of pH, Ionic Strength, and Temperature and Implications for Adhesion to Surfaces.

PubMed

Samandoulgou, Idrissa; Hammami, Riadh; Morales Rayas, Rocio; Fliss, Ismail; Jean, Julie

2015-11-01

Loss of ordered molecular structure in proteins is known to increase their adhesion to surfaces. The aim of this work was to study the stability of norovirus secondary and tertiary structures and its implications for viral adhesion to fresh foods and agrifood surfaces. The pH, ionic strength, and temperature conditions studied correspond to those prevalent in the principal vehicles of viral transmission (vomit and feces) and in the food processing and handling environment (pasteurization and refrigeration). The structures of virus-like particles representing GI.1, GII.4, and feline calicivirus (FCV) were studied using circular dichroism and intrinsic UV fluorescence. The particles were remarkably stable under most of the conditions. However, heating to 65°C caused losses of β-strand structure, notably in GI.1 and FCV, while at 75°C the α-helix content of GII.4 and FCV decreased and tertiary structures unfolded in all three cases. Combining temperature with pH or ionic strength caused variable losses of structure depending on the particle type. Regardless of pH, heating to pasteurization temperatures or higher would be required to increase GII.4 and FCV adhesion, while either low or high temperatures would favor GI.1 adhesion. Regardless of temperature, increased ionic strength would increase GII.4 adhesion but would decrease GI.1 adhesion. FCV adsorption would be greater at refrigeration, pasteurization, or high temperature combined with a low salt concentration or at a higher NaCl concentration regardless of temperature. Norovirus adhesion mediated by hydrophobic interaction may depend on hydrophobic residues normally exposed on the capsid surface at pH 3, pH 8, physiological ionic strength, and low temperature, while at pasteurization temperatures it may rely more on buried hydrophobic residues exposed upon structural rearrangement. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Rtools: a web server for various secondary structural analyses on single RNA sequences.

PubMed

Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

2016-07-08

The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dynamics and control of twisting bi-stable structures

NASA Astrophysics Data System (ADS)

Arrieta, Andres F.; van Gemmeren, Valentin; Anderson, Aaron J.; Weaver, Paul M.

2018-02-01

Compliance-based morphing structures have the potential to offer large shape adaptation, high stiffness and low weight, while reducing complexity, friction, and scalability problems of mechanism based systems. A promising class of structure that enables these characteristics are multi-stable structures given their ability to exhibit large deflections and rotations without the expensive need for continuous actuation, with the latter only required intermittently. Furthermore, multi-stable structures exhibit inherently fast response due to the snap-through instability governing changes between stable states, enabling rapid configuration switching between the discrete number of programmed shapes of the structure. In this paper, the design and utilisation of the inherent nonlinear dynamics of bi-stable twisting I-beam structures for actuation with low strain piezoelectric materials is presented. The I-beam structure consists of three compliant components assembled into a monolithic single element, free of moving parts, and showing large deflections between two stable states. Finite element analysis is utilised to uncover the distribution of strain across the width of the flange, guiding the choice of positioning for piezoelectric actuators. In addition, the actuation authority is maximised by calculating the generalised coupling coefficient for different positions of the piezoelectric actuators. The results obtained are employed to tailor and test I-beam designs exhibiting desired large deflection between stable states, while still enabling the activation of snap-through with the low strain piezoelectric actuators. To this end, the dynamic response of the I-beams to piezoelectric excitation is investigated, revealing that resonant excitations are insufficient to dynamically trigger snap-through. A novel bang-bang control strategy, which exploits the nonlinear dynamics of the structure successfully triggers both single and constant snap-through between the stable states of the bi-stable twisting I-beam structures. The obtained optimal piezoelectric actuator positioning is not necessarily intuitive and when used with the proposed dynamic actuation strategy serve as a blueprint for the actuation of such multi-stable compliant structures to produce fast and large deflections with highly embeddable actuators. This class of structures has potential applications in aerospace systems and soft/compliant robotics.

Matching problem for primary and secondary signals in dual-phase TPC detectors

NASA Astrophysics Data System (ADS)

Radics, B.; Burjons, E.; Rubbia, A.

2018-05-01

The problem of matching primary and secondary light signals, belonging to the same event, is presented in the context of dual-phase time projection chambers. In large scale detectors the secondary light emission could be delayed up to order of milliseconds, which, combined with high signal rates, could make the matching of the signals challenging. A possible approach is offered in the framework of the Stable Marriage and the College Admission problem, for both of which solutions are given by the Gale-Shapley algorithm.

Changes in Examination Performance in English Secondary Schools over the Course of a Decade: Searching for Patterns and Trends over Time

ERIC Educational Resources Information Center

Mangan, Jean; Pugh, Geoff; Gray, John

2005-01-01

The article explores changes in the examination performance of a random sample of 500 English secondary schools between 1992 and 2001. Using econometric methods, it concludes that: there is an overall deterministic trend in school performance but it is not stable, making prediction accuracy poor; the aggregate trend does not explain improvement…

Optimization of naltrexone diclofenac codrugs for sustained drug delivery across microneedle-treated skin.

PubMed

Ghosh, Priyanka; Lee, DoMin; Kim, Kyung Bo; Stinchcomb, Audra L

2014-01-01

The purpose of this work was to optimize the structure of codrugs for extended delivery across microneedle treated skin. Naltrexone, the model compound was linked with diclofenac, a nonspecific cyclooxygenase inhibitor to enhance the pore lifetime following microneedle treatment and develop a 7 day transdermal system for naltrexone. Four different codrugs of naltrexone and diclofenac were compared in terms of stability and solubility. Transdermal flux, permeability and skin concentration of both parent drugs and codrugs were quantified to form a structure permeability relationship. The results indicated that all codrugs bioconverted in the skin. The degree of conversion was dependent on the structure, phenol linked codrugs were less stable compared to the secondary alcohol linked structures. The flux of naltrexone across microneedle treated skin and the skin concentration of diclofenac were higher for the phenol linked codrugs. The polyethylene glycol link enhanced solubility of the codrugs, which translated into flux enhancement. The current studies indicated that formulation stability of codrugs and the flux of naltrexone can be enhanced via structure design optimization. The polyethylene glycol linked naltrexone diclofenac codrug is better suited for a 7 day drug delivery system both in terms of stability and drug delivery.

Prediction of RNA secondary structures: from theory to models and real molecules

NASA Astrophysics Data System (ADS)

Schuster, Peter

2006-05-01

RNA secondary structures are derived from RNA sequences, which are strings built form the natural four letter nucleotide alphabet, {AUGC}. These coarse-grained structures, in turn, are tantamount to constrained strings over a three letter alphabet. Hence, the secondary structures are discrete objects and the number of sequences always exceeds the number of structures. The sequences built from two letter alphabets form perfect structures when the nucleotides can form a base pair, as is the case with {GC} or {AU}, but the relation between the sequences and structures differs strongly from the four letter alphabet. A comprehensive theory of RNA structure is presented, which is based on the concepts of sequence space and shape space, being a space of structures. It sets the stage for modelling processes in ensembles of RNA molecules like evolutionary optimization or kinetic folding as dynamical phenomena guided by mappings between the two spaces. The number of minimum free energy (mfe) structures is always smaller than the number of sequences, even for two letter alphabets. Folding of RNA molecules into mfe energy structures constitutes a non-invertible mapping from sequence space onto shape space. The preimage of a structure in sequence space is defined as its neutral network. Similarly the set of suboptimal structures is the preimage of a sequence in shape space. This set represents the conformation space of a given sequence. The evolutionary optimization of structures in populations is a process taking place in sequence space, whereas kinetic folding occurs in molecular ensembles that optimize free energy in conformation space. Efficient folding algorithms based on dynamic programming are available for the prediction of secondary structures for given sequences. The inverse problem, the computation of sequences for predefined structures, is an important tool for the design of RNA molecules with tailored properties. Simultaneous folding or cofolding of two or more RNA molecules can be modelled readily at the secondary structure level and allows prediction of the most stable (mfe) conformations of complexes together with suboptimal states. Cofolding algorithms are important tools for efficient and highly specific primer design in the polymerase chain reaction (PCR) and help to explain the mechanisms of small interference RNA (si-RNA) molecules in gene regulation. The evolutionary optimization of RNA structures is illustrated by the search for a target structure and mimics aptamer selection in evolutionary biotechnology. It occurs typically in steps consisting of short adaptive phases interrupted by long epochs of little or no obvious progress in optimization. During these quasi-stationary epochs the populations are essentially confined to neutral networks where they search for sequences that allow a continuation of the adaptive process. Modelling RNA evolution as a simultaneous process in sequence and shape space provides answers to questions of the optimal population size and mutation rates. Kinetic folding is a stochastic process in conformation space. Exact solutions are derived by direct simulation in the form of trajectory sampling or by solving the master equation. The exact solutions can be approximated straightforwardly by Arrhenius kinetics on barrier trees, which represent simplified versions of conformational energy landscapes. The existence of at least one sequence forming any arbitrarily chosen pair of structures is granted by the intersection theorem. Folding kinetics is the key to understanding and designing multistable RNA molecules or RNA switches. These RNAs form two or more long lived conformations, and conformational changes occur either spontaneously or are induced through binding of small molecules or other biopolymers. RNA switches are found in nature where they act as elements in genetic and metabolic regulation. The reliability of RNA secondary structure prediction is limited by the accuracy with which the empirical parameters can be determined and by principal deficiencies, for example by the lack of energy contributions resulting from tertiary interactions. In addition, native structures may be determined by folding kinetics rather than by thermodynamics. We address the first problem by considering base pair probabilities or base pairing entropies, which are derived from the partition function of conformations. A high base pair probability corresponding to a low pairing entropy is taken as an indicator of a high reliability of prediction. Pseudoknots are discussed as an example of a tertiary interaction that is highly important for RNA function. Moreover, pseudoknot formation is readily incorporated into structure prediction algorithms. Some examples of experimental data on RNA secondary structures that are readily explained using the landscape concept are presented. They deal with (i) properties of RNA molecules with random sequences, (ii) RNA molecules from restricted alphabets, (iii) existence of neutral networks, (iv) shape space covering, (v) riboswitches and (vi) evolution of non-coding RNAs as an example of evolution restricted to neutral networks.

Artifacts Generated During Azoalkane Peroxy Radical Oxidative Stress Testing of Pharmaceuticals Containing Primary and Secondary Amines.

PubMed

Nefliu, Marcela; Zelesky, Todd; Jansen, Patrick; Sluggett, Gregory W; Foti, Christopher; Baertschi, Steven W; Harmon, Paul A

2015-12-01

We report artifactual degradation of pharmaceutical compounds containing primary and secondary amines during peroxy radical-mediated oxidative stress carried out using azoalkane initiators. Two degradation products were detected when model drug compounds dissolved in methanol/water were heated to 40°C with radical initiators such as 2,2'-azobis(2-methylpropionitrile) (AIBN). The primary artifact was identified as an α-aminonitrile generated from the reaction of the amine group of the model drug with formaldehyde and hydrogen cyanide, generated as byproducts of the stress reaction. A minor artifact was generated from the reaction between the amine group and isocyanic acid, also a byproduct of the stress reaction. We report the effects of pH, initiator/drug molar ratio, and type of azoalkane initiator on the formation of these artifacts. Mass spectrometry and nuclear magnetic resonance were used for structure elucidation, whereas mechanistic studies, including stable isotope labeling experiments, cyanide analysis, and experiments exploring the effects of butylated hydroxyanisole addition, were employed to support the degradation pathways. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Latent structure of the Wisconsin Card Sorting Test: a confirmatory factor analytic study.

PubMed

Greve, Kevin W; Stickle, Timothy R; Love, Jeffrey M; Bianchini, Kevin J; Stanford, Matthew S

2005-05-01

The present study represents the first large scale confirmatory factor analysis of the Wisconsin Card Sorting Test (WCST). The results generally support the three factor solutions reported in the exploratory factor analysis literature. However, only the first factor, which reflects general executive functioning, is statistically sound. The secondary factors, while likely reflecting meaningful cognitive abilities, are less stable except when all subjects complete all 128 cards. It is likely that having two discontinuation rules for the WCST has contributed to the varied factor analytic solutions reported in the literature and early discontinuation may result in some loss of useful information. Continued multivariate research will be necessary to better clarify the processes underlying WCST performance and their relationships to one another.

Parental education, children's performance and the transition to higher secondary education: trends in primary and secondary effects over five Dutch school cohorts (1965-99).

PubMed

Kloosterman, Rianne; Ruiter, Stijn; de Graaf, Paul M; Kraaykamp, Gerbert

2009-06-01

According to Boudon, social background affects educational transitions as a result of differences in children's academic performance (primary effects) and differences in transition probabilities given children's level of academic performance (secondary effects). This study addresses historical changes in both primary and secondary effects on the educational transition from primary school to higher secondary education in The Netherlands. In addition, it considers changes over time in the relative importance of these effects. The study compares five cohorts of Dutch pupils, specifically those enrolling in secondary education in 1965, 1977, 1989, 1993 and 1999, and it employs counterfactual analyses. The main findings are that secondary effects have been stable and primary effects have fluctuated to some extent. As a result, the proportion of the total effect of social background accounted for by primary effects has increased somewhat, from 53 per cent to 58 per cent.

Picometer resolution interferometric characterization of the dimensional stability of zero CTE CFRP

NASA Astrophysics Data System (ADS)

Cordero Machado, Jorge; Heinrich, Thomas; Schuldt, Thilo; Gohlke, Martin; Lucarelli, Stefano; Weise, Dennis; Johann, Ulrich; Peters, Achim; Braxmaier, Claus

2008-07-01

Highly stable but lightweight structural materials are essential for the realization of spaceborne optical instruments, for example telescopes. In terms of optical performance, usually tight tolerances on the absolute spacing between telescope mirrors have to be maintained from integration on ground to operation in final orbit. Furthermore, a certain stability of the telescope structure must typically be ensured in the measurement band. Particular challenging requirements have to be met for the LISA Mission (Laser Interferometer Space Antenna), where the spacing between primary and secondary mirror must be stable to a few picometers. Only few materials offer sufficient thermal stability to provide such performance. Candidates are for example Zerodur and Carbon-Fiber Reinforced Plastic (CFRP), where the latter is preferred in terms of mechanical stiffness and robustness. We are currently investigating the suitability of CFRP with respect to the LISA requirements by characterization of its dimensional stability with heterodyne laser interferometry. The special, highly symmetric interferometer setup offers a noise level of 2 pm/√Hz at 0.1Hz and above, and therefore represents a unique tool for this purpose. Various procedures for the determination of the coefficient of thermal expansion (CTE) have been investigated, both on a test sample with negative CTE, as well as on a CFRP tube specifically tuned to provide a theoretical zero expansion in the axial dimension.

dsRNA-protein interactions studied by molecular dynamics techniques. Unravelling dsRNA recognition by DCL1.

PubMed

Drusin, Salvador I; Suarez, Irina P; Gauto, Diego F; Rasia, Rodolfo M; Moreno, Diego M

2016-04-15

Double stranded RNA (dsRNA) participates in several biological processes, where RNA molecules acquire secondary structure inside the cell through base complementarity. The double stranded RNA binding domain (dsRBD) is one of the main protein folds that is able to recognize and bind to dsRNA regions. The N-terminal dsRBD of DCL1 in Arabidopsis thaliana (DCL1-1), in contrast to other studied dsRBDs, lacks a stable structure, behaving as an intrinsically disordered protein. DCL1-1 does however recognize dsRNA by acquiring a canonical fold in the presence of its substrate. Here we present a detailed modeling and molecular dynamics study of dsRNA recognition by DCL1-1. We found that DCL1-1 forms stable complexes with different RNAs and we characterized the residues involved in binding. Although the domain shows a binding loop substantially shorter than other homologs, it can still interact with the dsRNA and results in bending of the dsRNA A-type helix. Furthermore, we found that R8, a non-conserved residue located in the first dsRNA binding region, recognizes preferentially mismatched base pairs. We discuss our findings in the context of the function of DCL1-1 within the microRNA processing complex. Copyright © 2016 Elsevier Inc. All rights reserved.

Physical characterization of MxiH and PrgI, the needle component of the type III secretion apparatus from Shigella and Salmonella

PubMed Central

Darboe, Numukunda; Kenjale, Roma; Picking, Wendy L.; Picking, William D.; Middaugh, C. Russell

2006-01-01

Shigella and Salmonella use similar type III secretion systems for delivering effector proteins into host cells. This secretion system consists of a base anchored in both bacterial membranes and an extracellular “needle” that forms a rod-like structure exposed on the pathogen surface. The needle is composed of multiple subunits of a single protein and makes direct contact with host cells to facilitate protein delivery. The proteins that make up the needle of Shigella and Salmonella are MxiH and PrgI, respectively. These proteins are attractive vaccine candidates because of their essential role in virulence and surface exposure. We therefore isolated, purified, and characterized the monomeric forms of MxiH and PrgI. Their far-UV circular dichroism spectra show structural similarities with hints of subtle differences in their secondary structure. Both proteins are highly helical and thermally unstable, with PrgI having a midpoint of thermal unfolding (Tm) near 37°C and MxiH having a value near 42°C. The two proteins also have comparable intrinsic stabilities as measured by chemically induced (urea) unfolding. MxiH, however, with a free energy of unfolding (ΔG°0,un) of 1.6 kcal/mol, is slightly more stable than PrgI (1.2 kcal/mol). The relatively low m-values obtained for the urea-induced unfolding of the proteins suggest that they undergo only a small change in solvent-accessible surface area. This argues that when MxiH and PrgI are incorporated into the needle complex, they obtain a more stable structural state through the introduction of protein–protein interactions. PMID:16501225

Physical characterization of MxiH and PrgI, the needle component of the type III secretion apparatus from Shigella and Salmonella.

PubMed

Darboe, Numukunda; Kenjale, Roma; Picking, Wendy L; Picking, William D; Middaugh, C Russell

2006-03-01

Shigella and Salmonella use similar type III secretion systems for delivering effector proteins into host cells. This secretion system consists of a base anchored in both bacterial membranes and an extracellular "needle" that forms a rod-like structure exposed on the pathogen surface. The needle is composed of multiple subunits of a single protein and makes direct contact with host cells to facilitate protein delivery. The proteins that make up the needle of Shigella and Salmonella are MxiH and PrgI, respectively. These proteins are attractive vaccine candidates because of their essential role in virulence and surface exposure. We therefore isolated, purified, and characterized the monomeric forms of MxiH and PrgI. Their far-UV circular dichroism spectra show structural similarities with hints of subtle differences in their secondary structure. Both proteins are highly helical and thermally unstable, with PrgI having a midpoint of thermal unfolding (Tm) near 37 degrees C and MxiH having a value near 42 degrees C. The two proteins also have comparable intrinsic stabilities as measured by chemically induced (urea) unfolding. MxiH, however, with a free energy of unfolding (DeltaG degrees 0,un) of 1.6 kcal/mol, is slightly more stable than PrgI (1.2 kcal/mol). The relatively low m-values obtained for the urea-induced unfolding of the proteins suggest that they undergo only a small change in solvent-accessible surface area. This argues that when MxiH and PrgI are incorporated into the needle complex, they obtain a more stable structural state through the introduction of protein-protein interactions.

[Effect of Below-cloud Secondary Evaporation in Precipitations over the Loess Plateau Based on the Stable Isotopes of Hydrogen and Oxygen].

PubMed

Jin, Xiao-gang; Zhang, Ming-jun; Wang, Sheng-jie; Zhu, Xiao-fan; Dong, Lei; Ren, Zheng-guo; Chen, Fen-li

2015-04-01

Based on stable isotopes in 409 precipitation samples provided by GNIP and meteorological records at the eight stations in Loess Plateau from January 1985 to December 2004, as well as the trajectory model of HYSPLIT 4.9, the spatial and temporal variations of d-excess and Δ18O were analyzed. The spatial distribution of secondary evaporation rate and the impact of meteorological factors on below-cloud secondary evaporation were also discussed. The result showed that: (1) During summer and winter monsoon periods, Δ18O showed an uptrend variation and d-excess showed a downtrend variation from south to north in Loess Plateau. From east to west, Δ180 showed an uptrend variation only in summer monsoon period and a downtrend variation in winter monsoon period. The value of d-excess also showed a downtrend variation. Amplitude of variation Δ18O and d-excess could indicate the routes of monsoon. (2) Secondary evaporation existed on an annual basis, and it was relatively significant during the summer monsoon period, with ranges from 1.51% to 5.88% and an average rate of 3.87%. While winter monsoon became lower, the rates ranged from 1.06% to 5.46%, and the average rate dropped to 3.03%. Monsoon had larger influence on secondary evaporation in margin area of the plateau, while the influence on the central stations was little. (3) Temperature had the highest contribution to secondary evaporation, followed by precipitation amount and water vapor pressure, and relative humidity had a small contribution. Moreover, the influence of wind speed and altitude on secondary evaporation was weak.

Structures of the E46K Mutant-Type α-Synuclein Protein and Impact of E46K Mutation on the Structures of the Wild-Type α-Synuclein Protein

PubMed Central

2013-01-01

The E46K genetic missense mutation of the wild-type α-synuclein protein was recently identified in a family of Spanish origin with hereditary Parkinson’s disease. Detailed understanding of the structures of the monomeric E46K mutant-type α-synuclein protein as well as the impact of the E46K missense mutation on the conformations and free energy landscapes of the wild-type α-synuclein are required for gaining insights into the pathogenic mechanism of Parkinson’s disease. In this study, we use extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations to assess the secondary and tertiary structural properties as well as the conformational preferences of the monomeric wild-type and E46K mutant-type α-synuclein proteins in an aqueous solution environment. We also present the residual secondary structure component conversion stabilities with dynamics using a theoretical strategy, which we most recently developed. To the best of our knowledge, this study presents the first detailed comparison of the structural and thermodynamic properties of the wild-type and E46K mutant-type α-synuclein proteins in an aqueous solution environment at the atomic level with dynamics. We find that the E46K mutation results not only in local but also in long-range changes in the structural properties of the wild-type α-synuclein protein. The mutation site shows a significant decrease in helical content as well as a large increase in β-sheet structure formation upon E46K mutation. In addition, the β-sheet content of the C-terminal region increases significantly in the E46K mutant-type αS in comparison to the wild-type αS. Our theoretical strategy developed to assess the thermodynamic preference of secondary structure transitions indicates that this shift in secondary structure is the result of a decrease in the thermodynamic preference of turn to helix conversions while the coil to β-sheet preference increases for these residues. Long-range intramolecular protein interactions of the C-terminal with the N-terminal and NAC regions increase upon E46K mutation, resulting in more compact structures for the E46K mutant-type rather than wild-type αS. However, the E46K mutant-type αS structures are less stable than the wild-type αS. Overall, our results show that the E46K mutant-type αS has a higher propensity to aggregate than the wild-type αS and that the N-terminal and C-terminal regions are reactive toward fibrillization and aggregation upon E46K mutation and we explain the associated reasons based on the structural properties herein. Small molecules or drugs that can block the specific residues forming abundant β-sheet structure, which we report here, might help to reduce the reactivity of these intrinsically disordered fibrillogenic proteins toward aggregation and their toxicity. PMID:23374074

Seasonal trophic structure of the Scotia Sea pelagic ecosystem considered through biomass spectra and stable isotope analysis

NASA Astrophysics Data System (ADS)

Tarling, G. A.; Stowasser, G.; Ward, P.; Poulton, A. J.; Zhou, M.; Venables, H. J.; McGill, R. A. R.; Murphy, E. J.

2012-01-01

The biomass size structure of pelagic communities provides a system level perspective that can be instructive when considering trophic interactions. Such perspectives can become even more powerful when combined with taxonomic information and stable isotope analysis. Here we apply these approaches to the pelagic community of the Scotia Sea (Southern Ocean) and consider the structure and development of trophic interactions over different years and seasons. Samples were collected from three open-ocean cruises during the austral spring 2006, summer 2008 and autumn 2009. Three main sampling techniques were employed: sampling bottles for microplankton (0-50 m), vertically hauled fine meshed nets for mesozooplankton (0-400 m) and coarse-meshed trawls for macrozooplankton and nekton (0-1000 m). All samples were identified to the lowest practicable taxonomic level and their abundance, individual body weight and biomass (in terms of carbon) estimated. Slopes of normalised biomass spectrum versus size showed a significant but not substantial difference between cruises and were between -1.09 and -1.06. These slopes were shallower than expected for a community at equilibrium and indicated that there was an accumulation of biomass in the larger size classes (10 1-10 5 mg C ind -1). A secondary structure of biomass domes was also apparent, with the domes being 2.5-3 log 10 intervals apart in spring and summer and 2 log 10 intervals apart in autumn. The recruitment of copepod-consuming macrozooplankton, Euphausia triacantha and Themisto gaudichaudii into an additional biomass dome was responsible for the decrease in the inter-dome interval in autumn. Predator to prey mass ratios estimated from stable isotope analysis reached a minimum in autumn while the estimated trophic level of myctophid fish was highest in that season. This reflected greater amounts of internal recycling and increased numbers of trophic levels in autumn compared to earlier times of the year. The accumulation of biomass in larger size classes throughout the year in the Scotia Sea may reflect the prevalence of species that store energy and have multiyear life-cycles.

RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

ERIC Educational Resources Information Center

Ellington, Roni; Wachira, James; Nkwanta, Asamoah

2010-01-01

The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses…

Fourier-based classification of protein secondary structures.

PubMed

Shu, Jian-Jun; Yong, Kian Yan

2017-04-15

The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to classify protein secondary structures, but are faced with a significant number of misclassifications. The paper presents a technique for the classification of protein secondary structures based on protein "signal-plotting" and the use of the Fourier technique for digital signal processing. New indices are proposed to classify protein secondary structures by analyzing hydrophobicity profiles. The approach is simple and straightforward. Results show that the more types of protein secondary structures can be classified by means of these newly-proposed indices. Copyright © 2017 Elsevier Inc. All rights reserved.

Engineered Human Antibody Constant Domains with Increased Stability*S⃞

PubMed Central

Gong, Rui; Vu, Bang K.; Feng, Yang; Prieto, DaRue A.; Dyba, Marzena A.; Walsh, Joseph D.; Prabakaran, Ponraj; Veenstra, Timothy D.; Tarasov, Sergey G.; Ishima, Rieko; Dimitrov, Dimiter S.

2009-01-01

The immunoglobulin (Ig) constant CH2 domain is critical for antibody effector functions. Isolated CH2 domains are promising as scaffolds for construction of libraries containing diverse binders that could also confer some effector functions. However, previous work has shown that an isolated murine CH2 domain is relatively unstable to thermally induced unfolding. To explore unfolding mechanisms of isolated human CH2 and increase its stability γ1 CH2 was cloned and a panel of cysteine mutants was constructed. Human γ1 CH2 unfolded at a higher temperature (Tm = 54.1 °C, as measured by circular dichroism) than that previously reported for a mouse CH2 (41 °C). One mutant (m01) was remarkably stable (Tm = 73.8 °C). Similar results were obtained by differential scanning calorimetry. This mutant was also significantly more stable than the wild-type CH2 against urea induced unfolding (50% unfolding at urea concentration of 6.8 m versus 4.2 m). The m01 was highly soluble and monomeric. The existence of the second disulfide bond in m01 and its correct position were demonstrated by mass spectrometry and nuclear magnetic resonance spectroscopy, respectively. The loops were on average more flexible than the framework in both CH2 and m01, and the overall secondary structure was not affected by the additional disulfide bond. These data suggest that a human CH2 domain is relatively stable to unfolding at physiological temperature, and that both CH2 and the highly stable mutant m01 are promising new scaffolds for the development of therapeutics against human diseases. PMID:19307178

Deciphering the shape and deformation of secondary structures through local conformation analysis

PubMed Central

2011-01-01

Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons. PMID:21284872

Deciphering the shape and deformation of secondary structures through local conformation analysis.

PubMed

Baussand, Julie; Camproux, Anne-Claude

2011-02-01

Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

Stable, concentrated solutions of high molecular weight polyaniline and articles therefrom

DOEpatents

Mattes, Benjamin R.; Wang, Hsing-Lin

2000-01-01

Stable, concentrated solutions of high molecular weight polyaniline. In order to process high quality fibers and other articles possessing good mechanical properties, it is known that solution concentrations of the chosen polymer should be in the range from 15-30% (w/w). Moreover, it is desirable to use the highest molecular weight consistent with the solubility properties of the polymer. However, such solutions are inherently unstable, forming gels before processing can be achieved. The present invention describes the addition gel inhibitors (GIs) to the polymer solution, thereby permitting high concentrations (>15% (w/w)) of high molecular weight ((M.sub.w)>120,000, and (M.sub.n)>30,000) emeraldine base (EB) polyaniline to be dissolved. Secondary amines have been used for this purpose in concentrations which are small compared to those which might otherwise be used in a cosolvent role therefor. The resulting solutions are useful for generating excellent fibers, films, coatings and other objects, since the solutions are stable for significant time periods, and the GIs are present in too small concentrations to cause polymer deterioration. It is demonstrated that the GIs found to be useful do not act as cosolvents, and that gelation times of the solutions are directly proportional to the concentration of GI. In particular, there is a preferred concentration of GI, which if exceeded causes structural and electrical conductivity degradation of resulting articles. Heating of the solutions significantly improves solubility.

A comparative study of methanol as a supplementary carbon source for enhancing denitrification in primary and secondary anoxic zones.

PubMed

Ginige, Maneesha P; Bowyer, Jocelyn C; Foley, Leah; Keller, Jürg; Yuan, Zhiguo

2009-04-01

A comparative study on the use of methanol as a supplementary carbon source to enhance denitrification in primary and secondary anoxic zones is reported. Three lab-scale sequencing batch reactors (SBR) were operated to achieve nitrogen and carbon removal from domestic wastewater. Methanol was added to the primary anoxic period of the first SBR, and to the secondary anoxic period of the second SBR. No methanol was added to the third SBR, which served as a control. The extent of improvement on the denitrification performance was found to be dependent on the reactor configuration. Addition to the secondary anoxic period is more effective when very low effluent nitrate levels are to be achieved and hence requires a relatively large amount of methanol. Adding a small amount of methanol to the secondary anoxic period may cause nitrite accumulation, which does not improve overall nitrogen removal. In the latter case, methanol should be added to the primary anoxic period. The addition of methanol can also improve biological phosphorus removal by creating anaerobic conditions and increasing the availability of organic carbon in wastewater for polyphosphate accumulating organisms. This potentially provides a cost-effective approach to phosphorus removal from wastewater with a low carbon content. New fluorescence in situ hybridisation (FISH) probes targeting methanol-utilising denitrifiers were designed using stable isotope probing. Microbial structure analysis of the sludges using the new and existing FISH probes clearly showed that the addition of methanol stimulated the growth of specific methanol-utilizing denitrifiers, which improved the capability of sludge to use methanol and ethanol for denitrification, but reduced its capability to use wastewater COD for denitrification. Unlike acetate, long-term application of methanol has no negative impact on the settling properties of the sludge.

Comparison of stem morphology and anatomy of two alfalfa clonal lines exhibiting divergent cell wall composition.

PubMed

Gronwald, John W; Bucciarelli, Bruna

2013-08-30

In previous research, two alfalfa clonal lines (252 and 1283) were identified that exhibited environmentally stable differences in stem cell walls. Compared with stems of 1283, stems of 252 have a higher cell wall concentration and greater amounts of lignin and cellulose but reduced levels of pectic sugar residues. These results suggest greater deposition of secondary xylem and a reduction in pith in stems of 252 compared with 1283. The stem morphology and anatomy of first-cut and second-cut harvests of field-grown 1283 and 252 were examined. For both harvests, stems of 1283 were thicker and had a higher leaf/stem ratio compared with stems of 252. Stem cross-sections of both genotypes were stained for lignin, and the proportions of stem area that were pith and secondary xylem were measured using ImageJ. Stems of 252 exhibited greater deposition of secondary xylem and a reduction in pith proportion compared with stems of 1283 for the first-cut harvest, but this difference was not statistically significant for the second-cut harvest. The results indicate that the proportions of secondary xylem and pith are not environmentally stable in these two genotypes and hence cannot be the sole basis for the differences in cell wall concentration/composition. © 2012 Society of Chemical Industry.

Subunit Conformations and Assembly States of a DNA Translocating Motor: The Terminase of Bacteriophage P22

PubMed Central

Němeček, Daniel; Gilcrease, Eddie B.; Kang, Sebyung; Prevelige, Peter E.; Casjens, Sherwood; Thomas, George J.

2007-01-01

Bacteriophage P22, a podovirus infecting strains of Salmonella typhimurium, packages a 42 kbp genome using a headful mechanism. DNA translocation is accomplished by the phage terminase, a powerful molecular motor consisting of large and small subunits. Although many of the structural proteins of the P22 virion have been well characterized, little is known about the terminase subunits and their molecular mechanism of DNA translocation. We report here structural and assembly properties of ectopically expressed and highly purified terminase large and small subunits. The large subunit (gp2), which contains the nuclease and ATPase activities of terminase, exists as a stable monomer with an α/β fold. The small subunit (gp3), which recognizes DNA for packaging and may regulate gp2 activity, exhibits a highly α-helical secondary structure and self-associates to form a stable oligomeric ring in solution. For wildtype gp3, the ring contains nine subunits, as demonstrated by hydrodynamic measurements, electron microscopy and native mass spectrometry. We have also characterized a gp3 mutant (Ala 112 → Thr) that forms a ten subunit ring, despite a subunit fold indistinguishable from wildtype. Both the nonameric and decameric gp3 rings exhibit nonspecific DNA binding activity, and gp2 is able to bind strongly to the DNA/gp3 complex but not to DNA alone. We propose a scheme for the roles of P22 terminase large and small subunits in the recruitment and packaging of viral DNA and discuss the model in relation to proposals for terminase-driven DNA translocation in other phages. PMID:17945256

Hierarchical structure in sharply divided phase space for the piecewise linear map

NASA Astrophysics Data System (ADS)

Akaishi, Akira; Aoki, Kazuki; Shudo, Akira

2017-05-01

We have studied a two-dimensional piecewise linear map to examine how the hierarchical structure of stable regions affects the slow dynamics in Hamiltonian systems. In the phase space there are infinitely many stable regions, each of which is polygonal-shaped, and the rest is occupied by chaotic orbits. By using symbolic representation of stable regions, a procedure to compute the edges of the polygons is presented. The stable regions are hierarchically distributed in phase space and the edges of the stable regions show the marginal instability. The cumulative distribution of the recurrence time obeys a power law as ˜t-2 , the same as the one for the system with phase space, which is composed of a single stable region and chaotic components. By studying the symbol sequence of recurrence trajectories, we show that the hierarchical structure of stable regions has no significant effect on the power-law exponent and that only the marginal instability on the boundary of stable regions is responsible for determining the exponent. We also discuss the relevance of the hierarchical structure to those in more generic chaotic systems.

Conjugation of hydroxyapatite nanocrystals with human immunoglobulin G for nanomedical applications.

PubMed

Iafisco, Michele; Varoni, Elena; Di Foggia, Michele; Pietronave, Stefano; Fini, Milena; Roveri, Norberto; Rimondini, Lia; Prat, Maria

2012-02-01

Inorganic nanosized drug carriers are a promising field in nanomedicine applied to cancer. Their conjugation with antibodies combines the properties of the nanoparticles themselves with the specific and selective recognition ability of the antibodies to antigens. Biomimetic carbonate-hydroxyapatite (HA) nanoparticles were synthesized and fully characterized; human IgGs, used as model antibodies, were coupled to these nanocrystals. The maximum loading amount, the interaction modelling, the preferential orientation and the secondary structure modifications were evaluated using theoretical models (Langmuir, Freundlich and Langmuir-Freundlich) spectroscopic (UV-Vis, Raman), calorimetric (TGA), and immunochemical techniques (ELISA, Western Blot). HA nanoparticles of about 30 nm adsorbed human IgGs, in a dose-dependent, saturable and stable manner with micromolar affinity and adsorption capability around 2.3 mg/m(2). Adsorption isotherm could be described by Langmuir-Freundlich model, and was due to both energetically homogeneous and heterogeneous binding sites on HA surface, mainly of electrostatic nature. Binding did not induce secondary structure modification of IgGs. A preferential IgG end-on orientation with the involvement of IgG Fc moiety in the adsorption seems most probable due to the steric hindrance of their Fab domains. Biomimetic HA nanocrystals are suitable substrates to produce nanoparticles which can be functionalized with antibodies for efficient targeted drug delivery to tumours. Copyright © 2011 Elsevier B.V. All rights reserved.

Magnetic field controlled floating-zone single crystal growth of intermetallic compounds

NASA Astrophysics Data System (ADS)

Hermann, R.; Gerbeth, G.; Priede, J.

2013-03-01

Radio-frequency (RF) floating zone single crystal growth is an important technique for the preparation of single bulk crystals. The advantage of the floating-zone method is the crucible-free growth of single crystals of reactive materials with high melting points. The strong heat diffusion on the surface, as well as the melt convection in the molten zone due to induction heating, often leads to an undesired solid-liquid interface geometry with a concave (towards the solid phase) outer rim. These concave parts aggravate the single crystal growth over the full cross-section. A two-phase stirrer was developed at IFW Dresden in order to avoid the problems connected with these concave parts. It acts as a magnetic field pump and changes the typical double vortex structure to a single roll structure, thus pushing hot melt into the regions where the concave parts may arise. The current in the secondary coil is induced by the primary coil, and the capacitor and the resistance of the secondary circuit are adjusted to get a stable 90 degree phase-shift between the coil currents. Single crystal growth of industrial relevant RuAl and TiAl intermetallic compounds was performed based on the material parameters and using the adjusted two-phase stirrer. Very recently, the magnetic system was applied to the crystal growth of biocompatible TiNb alloys and antiferromagnetic Heusler MnSi compounds.

DNA Replication Dynamics of the GGGGCC Repeat of the C9orf72 Gene.

PubMed

Thys, Ryan Griffin; Wang, Yuh-Hwa

2015-11-27

DNA has the ability to form a variety of secondary structures in addition to the normal B-form DNA, including hairpins and quadruplexes. These structures are implicated in a number of neurological diseases and cancer. Expansion of a GGGGCC repeat located at C9orf72 is associated with familial amyotrophic lateral sclerosis and frontotemporal dementia. This repeat expands from two to 24 copies in normal individuals to several hundreds or thousands of repeats in individuals with the disease. Biochemical studies have demonstrated that as little as four repeats have the ability to form a stable DNA secondary structure known as a G-quadruplex. Quadruplex structures have the ability to disrupt normal DNA processes such as DNA replication and transcription. Here we examine the role of GGGGCC repeat length and orientation on DNA replication using an SV40 replication system in human cells. Replication through GGGGCC repeats leads to a decrease in overall replication efficiency and an increase in instability in a length-dependent manner. Both repeat expansions and contractions are observed, and replication orientation is found to influence the propensity for expansions or contractions. The presence of replication stress, such as low-dose aphidicolin, diminishes replication efficiency but has no effect on instability. Two-dimensional gel electrophoresis analysis demonstrates a replication stall with as few as 20 GGGGCC repeats. These results suggest that replication of the GGGGCC repeat at C9orf72 is perturbed by the presence of expanded repeats, which has the potential to result in further expansion, leading to disease. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Production and characterization of genetically modified human IL-11 variants.

PubMed

Sano, Emiko; Takei, Toshiaki; Ueda, Takuya; Tsumoto, Kouhei

2017-02-01

Interleukin-11 (IL-11) has been expected as a drug on severe thrombocytopenia caused by myelo-suppressive chemotherapy. Whereas, development of IL-11 inhibitor is also expected for a treatment against IL-11 related cancer progression. Here, we will demonstrate the creation of various kinds of genetically modified hIL-11s. Modified vectors were constructed by introducing N- or O-glycosylation site on the region of hIL-11 that does not belong to the core α-helical motif based on the predicted secondary structure. N-terminal (N: between 22 to 23 aa), the first loop (M1:70 to 71 aa), the second loop (M2:114-115 aa), the third loop (M3:160-161 aa) and C-terminal (C: 200- aa) were selected for modification. A large scale production system was established and the characteristics of modified hIL-11s were evaluated. The structure was analyzed by amino acid sequence and composition analysis and CD-spectra. Glycan was assessed by monosaccharide composition analysis. Growth promoting activity and biological stability were analyzed by proliferation of T1165 cells. N-terminal modified proteins were well glycosylated and produced. Growth activity of 3NN with NASNASNAS sequence on N-terminal was about tenfold higher than wild type (WT). Structural and biological stabilities of 3NN were also better than WT and residence time in mouse blood was longer than WT. M1 variants lacked growth activity though they are well glycosylated and secondary structure is very stable. Both of 3NN and OM1 with AAATPAPG on M1 associated with hIL-11R strongly. These results indicate N-terminal and M1 variants will be expected for practical use as potent agonists or antagonists of hIL-11. Copyright © 2016 Elsevier B.V. All rights reserved.

A stable wireless energy transmission system for gastrointestinal microsystems.

PubMed

Xin, W H; Yan, G Z; Wang, W X

2010-01-01

A wireless energy transmission system using a Helmholtz primary coil outside and a 3-dimensional secondary coil inside the body is introduced. It is designed to transmit stable power to a gastrointestinal microsystem regardless of its position and orientation when working in the gastric tract. Up to 310 mW of usable DC power can be delivered under worst-case geometrical conditions. Measured data of the system performance are presented and evaluated.

Crystal structures of hydrates of simple inorganic salts. III. Water-rich aluminium halide hydrates: AlCl3 · 15H2O, AlBr3 · 15H2O, AlI3 · 15H2O, AlI3 · 17H2O and AlBr3 · 9H2O.

PubMed

Schmidt, Horst; Hennings, Erik; Voigt, Wolfgang

2014-09-01

Water-rich aluminium halide hydrate structures are not known in the literature. The highest known water content per Al atom is nine for the perchlorate and fluoride. The nonahydrate of aluminium bromide, stable pentadecahydrates of aluminium chloride, bromide and iodide, and a metastable heptadecahydrate of the iodide have now been crystallized from low-temperature solutions. The structures of these hydrates were determined and are discussed in terms of the development of cation hydration spheres. The pentadecahydrate of the chloride and bromide are isostructural. In AlI(3) · 15H2O, half of the Al(3+) cations are surrounded by two complete hydration spheres, with six H2O in the primary and 12 in the secondary. For the heptadecahydrate of aluminium iodide, this hydration was found for every Al(3+).

The yeast Pif1 helicase prevents genomic instability caused by G-quadruplex-forming CEB1 sequences in vivo.

PubMed

Ribeyre, Cyril; Lopes, Judith; Boulé, Jean-Baptiste; Piazza, Aurèle; Guédin, Aurore; Zakian, Virginia A; Mergny, Jean-Louis; Nicolas, Alain

2009-05-01

In budding yeast, the Pif1 DNA helicase is involved in the maintenance of both nuclear and mitochondrial genomes, but its role in these processes is still poorly understood. Here, we provide evidence for a new Pif1 function by demonstrating that its absence promotes genetic instability of alleles of the G-rich human minisatellite CEB1 inserted in the Saccharomyces cerevisiae genome, but not of other tandem repeats. Inactivation of other DNA helicases, including Sgs1, had no effect on CEB1 stability. In vitro, we show that CEB1 repeats formed stable G-quadruplex (G4) secondary structures and the Pif1 protein unwinds these structures more efficiently than regular B-DNA. Finally, synthetic CEB1 arrays in which we mutated the potential G4-forming sequences were no longer destabilized in pif1Delta cells. Hence, we conclude that CEB1 instability in pif1Delta cells depends on the potential to form G-quadruplex structures, suggesting that Pif1 could play a role in the metabolism of G4-forming sequences.

Jealousy Graphs: Structure and Complexity of Decentralized Stable Matching

DTIC Science & Technology

2013-01-01

REPORT Jealousy Graphs: Structure and Complexity of Decentralized Stable Matching 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The stable matching...Franceschetti 858-822-2284 3. DATES COVERED (From - To) Standard Form 298 (Rev 8/98) Prescribed by ANSI Std. Z39.18 - Jealousy Graphs: Structure and...market. Using this structure, we are able to provide a ner analysis of the complexity of a subclass of decentralized matching markets. Jealousy

Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants.

PubMed

Rathner, Petr; Rathner, Adriana; Horničáková, Michaela; Wohlschlager, Christian; Chandra, Kousik; Kohoutová, Jaroslava; Ettrich, Rüdiger; Wimmer, Reinhard; Müller, Norbert

2015-09-01

The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this "missing link", we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1-45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Computer-Aided Design of RNA Origami Structures.

PubMed

Sparvath, Steffen L; Geary, Cody W; Andersen, Ebbe S

2017-01-01

RNA nanostructures can be used as scaffolds to organize, combine, and control molecular functionalities, with great potential for applications in nanomedicine and synthetic biology. The single-stranded RNA origami method allows RNA nanostructures to be folded as they are transcribed by the RNA polymerase. RNA origami structures provide a stable framework that can be decorated with functional RNA elements such as riboswitches, ribozymes, interaction sites, and aptamers for binding small molecules or protein targets. The rich library of RNA structural and functional elements combined with the possibility to attach proteins through aptamer-based binding creates virtually limitless possibilities for constructing advanced RNA-based nanodevices.In this chapter we provide a detailed protocol for the single-stranded RNA origami design method using a simple 2-helix tall structure as an example. The first step involves 3D modeling of a double-crossover between two RNA double helices, followed by decoration with tertiary motifs. The second step deals with the construction of a 2D blueprint describing the secondary structure and sequence constraints that serves as the input for computer programs. In the third step, computer programs are used to design RNA sequences that are compatible with the structure, and the resulting outputs are evaluated and converted into DNA sequences to order.

The dynamics of interacting salt structures and associated fluid flow in the western Norwegian-Danish Basin

NASA Astrophysics Data System (ADS)

Olsen, Mikkel S.; Clausen, Ole R.; Andresen, Katrine J.; Korstgård, John A.

2015-04-01

Minor secondary structures observed along the flanks of major salt structures in the Norwegian-Danish Basin appear to be generated mainly during the early stages of halokinesis. Seismic anomalies in the cover sediments at the flanks of the major salt structures and in relation to one of the secondary structures show several circular patterns. The circular patterns are generally interpreted as faults related to collapsing salt, indicating a subtle and dynamic cannibalization relationship between the secondary structure and the main diapir. High-amplitude reflections interpreted as either entrapped gas along the circular faults or diagenetic changes induced by the fluids originating from the salt-sediment interface generally enhances the seismic appearance of the circular faults, but potentially also disturb the seismic imaging of the faults. Other secondary salt structures, with a similar geometry, do not show sign of collapse, apparently due to a greater distance from the main salt structures and therefore not within the reach of being cannibalized by these. The observations furthermore suggest a trend showing a more advanced development of the main salt structures when the secondary structures are cannibalized. The lateral distribution of the main salt structures thus appears to be controlled not only by the initial thickness of the Zechstein salt, and possible underlying structures, but also by subtle variations in the location and evolution of secondary structures. The secondary structures have a major impact on the drainage of the deep Mesozoic succession as indicated by the fluid flow pattern also observed in the study, which emphasizes that a detailed mapping of salt structures including secondary structures at the flanks is of major importance during evaluation of petroleum systems in areas dominated by halokinesis.

Distinct Secondary Structures of the Leucine-Rich Repeat Proteoglycans Decorin and Biglycan: Glycosylation-Dependent Conformational Stability

NASA Technical Reports Server (NTRS)

Krishnan, Priya; Hocking, Anne M.; Scholtz, J. Martin; Pace, C. Nick; Holik, Kimberly K.; McQuillan, David J.

1998-01-01

Biglycan and decorin, closely related small leucine-rich repeat proteoglycans, have been overexpressed in eukaryotic cers and two major glycoforms isolated under native conditions: a proteoglycan substituted with glycosaminoglycan chains; and a core protein form secreted devoid of glycosaminoglycans. A comparative biophysical study of these glycoforms has revealed that the overall secondary structures of biglycan and decorin are different. Far-UV Circular Dichroism (CD) spectroscopy of decorin and biglycan proteoglycans indicates that, although they are predominantly Beta-sheet, biglycan has a significantly higher content of alpha-helical structure. Decorin proteoglycan and core protein are very similar, whereas the biglycan core protein exhibits closer similarity to the decorin glycoforms than to. the biglycan proteoglycan form. However, enzymatic removal of the chondroitin sulfate chains from biglycan proteoglycan does not induce a shift to the core protein structure, suggesting that the fmal form is influenced by polysaccharide addition only during biosynthesis. Fluorescence emission spectroscopy demonstrated that the single tryptophan residue, which is at a conserved position at the C-terminal domain of both biglycan and decorin, is found in similar microenvironments. This indicates that at least in this specific domain, the different glycoforms do exhibit apparent conservation of structure. Exposure of decorin and biglycan to 10 M urea resulted in an increase in fluorescent intensity, which indicates that the emission from tryptophan in the native state is quenched. Comparison of urea-induced protein unfolding curves provided further evidence that decorin and biglycan assume different structures in solution. Decorin proteoglycan and core protein unfold in a manner similar to a classic two-state model, in which there is a steep transition to an unfolded state between 1-2 M urea. The biglycan core protein also shows a similar steep transition. However, biglycan proteoglycan shows a broad unfolding transition between 1-6 M urea, probably indicating the presence of stable unfolding intermediates.

Isolation and in silico analysis of a novel H+-pyrophosphatase gene orthologue from the halophytic grass Leptochloa fusca

NASA Astrophysics Data System (ADS)

Rauf, Muhammad; Saeed, Nasir A.; Habib, Imran; Ahmed, Moddassir; Shahzad, Khurram; Mansoor, Shahid; Ali, Rashid

2017-02-01

Structure prediction can provide information about function and active sites of protein which helps to design new functional proteins. H+-pyrophosphatase is transmembrane protein involved in establishing proton motive force for active transport of Na+ across membrane by Na+/H+ antiporters. A full length novel H+-pyrophosphatase gene was isolated from halophytic grass Leptochloa fusca using RT-PCR and RACE method. Full length LfVP1 gene sequence of 2292 nucleotides encodes protein of 764 amino acids. DNA and protein sequences were used for characterization using bioinformatics tools. Various important potential sites were predicted by PROSITE webserver. Primary structural analysis showed LfVP1 as stable protein and Grand average hydropathy (GRAVY) indicated that LfVP1 protein has good hydrosolubility. Secondary structure analysis showed that LfVP1 protein sequence contains significant proportion of alpha helix and random coil. Protein membrane topology suggested the presence of 14 transmembrane domains and presence of catalytic domain in TM3. Three dimensional structure from LfVP1 protein sequence also indicated the presence of 14 transmembrane domains and hydrophobicity surface model showed amino acid hydrophobicity. Ramachandran plot showed that 98% amino acid residues were predicted in the favored region.

Conformational Analysis on structural perturbations of the zinc finger NEMO

NASA Astrophysics Data System (ADS)

Godwin, Ryan; Salsbury, Freddie; Salsbury Group Team

2014-03-01

The NEMO (NF-kB Essential Modulator) Zinc Finger protein (2jvx) is a functional Ubiquitin-binding domain, and plays a role in signaling pathways for immune/inflammatory responses, apoptosis, and oncogenesis [Cordier et al., 2008]. Characterized by 3 cysteines and 1 histidine residue at the active site, the biologically occurring, bound zinc configuration is a stable structural motif. Perturbations of the zinc binding residues suggest conformational changes in the 423-atom protein characterized via analysis of all-atom molecular dynamics simulations. Structural perturbations include simulations with and without a zinc ion and with and without de-protonated cysteines, resulting in four distinct configurations. Simulations of various time scales show consistent results, yet the longest, GPU driven, microsecond runs show more drastic structural and dynamic fluctuations when compared to shorter duration time-scales. The last cysteine residue (26 of 28) and the helix on which it resides exhibit a secondary, locally unfolded conformation in addition to its normal bound conformation. Combined analytics elucidate how the presence of zinc and/or protonated cysteines impact the dynamics and energetic fluctuations of NEMO. Comprehensive Cancer Center of Wake Forest University Computational Biosciences shared resource supported by NCI CCSG P30CA012197.

Correlated Measurements of the Disturbances of Geomagnetic Field and Changes of Secondary Particle Fluxes at Aragats-Space Environmental Center (ASEC)

DTIC Science & Technology

2010-02-01

Fluxes at Aragats-Space Environmental Center (ASEC) Ashot A. Chilingarian Alikhanyan Physics Institute Cosmic Ray Division 2 Alikhanian...GMS occurred during 23rd Solar activity cycle demonstrate that Cosmic Ray increase during GMS occurs coherently (or ~ 1 hour in advance) with abrupt...data on Solar bursts and secondary cosmic ray data. The magnetometer operates stable, noise level is low. 15. SUBJECT TERMS

Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment.

PubMed

Li, Yaohang; Liu, Hui; Rata, Ionel; Jakobsson, Eric

2013-02-25

The rapidly increasing number of protein crystal structures available in the Protein Data Bank (PDB) has naturally made statistical analyses feasible in studying complex high-order inter-residue correlations. In this paper, we report a context-based secondary structure potential (CSSP) for assessing the quality of predicted protein secondary structures generated by various prediction servers. CSSP is a sequence-position-specific knowledge-based potential generated based on the potentials of mean force approach, where high-order inter-residue interactions are taken into consideration. The CSSP potential is effective in identifying secondary structure predictions with good quality. In 56% of the targets in the CB513 benchmark, the optimal CSSP potential is able to recognize the native secondary structure or a prediction with Q3 accuracy higher than 90% as best scored in the predicted secondary structures generated by 10 popularly used secondary structure prediction servers. In more than 80% of the CB513 targets, the predicted secondary structures with the lowest CSSP potential values yield higher than 80% Q3 accuracy. Similar performance of CSSP is found on the CASP9 targets as well. Moreover, our computational results also show that the CSSP potential using triplets outperforms the CSSP potential using doublets and is currently better than the CSSP potential using quartets.

Phase Stability and Electronic Structure of Prospective Sb-Based Mixed Sulfide and Iodide 3D Perovskite (CH3NH3)SbSI2.

PubMed

Li, Tianyang; Wang, Xiaoming; Yan, Yanfa; Mitzi, David B

2018-06-29

Lead-free antimony-based mixed sulfide and iodide perovskite phases have recently been reported to be synthesized experimentally and to exhibit reasonable photovoltaic performance. Through a combination of experimental validation and computational analysis, we show no evidence of the formation of the mixed sulfide and iodide perovskite phase, MASbSI 2 (MA = CH 3 NH 3 + ), and instead that the main products are a mixture of the binary and ternary compounds (Sb 2 S 3 and MA 3 Sb 2 I 9 ). Density functional theory calculations also indicate that such a mixed sulfide and iodide perovskite phase should be thermodynamically less stable compared with binary/ternary anion-segregated secondary phases and less likely to be synthesized under equilibrium conditions. Additionally, band structure calculations show that this mixed sulfide and iodide phase, if possible to synthesize (e.g., under nonequilibrium conditions), should have a suitable direct band gap for photovoltaic application.

Characterization and assembly of a GFP-tagged cylindriform silk into hexameric complexes.

PubMed

Öster, Carl; Svensson Bonde, Johan; Bülow, Leif; Dicko, Cedric

2014-04-01

Spider silk has been studied extensively for its attractive mechanical properties and potential applications in medicine and industry. The production of spider silk, however, has been lagging behind for lack of suitable systems. Our approach focuses on solving the production of spider silk by designing, expressing, purifying and characterizing the silk from cylindriform glands. We show that the cylindriform silk protein, in contrast to the commonly used dragline silk protein, is fully folded and stable in solution. With the help of GFP as a fusion tag we enhanced the expression of the silk protein in Escherichia coli and could optimize the downstream processing. Secondary structures analysis by circular dichroism and FTIR shows that the GFP-silk fusion protein is predominantly α-helical, and that pH can trigger a α- to β-transition resulting in aggregation. Structural analysis by small angle X-ray scattering suggests that the GFP-Silk exists in the form of a hexamer in solution. Copyright © 2013 Wiley Periodicals, Inc.

A Key concept in Magnesium Secondary Battery Electrolytes.

PubMed

Bertasi, Federico; Hettige, Chaminda; Sepehr, Fatemeh; Bogle, Xavier; Pagot, Gioele; Vezzù, Keti; Negro, Enrico; Paddison, Stephen J; Greenbaum, Steve G; Vittadello, Michele; Di Noto, Vito

2015-09-21

A critical roadblock toward practical Mg-based energy storage technologies is the lack of reversible electrolytes that are safe and electrochemically stable. Here, we report on high-performance electrolytes based on 1-ethyl-3-methylimidazolium chloride (EMImCl) doped with AlCl3 and highly amorphous δ-MgCl2 . The phase diagram of the electrolytes reveals the presence of four thermal transitions that strongly depend on salt content. High-level density functional theory (DFT)-based electronic structure calculations substantiate the structural and vibrational assignment of the coordination complexes. A 3D chloride-concatenated dynamic network model accounts for the outstanding redox behaviour and the electric and magnetic properties, providing insight into the conduction mechanism of the electrolytes. Mg anode cells assembled using the electrolytes were cyclically discharged at a high rate (35 mA g(-1) ), exhibiting an initial capacity of 80 mA h g(-1) and a steady-state voltage of 2.3 V. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High temperature unfolding of a truncated hemoglobin by molecular dynamics simulation.

PubMed

Sharma, Ravi Datta; Kanwal, Rajnee; Lynn, Andrew M; Singh, Prerna; Pasha, Syed Tazeen; Fatma, Tasneem; Jawaid, Safdar

2013-09-01

Heme containing proteins are associated with peroxidase activity. The proteins like hemoglobin, myoglobins, cytochrome c and micro-peroxidase other than peroxidases have been shown to exhibit weak peroxidase-like activity. This weak peroxidase-like activity in hemoglobin-like molecules is due to heme moiety. We conducted molecular dynamics (MD) studies to decipher the unfolding path of Ba-Glb (a truncated hemoglobin from Bacillus anthracis) and the role of heme moiety to its unfolding path. The similar unfolding path is also observed in vitro by UV/VIS spectroscopy. The data confirmed that the unfolding of Ba-Glb follows a three state process with a meta-stable (intermediate) state between the native and unfolded conformations. The present study is supported by several unfolding parameters like root-mean-square-deviation (RMSD), dictionary of protein secondary structure (DSSP), and free energy landscape. Understanding the structure of hemoglobin like proteins in unicellular dreaded pathogens like B. anthracis will pave way for newer drug discovery targets and in the disease management of anthrax.

Structure, stability, thermodynamic properties, and IR spectra of the protonated water decamer H+(H2O)10.

PubMed

Karthikeyan, S; Kim, Kwang S

2009-08-13

Protonated water clusters H+(H2O)n favor two-dimensional (2D) structures for n < or = 7 at low temperatures. At 0 K, the 2D and three-dimensional (3D) structures for n = 8 are almost isoenergetic, and the 3D structures for n > 9 tend to be more stable. However, for n = 9, the netlike structures are likely to be more stable above 150 K. In this regard, we investigate the case of n = 10 to find which structure is more stable between the 3D structure and the netlike structure around 150 and 250 K. We use density functional theory, Møller-Plesset second-order perturbation theory, and coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). At the complete basis set limit for the CCSD(T) level of theory, three isomers of 3D cage structure are much more stable in zero point energy corrected binding energy and in free binding energies at 150 K than the lowest energy netlike structures, while the netlike structure would be more stable around approximately 250 K. The predicted vibrational spectra are in good agreement with the experiment. One of the three isomers explains the experimental IR observation of an acceptor (A) type peak of a dangling hydrogen atom.

New two-dimensional V-V binary compounds with a honeycomb-like structure: a first-principles study

NASA Astrophysics Data System (ADS)

Xiao, Wen-Zhi; Xiao, Gang; Rong, Qing-Yan; Wang, Ling-Ling

2018-03-01

We systematically search for the stable structures of two-dimensional (2D) V-V binary compounds with honeycomb-like structure by using the first-principles calculation. We identify 26 stable structures out of 54 2D V-V compounds based on various assessments of stabilities: total energy, thermodynamics, and mechanics. Among them, 12 2D V-V compounds are previously unrecognized structures. For each class V-V isomer, the most stable structures are found to be β-AsP, β-SbAs, α-BiAs, α-BiSb, α 2-SbP, and α 2-BiP. For all isomers of the AsP, they are always stable, and hence PAs monolayer is most likely to be prepared experimentally. All the stable structures are semiconductors with bandgaps ranging from 0.06 eV to 2.52 eV at the Heyd-Scuseria-Ernzerhof level. Therefore, they are potential materials for versatile semiconductor devices. Our findings provide a new clue to facilitate the design of 2D materials for potential applications.

R-chie: a web server and R package for visualizing RNA secondary structures

PubMed Central

Lai, Daniel; Proctor, Jeff R.; Zhu, Jing Yun A.; Meyer, Irmtraud M.

2012-01-01

Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R-chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems. PMID:22434875

Heparin monotherapy or bivalirudin during percutaneous coronary intervention in patients with non-ST-segment-elevation acute coronary syndromes or stable ischemic heart disease: results from the Evaluation of Drug-Eluting Stents and Ischemic Events registry.

PubMed

Bangalore, Sripal; Pencina, Michael J; Kleiman, Neal S; Cohen, David J

2014-06-01

The use of bivalirudin versus unfractionated heparin monotherapy in patients without ST-segment-elevation myocardial infarction is not well defined. The study population consisted of patients enrolled in the Evaluation of Drug-Eluting Stents and Ischemic Events (EVENT) registry with either non-ST-segment-elevation acute coronary syndromes or stable ischemic heart disease, who underwent percutaneous coronary intervention with either unfractionated heparin or bivalirudin monotherapy. Propensity score matching was used to adjust for baseline characteristics. The primary bleeding (in-hospital composite bleeding-access site bleeding, thrombolysis in myocardial infarction major/minor bleeding, or transfusion) and primary (in-hospital death/myocardial infarction) and secondary ischemic outcomes (death/myocardial infarction/unplanned repeat revascularization at 12 months) were evaluated. Propensity score matching yielded 1036 patients with non-ST-segment-elevation acute coronary syndromes and 2062 patients with stable ischemic heart disease. For the non-ST-segment-elevation acute coronary syndrome cohort, bivalirudin use was associated with lower bleeding (difference, -3.3% [-0.8% to -5.8%]; P=0.01; number need to treat=30) without increase in either primary (difference, 1.2% [4.1% to -1.8%]; P=0.45) or secondary ischemic outcomes, including stent thrombosis (difference, 0.0% [1.3% to -1.3%]; P=1.00). Similarly, in the stable ischemic heart disease cohort, bivalirudin use was associated with lower bleeding (difference, -1.8% [-0.4% to -3.3%]; P=0.01; number need to treat=53) without increase in either primary (difference, 0.4% [2.3% to -1.5%]; P=0.70) or secondary ischemic outcomes, including stent thrombosis (difference, 0.0% [0.7% to -0.7%]; P=1.00) when compared with unfractionated heparin monotherapy. Among patients with non-ST-segment-elevation acute coronary syndromes or stable ischemic heart disease undergoing percutaneous coronary intervention, bivalirudin use during percutaneous coronary intervention when compared with unfractionated heparin monotherapy was associated with lower bleeding without significant increase in ischemic outcomes or stent thrombosis. © 2014 American Heart Association, Inc.

Characterising RNA secondary structure space using information entropy

PubMed Central

2013-01-01

Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free grammars (SCFGs), which generate a probability distribution over secondary structures. It is, however, unclear how this probability distribution changes as a function of the input alignment. As prediction programs typically only return a single secondary structure, better characterisation of the underlying probability space of RNA secondary structures is of great interest. In this work, we show how to efficiently compute the information entropy of the probability distribution over RNA secondary structures produced for RNA alignments by a phylo-SCFG, and implement it for the PPfold model. We also discuss interpretations and applications of this quantity, including how it can clarify reasons for low prediction reliability scores. PPfold and its source code are available from http://birc.au.dk/software/ppfold/. PMID:23368905

Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy

PubMed Central

Garmann, Rees F.; Gopal, Ajaykumar; Athavale, Shreyas S.; Knobler, Charles M.; Gelbart, William M.; Harvey, Stephen C.

2015-01-01

The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures. PMID:25752599

3D-nanostructured Au electrodes for the event-specific detection of MON810 transgenic maize.

PubMed

Fátima Barroso, M; Freitas, Maria; Oliveira, M Beatriz P P; de-Los-Santos-Álvarez, Noemí; Lobo-Castañón, María Jesús; Delerue-Matos, Cristina

2015-03-01

In the present work, the development of a genosensor for the event-specific detection of MON810 transgenic maize is proposed. Taking advantage of nanostructuration, a cost-effective three dimensional electrode was fabricated and a ternary monolayer containing a dithiol, a monothiol and the thiolated capture probe was optimized to minimize the unspecific signals. A sandwich format assay was selected as a way of precluding inefficient hybridization associated with stable secondary target structures. A comparison between the analytical performance of the Au nanostructured electrodes and commercially available screen-printed electrodes highlighted the superior performance of the nanostructured ones. Finally, the genosensor was effectively applied to detect the transgenic sequence in real samples, showing its potential for future quantitative analysis. Copyright © 2014 Elsevier B.V. All rights reserved.

Regularities in Low-Temperature Phosphatization of Silicates

NASA Astrophysics Data System (ADS)

Savenko, A. V.

2018-01-01

The regularities in low-temperature phosphatization of silicates are defined from long-term experiments on the interaction between different silicate minerals and phosphate-bearing solutions in a wide range of medium acidity. It is shown that the parameters of the reaction of phosphatization of hornblende, orthoclase, and labradorite have the same values as for clayey minerals (kaolinite and montmorillonite). This effect may appear, if phosphotization proceeds, not after silicate minerals with a different structure and composition, but after a secondary silicate phase formed upon interaction between silicates and water and stable in a certain pH range. Variation in the parameters of the reaction of phosphatization at pH ≈ 1.8 is due to the stability of the silicate phase different from that at higher pH values.

Application and research of recyclable cables in foundation pit support engineering

NASA Astrophysics Data System (ADS)

Zheng, Suping

2018-05-01

Anchoring cables are widely used in the construction of foundation pit as a temporary support structure. After the construction is completed, the anchor cables left in the ground will not only cause environmental pollution but also cause a great waste of resources. The emergence of recyclable cable technology, to avoid such problems, to achieve the secondary use of the anchor cable, excavation in the excavation project is more and more widely used. Combined with the design and construction of recoverable anchor cable in engineering practice, the application effect of recoverable anchor cable in foundation pit support is analyzed, and the conclusion that the support effect of recoverable anchor cable is stable and safe can be obtained Recyclable anchor cable in the future support projects to provide a reference.

BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra.

PubMed

Micsonai, András; Wien, Frank; Bulyáki, Éva; Kun, Judit; Moussong, Éva; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József

2018-06-11

Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.

Structurally coloured secondary particles composed of black and white colloidal particles.

PubMed

Takeoka, Yukikazu; Yoshioka, Shinya; Teshima, Midori; Takano, Atsushi; Harun-Ur-Rashid, Mohammad; Seki, Takahiro

2013-01-01

This study investigated the colourful secondary particles formed by controlling the aggregation states of colloidal silica particles and the enhancement of the structural colouration of the secondary particles caused by adding black particles. We obtained glossy, partially structurally coloured secondary particles in the absence of NaCl, but matte, whitish secondary particles were obtained in the presence of NaCl. When a small amount of carbon black was incorporated into both types of secondary particles, the incoherent multiple scattering of light from the amorphous region was considerably reduced. However, the peak intensities in the reflection spectra, caused by Bragg reflection and by coherent single wavelength scattering, were only slightly decreased. Consequently, a brighter structural colour of these secondary particles was observed with the naked eye. Furthermore, when magnetite was added as a black particle, the coloured secondary particles could be moved and collected by applying an external magnetic field.

Structurally Coloured Secondary Particles Composed of Black and White Colloidal Particles

PubMed Central

Takeoka, Yukikazu; Yoshioka, Shinya; Teshima, Midori; Takano, Atsushi; Harun-Ur-Rashid, Mohammad; Seki, Takahiro

2013-01-01

This study investigated the colourful secondary particles formed by controlling the aggregation states of colloidal silica particles and the enhancement of the structural colouration of the secondary particles caused by adding black particles. We obtained glossy, partially structurally coloured secondary particles in the absence of NaCl, but matte, whitish secondary particles were obtained in the presence of NaCl. When a small amount of carbon black was incorporated into both types of secondary particles, the incoherent multiple scattering of light from the amorphous region was considerably reduced. However, the peak intensities in the reflection spectra, caused by Bragg reflection and by coherent single wavelength scattering, were only slightly decreased. Consequently, a brighter structural colour of these secondary particles was observed with the naked eye. Furthermore, when magnetite was added as a black particle, the coloured secondary particles could be moved and collected by applying an external magnetic field. PMID:23917891

Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication.

PubMed

Compton, L A; Johnson, W C

1986-05-15

Inverse circular dichroism (CD) spectra are presented for each of the five major secondary structures of proteins: alpha-helix, antiparallel and parallel beta-sheet, beta-turn, and other (random) structures. The fraction of the each secondary structure in a protein is predicted by forming the dot product of the corresponding inverse CD spectrum, expressed as a vector, with the CD spectrum of the protein digitized in the same way. We show how this method is based on the construction of the generalized inverse from the singular value decomposition of a set of CD spectra corresponding to proteins whose secondary structures are known from X-ray crystallography. These inverse spectra compute secondary structure directly from protein CD spectra without resorting to least-squares fitting and standard matrix inversion techniques. In addition, spectra corresponding to the individual secondary structures, analogous to the CD spectra of synthetic polypeptides, are generated from the five most significant CD eigenvectors.

Photoconversion changes bilin chromophore conjugation and protein secondary structure in the violet/orange cyanobacteriochrome NpF2164g3' [corrected].

PubMed

Lim, Sunghyuk; Rockwell, Nathan C; Martin, Shelley S; Dallas, Jerry L; Lagarias, J Clark; Ames, James B

2014-06-01

Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors distantly related to phytochromes. All CBCRs examined to date utilize a conserved Cys residue to form a covalent thioether linkage to the bilin chromophore. In the insert-Cys CBCR subfamily, a second conserved Cys can covalently link to the bilin C10 methine bridge, allowing detection of near-UV to blue light. The best understood insert-Cys CBCR is the violet/orange CBCR NpF2164g3 from Nostoc punctiforme, which has a stable second linkage in the violet-absorbing dark state. Photoconversion of NpF2164g3 leads to elimination of the second linkage and formation of an orange-absorbing photoproduct. We recently reported NMR chemical shift assignments for the orange-absorbing photoproduct state of NpF2164g3. We here present equivalent information for its violet-absorbing dark state. In both photostates, NpF2164g3 is monomeric in solution and regions containing the two conserved Cys residues essential for photoconversion are structurally disordered. In contrast to blue light receptors such as phototropin, NpF2164g3 is less structurally ordered in the dark state than in the photoproduct. The insert-Cys insertion loop and C-terminal helix exhibit light-dependent structural changes. Moreover, a motif containing an Asp residue also found in other CBCRs and in phytochromes adopts a random-coil structure in the dark state but a stable α-helix structure in the photoproduct. NMR analysis of the chromophore is consistent with a less ordered dark state, with A-ring resonances only resolved in the photoproduct. The C10 atom of the bilin chromophore exhibits a drastic change in chemical shift upon photoconversion, changing from 34.5 ppm (methylene) in the dark state to 115 ppm (methine) in the light-activated state. Our results provide structural insight into the two-Cys photocycle of NpF2164g3 and the structurally diverse mechanisms used for light perception by the larger phytochrome superfamily.

Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state

PubMed Central

Warfield, Becka M.

2017-01-01

RNA aptamers are oligonucleotides that bind with high specificity and affinity to target ligands. In the absence of bound ligand, secondary structures of RNA aptamers are generally stable, but single-stranded and loop regions, including ligand binding sites, lack defined structures and exist as ensembles of conformations. For example, the well-characterized theophylline-binding aptamer forms a highly stable binding site when bound to theophylline, but the binding site is unstable and disordered when theophylline is absent. Experimental methods have not revealed at atomic resolution the conformations that the theophylline aptamer explores in its unbound state. Consequently, in the present study we applied 21 microseconds of molecular dynamics simulations to structurally characterize the ensemble of conformations that the aptamer adopts in the absence of theophylline. Moreover, we apply Markov state modeling to predict the kinetics of transitions between unbound conformational states. Our simulation results agree with experimental observations that the theophylline binding site is found in many distinct binding-incompetent states and show that these states lack a binding pocket that can accommodate theophylline. The binding-incompetent states interconvert with binding-competent states through structural rearrangement of the binding site on the nanosecond to microsecond timescale. Moreover, we have simulated the complete theophylline binding pathway. Our binding simulations supplement prior experimental observations of slow theophylline binding kinetics by showing that the binding site must undergo a large conformational rearrangement after the aptamer and theophylline form an initial complex, most notably, a major rearrangement of the C27 base from a buried to solvent-exposed orientation. Theophylline appears to bind by a combination of conformational selection and induced fit mechanisms. Finally, our modeling indicates that when Mg2+ ions are present the population of binding-competent aptamer states increases more than twofold. This population change, rather than direct interactions between Mg2+ and theophylline, accounts for altered theophylline binding kinetics. PMID:28437473

A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data

PubMed Central

Sturm, Marc; Quinten, Sascha; Huber, Christian G.; Kohlbacher, Oliver

2007-01-01

We propose a new model for predicting the retention time of oligonucleotides. The model is based on ν support vector regression using features derived from base sequence and predicted secondary structure of oligonucleotides. Because of the secondary structure information, the model is applicable even at relatively low temperatures where the secondary structure is not suppressed by thermal denaturing. This makes the prediction of oligonucleotide retention time for arbitrary temperatures possible, provided that the target temperature lies within the temperature range of the training data. We describe different possibilities of feature calculation from base sequence and secondary structure, present the results and compare our model to existing models. PMID:17567619

Microstructure and phase composition characterization in a Co{sub 38}Ni{sub 33}Al{sub 29} ferromagnetic shape memory alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, J.B.

2016-08-15

Transmission electron microscopy was performed to investigate the microstructures of a secondary phase and its surrounding matrix in a Co{sub 38}Ni{sub 33}Al{sub 29} ferromagnetic shape memory alloy. The secondary phase shows a γ′ L1{sub 2} structure exhibiting a dendritic morphology with enclosed B2 austenite regions while the matrix shows the L1{sub 0} martensitic structure. A secondary phase-austenite-martensite sandwich structure with residual austenite ranging from several hundred nanometers to several micrometers wide is observed at the secondary phase-martensite interface due to the depletion of Co and enrichment of Al in the chemical gradient zone and the effect of the strong martensiticmore » start temperature dependency of the element concentrations. The crystallographic orientation relationship of the secondary phase and the B2 austenite fits the Kurdjumov-Sachs relationship. - Highlights: •The secondary phase has a γ′ L1{sub 2} structure exhibiting a dendritic morphology. •A secondary phase-austenite-martensite sandwich structure is observed. •The structural sandwich structure is due to elemental composition variation. •The secondary phase and the B2 austenite fit the Kurdjumov-Sachs relationship.« less

Contributions of detrital subsidies to aboveground spiders during secondary succession, revealed by radiocarbon and stable isotope signatures.

PubMed

Haraguchi, Takashi F; Uchida, Masao; Shibata, Yasuyuki; Tayasu, Ichiro

2013-04-01

Prey subsidies originating from detritus add nutrients and energy to arboreal communities. Measurement of this subsidy is required in the understanding of how food web dynamics respond to changes in surrounding environments. Shrub spiders are one of the key predators involved in food web coupling. We evaluate the effects of potential changes in prey availabilities during secondary succession on the contribution of subsidy from detrital food webs to shrub spiders and how different spider feeding guilds used the subsidy of prey from detrital food webs. We measured the relative importance of the subsidy for the spider feeding guilds, using the ratios of stable isotopes of C (δ(13)C), and N (δ(15)N) and C isotope discrimination (Δ(14)C). Diet age was calculated from Δ(14)C values, because old diet ages of spiders indicate that the spiders consume prey from detrital food sources. Dominant aerial prey (Diptera) had a distinctively old diet age compared with arboreal prey, which indicates that aerial prey were subsidized from detrital food webs. Sit-and-wait spiders tended to have an older diet age than active hunting spiders, which indicates that sit-and-wait spiders depended more on subsidies. Diet age varied only slightly for spiders in stands of different ages, indicating that rates at which spiders use grazing and detrital prey are probably determined more by foraging strategies and not by stand age. A dominance of sit-and-wait predators will lead to higher detrital subsidy inputs in shrub habitats. This study highlights the effect of shrub spider community structure (feeding guild composition) on the volume of the subsidy received from the detrital food web.

Design and methodology of the COACH-2 (Comparative study on guideline adherence and patient compliance in heart failure patients) study: HF clinics versus primary care in stable patients on optimal therapy.

PubMed

Luttik, M L A; Brons, M; Jaarsma, T; Hillege, H L; Hoes, A; de Jong, R; Linssen, G; Lok, D J; Berger, M; van Veldhuisen, D J

2012-08-01

Since the number of heart failure (HF) patients is still growing and long-term treatment of HF patients is necessary, it is important to initiate effective ways for structural involvement of primary care services in HF management programs. However, evidence on whether and when patients can be referred back to be managed in primary care is lacking. To determine whether long-term patient management in primary care, after initial optimisation of pharmacological and non-pharmacological treatment in a specialised HF clinic, is equally effective as long-term management in a specialised HF clinic in terms of guideline adherence and patient compliance. The study is designed as a randomised, controlled, non-inferiority trial. Two-hundred patients will be randomly assigned to be managed and followed in primary care or in a HFclinic. Patients are eligible to participate if they are (1) clinically stable, (2) optimally up-titrated on medication (according to ESC guidelines) and, (3) have received optimal education and counselling on pre-specified issues regarding HF and its treatment. Furthermore, close cooperation between secondary and primary care in terms of back referral to or consultation of the HF clinic will be provided.The primary outcome will be prescriber adherence and patient compliance with medication after 12 months. Secondary outcomes measures will be readmission rate, mortality, quality of life and patient compliance with other lifestyle changes. The results of the study will add to the understanding of the role of primary care and HF clinics in the long-term follow-up of HF patients.

The landscape of the non-canonical RNA-binding site of Gemin5 unveils a feedback loop counteracting the negative effect on translation.

PubMed

Francisco-Velilla, Rosario; Fernandez-Chamorro, Javier; Dotu, Ivan; Martinez-Salas, Encarnación

2018-05-16

Gemin5 is a predominantly cytoplasmic protein that downregulates translation, beyond controlling snRNPs assembly. The C-terminal region harbors a non-canonical RNA-binding site consisting of two domains, RBS1 and RBS2, which differ in RNA-binding capacity and the ability to modulate translation. Here, we show that these domains recognize distinct RNA targets in living cells. Interestingly, the most abundant and exclusive RNA target of the RBS1 domain was Gemin5 mRNA. Biochemical and functional characterization of this target demonstrated that RBS1 polypeptide physically interacts with a predicted thermodynamically stable stem-loop upregulating mRNA translation, thereby counteracting the negative effect of Gemin5 protein on global protein synthesis. In support of this result, destabilization of the stem-loop impairs the stimulatory effect on translation. Moreover, RBS1 stimulates translation of the endogenous Gemin5 mRNA. Hence, although the RBS1 domain downregulates global translation, it positively enhances translation of RNA targets carrying thermodynamically stable secondary structure motifs. This mechanism allows fine-tuning the availability of Gemin5 to play its multiple roles in gene expression control.

The turn of the screw: an exercise in protein secondary structure.

PubMed

Pikaart, Michael

2011-01-01

An exercise using simple paper strips to illustrate protein helical and sheet secondary structures is presented. Drawing on the rich historical context of the use of physical models in protein biochemistry by early practitioners, in particular Linus Pauling, the purpose of this activity is to cultivate in students a hands-on, intuitive sense of protein secondary structure and to complement the common computer-based structural portrayals often used in teaching biochemistry. As students fold these paper strips into model secondary structures, they will better grasp how intramolecular hydrogen bonds form in the folding of a polypeptide into secondary structure, and how these hydrogen bonds direct the overall shape of helical and sheet structures, including the handedness of the α-helix and the difference between right- and the left-handed twist. Copyright © 2010 Wiley Periodicals, Inc.

VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program.

PubMed

Yahyavi, Masoumeh; Falsafi-Zadeh, Sajad; Karimi, Zahra; Kalatarian, Giti; Galehdari, Hamid

2014-01-01

The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its trajectories during simulation for known structures available at the Protein Data Bank (PDB). The program helps to calculate (1) percentage SS, (2) SS occurrence in each residue, (3) percentage SS during simulation, and (4) percentage residues in all SS types during simulation. The VMD-SS plug-in was designed using TCL script and stride to calculate secondary structure features. The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755.

Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution

PubMed Central

Chursov, Andrey; Frishman, Dmitrij; Shneider, Alexander

2013-01-01

Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary structures of mRNA coding regions, a previously unknown factor in bacterial evolution, by comparing the structural consequences of mutations in essential and nonessential Escherichia coli genes accumulated over 40 000 generations in the course of the ‘long-term evolution experiment’. We monitored the extent to which mutations influence minimum free energy (MFE) values, assuming that a substantial change in MFE is indicative of structural perturbation. Our principal finding is that purifying selection tends to eliminate those mutations in essential genes that lead to greater changes of MFE values and, therefore, may be more disruptive for the corresponding mRNA secondary structures. This effect implies that synonymous mutations disrupting mRNA secondary structures may directly affect the fitness of the organism. These results demonstrate that the need to maintain intact mRNA structures imposes additional evolutionary constraints on bacterial genomes, which go beyond preservation of structure and function of the encoded proteins. PMID:23783573

The Visit-Data Warehouse: Enabling Novel Secondary Use of Health Information Exchange Data

PubMed Central

Fleischman, William; Lowry, Tina; Shapiro, Jason

2014-01-01

Introduction/Objectives: Health Information Exchange (HIE) efforts face challenges with data quality and performance, and this becomes especially problematic when data is leveraged for uses beyond primary clinical use. We describe a secondary data infrastructure focusing on patient-encounter, nonclinical data that was built on top of a functioning HIE platform to support novel secondary data uses and prevent potentially negative impacts these uses might have otherwise had on HIE system performance. Background: HIE efforts have generally formed for the primary clinical use of individual clinical providers searching for data on individual patients under their care, but many secondary uses have been proposed and are being piloted to support care management, quality improvement, and public health. Description of the HIE and Base Infrastructure: This infrastructure review describes a module built into the Healthix HIE. Healthix, based in the New York metropolitan region, comprises 107 participating organizations with 29,946 acute-care beds in 383 facilities, and includes more than 9.2 million unique patients. The primary infrastructure is based on the InterSystems proprietary Caché data model distributed across servers in multiple locations, and uses a master patient index to link individual patients’ records across multiple sites. We built a parallel platform, the “visit data warehouse,” of patient encounter data (demographics, date, time, and type of visit) using a relational database model to allow accessibility using standard database tools and flexibility for developing secondary data use cases. These four secondary use cases include the following: (1) tracking encounter-based metrics in a newly established geriatric emergency department (ED), (2) creating a dashboard to provide a visual display as well as a tabular output of near-real-time de-identified encounter data from the data warehouse, (3) tracking frequent ED users as part of a regional-approach to case management intervention, and (4) improving an existing quality improvement program that analyzes patients with return visits to EDs within 72 hours of discharge. Results/Lessons Learned: Setting up a separate, near-real-time, encounters-based relational database to complement an HIE built on a hierarchical database is feasible, and may be necessary to support many secondary uses of HIE data. As of November 2014, the visit-data warehouse (VDW) built by Healthix is undergoing technical validation testing and updates on an hourly basis. We had to address data integrity issues with both nonstandard and missing HL7 messages because of varied HL7 implementation across the HIE. Also, given our HIEs federated structure, some sites expressed concerns regarding data centralization for the VDW. An established and stable HIE governance structure was critical in overcoming this initial reluctance. Conclusions: As secondary use of HIE data becomes more prevalent, it may be increasingly necessary to build separate infrastructure to support secondary use without compromising performance. More research is needed to determine optimal ways of building such infrastructure and validating its use for secondary purposes. PMID:25848595

Conjugation of cytochrome c with ferrocene-terminated hyperbranched polymer and its influence on protein structure, conformation and function.

PubMed

Xiao, Fengjuan; Yue, Lin; Li, Song; Li, Xinxin

2016-06-05

Interaction mechanism of a new hyperbranched polyurethane-based ferrocene (HPU-Fc) with cytochrome c (cyt c) and cyt c structure and conformation change induced by HPU-Fc were investigated using cyclic voltammogram(CV), differential pulse voltammetry (DPV), circular dichroism (CD), fluorescence, synchronous fluorescence and absorbance spectroscopy technique. The peroxidase activity of cyt c in the presence of HPU-Fc was also studied. The structure and conformation of protein are relatively stable at moderate concentration of HPU-Fc without obvious perturbation of the heme pocket and significant changes in protein secondary structure. Conjugation of cyt c with excessive HPU-Fc (over about 3 times of cyt c) slightly changed the α-helix structure in protein, disturbed the microenvironment around heme as well as away from the heme crevice, which caused the changes of the electrochemical behavior and the absorption spectra. Reasonable amount of HPU-Fc has no significant influence on the protein enzymatic activity, while excess HPU-Fc may cause a conformation not suitable for H2O2 activation and guaiacol oxidation. The interaction of HPU-Fc with cyt c and the conservation of protein function at suitable HPU-Fc amount make prepared complex promising for the synergistic anticancer therapy. Copyright © 2016 Elsevier B.V. All rights reserved.

Secondary Ion Mass Spectrometry for Mg Tracer Diffusion: Issues and Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuggle, Jay; Giordani, Andrew; Kulkarni, Nagraj S

2014-01-01

A Secondary Ion Mass Spectrometry (SIMS) method has been developed to measure stable Mg isotope tracer diffusion. This SIMS method was then used to calculate Mg self- diffusivities and the data was verified against historical data measured using radio tracers. The SIMS method has been validated as a reliable alternative to the radio-tracer technique for the measurement of Mg self-diffusion coefficients and can be used as a routine method for determining diffusion coefficients.

Sleep Disturbance, Daytime Symptoms, and Functional Performance in Patients With Stable Heart Failure: A Mediation Analysis.

PubMed

Jeon, Sangchoon; Redeker, Nancy S

2016-01-01

Sleep disturbance is common among patients with heart failure (HF) who also experience symptom burden and poor functional performance. We evaluated the extent to which sleep-related, daytime symptoms (fatigue, excessive daytime sleepiness, and depressive symptoms) mediate the relationship between sleep disturbance and functional performance among patients with stable HF. We recruited patients with stable HF for this secondary analysis of data from a cross-sectional, observational study. Participants completed unattended ambulatory polysomnography from which the Respiratory Disturbance Index was calculated, along with a Six-Minute Walk Test, questionnaires to elicit sleep disturbance (Pittsburgh Sleep Quality Index, Insomnia Symptoms from the Sleep Habits Questionnaire), daytime symptoms (Center for Epidemiologic Studies Depression Scale, Global Fatigue Index, Epworth Sleepiness Scale), and self-reported functional performance (Medical Outcomes Study SF36 V2 Physical Function Scale). We used structural equation modeling with latent variables for the key analysis. Follow-up, exploratory regression analysis with bootstrapped samples was used to examine the extent to which individual daytime symptoms mediated effects of sleep disturbance on functional performance after controlling for clinical and demographic covariates. The sample included 173 New York Heart Association Class I-IV HF patients (n = 60/34.7% women; M = 60.7, SD = 16.07 years of age). Daytime symptoms mediated the relationship between sleep disturbance and functional performance. Fatigue and depression mediated the relationship between insomnia symptoms and self-reported functional performance, whereas fatigue and sleepiness mediated the relationship between sleep quality and functional performance. Sleepiness mediated the relationship between the respiratory index and self-reported functional performance only in people who did not report insomnia. Daytime symptoms explain the relationships between sleep disturbance and functional performance in stable HF.

A generalized analysis of hydrophobic and loop clusters within globular protein sequences

PubMed Central

Eudes, Richard; Le Tuan, Khanh; Delettré, Jean; Mornon, Jean-Paul; Callebaut, Isabelle

2007-01-01

Background Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet. Results The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated within banks of experimental structures, considered at different levels of sequence redundancy. The 294 more frequent hydrophobic cluster species were analyzed with regard to their association with the different secondary structures (frequencies of association with secondary structures and secondary structure propensities). Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for α-helices or β-strands. Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster species. We also investigated the behavior of loop forming clusters, using a "PGDNS" alphabet. These loop clusters do not overlap with hydrophobic clusters and are highly associated with coils. Finally, the structural information contained in the hydrophobic structural words, as deduced from experimental structures, was compared to the PSI-PRED predictions, revealing that β-strands and especially α-helices are generally over-predicted within the limits of typical β and α hydrophobic clusters. Conclusion The dictionary of hydrophobic clusters described here can help the HCA user to interpret and compare the HCA plots of globular protein sequences, as well as provides an original fundamental insight into the structural bricks of protein folds. Moreover, the novel loop cluster analysis brings additional information for secondary structure prediction on the whole sequence through a generalized cluster analysis (GCA), and not only on regular secondary structures. Such information lays the foundations for developing a new and original tool for secondary structure prediction. PMID:17210072

Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent?

PubMed Central

Siwy, Christopher M.

2017-01-01

By applying REMD simulations we have performed comparative analysis of the conformational ensembles of amino-truncated Aβ10-40 peptide produced with five force fields, which combine four protein parameterizations (CHARMM36, CHARMM22*, CHARMM22/cmap, and OPLS-AA) and two water models (standard and modified TIP3P). Aβ10-40 conformations were analyzed by computing secondary structure, backbone fluctuations, tertiary interactions, and radius of gyration. We have also calculated Aβ10-40 3JHNHα-coupling and RDC constants and compared them with their experimental counterparts obtained for the full-length Aβ1-40 peptide. Our study led us to several conclusions. First, all force fields predict that Aβ adopts unfolded structure dominated by turn and random coil conformations. Second, specific TIP3P water model does not dramatically affect secondary or tertiary Aβ10-40 structure, albeit standard TIP3P model favors slightly more compact states. Third, although the secondary structures observed in CHARMM36 and CHARMM22/cmap simulations are qualitatively similar, their tertiary interactions show little consistency. Fourth, two force fields, OPLS-AA and CHARMM22* have unique features setting them apart from CHARMM36 or CHARMM22/cmap. OPLS-AA reveals moderate β-structure propensity coupled with extensive, but weak long-range tertiary interactions leading to Aβ collapsed conformations. CHARMM22* exhibits moderate helix propensity and generates multiple exceptionally stable long- and short-range interactions. Our investigation suggests that among all force fields CHARMM22* differs the most from CHARMM36. Fifth, the analysis of 3JHNHα-coupling and RDC constants based on CHARMM36 force field with standard TIP3P model led us to an unexpected finding that in silico Aβ10-40 and experimental Aβ1-40 constants are generally in better agreement than these quantities computed and measured for identical peptides, such as Aβ1-40 or Aβ1-42. This observation suggests that the differences in the conformational ensembles of Aβ10-40 and Aβ1-40 are small and the former can be used as proxy of the full-length peptide. Based on this argument, we concluded that CHARMM36 force field with standard TIP3P model produces the most accurate representation of Aβ10-40 conformational ensemble. PMID:28085875

Nicked apomyoglobin: a noncovalent complex of two polypeptide fragments comprising the entire protein chain.

PubMed

Musi, Valeria; Spolaore, Barbara; Picotti, Paola; Zambonin, Marcello; De Filippis, Vincenzo; Fontana, Angelo

2004-05-25

Limited proteolysis of the 153-residue chain of horse apomyoglobin (apoMb) by thermolysin results in the selective cleavage of the peptide bond Pro88-Leu89. The N-terminal (residues 1-88) and C-terminal (residues 89-153) fragments of apoMb were isolated to homogeneity and their conformational and association properties investigated in detail. Far-UV circular dichroism (CD) measurements revealed that both fragments in isolation acquire a high content of helical secondary structure, while near-UV CD indicated the absence of tertiary structure. A 1:1 mixture of the fragments leads to a tight noncovalent protein complex (1-88/89-153, nicked apoMb), characterized by secondary and tertiary structures similar to those of intact apoMb. The apoMb complex binds heme in a nativelike manner, as given by CD measurements in the Soret region. Second-derivative absorption spectra in the 250-300 nm region provided evidence that the degree of exposure of Tyr residues in the nicked species is similar to that of the intact protein at neutral pH. Also, the microenvironment of Trp residues, located in positions 7 and 14 of the 153-residue chain of the protein, is similar in both protein species, as given by fluorescence emission data. Moreover, in analogy to intact apoMb, the nicked protein binds the hydrophobic dye 1-anilinonaphthalene-8-sulfonate (ANS). Taken together, our results indicate that the two proteolytic fragments 1-88 and 89-153 of apoMb adopt partly folded states characterized by sufficiently nativelike conformational features that promote their specific association and mutual stabilization into a nicked protein species much resembling in its structural features intact apoMb. It is suggested that the formation of a noncovalent complex upon fragment complementation can mimic the protein folding process of the entire protein chain, with the difference that the folding of the complementary fragments is an intermolecular process. In particular, this study emphasizes the importance of interactions between marginally stable elements of secondary structure in promoting the tertiary contacts of a native protein. Considering that apoMb has been extensively used as a paradigm in protein folding studies for the past few decades, the novel fragment complementing system of apoMb here described appears to be very useful for investigating the initial as well as late events in protein folding.

Structures and Free Energy Landscapes of the Wild-Type and A30P Mutant-Type α-Synuclein Proteins with Dynamics

PubMed Central

2013-01-01

The genetic missense A30P mutation of the wild-type α-synuclein protein results in the replacement of the 30th amino acid residue from alanine (Ala) to proline (Pro) and was initially found in the members of a German family who developed Parkinson’s disease. Even though the structures of these proteins have been measured before, detailed understanding about the structures and their relationships with free energy landscapes is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson’s disease. We report the secondary and tertiary structures and conformational free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins in an aqueous solution environment via extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations. In addition, we present the residual secondary structure component transition stabilities at the atomic level with dynamics in terms of free energy change calculations using a new strategy that we reported most recently. Our studies yield new interesting results; for instance, we find that the A30P mutation has local as well as long-range effects on the structural properties of the wild-type α-synuclein protein. The helical content at Ala18-Gly31 is less prominent in comparison to the wild-type α-synuclein protein. The β-sheet structure abundance decreases in the N-terminal region upon A30P mutation of the wild-type α-synuclein, whereas the NAC and C-terminal regions possess larger tendencies for β-sheet structure formation. Long-range intramolecular protein interactions are less abundant upon A30P mutation, especially between the NAC and C-terminal regions, which is linked to the less compact and less stable structures of the A30P mutant-type rather than the wild-type α-synuclein protein. Results including the usage of our new strategy for secondary structure transition stabilities show that the A30P mutant-type α-synuclein tendency toward aggregation is higher than the wild-type α-synuclein but we also find that the C-terminal and NAC regions of the A30P mutant-type α-synuclein are reactive toward fibrillzation and aggregation based on atomic level studies with dynamics in an aqueous solution environment. Therefore, we propose that small molecules or drugs blocking the specific residues, which we report herein, located in the NAC- and C-terminal regions of the A30P mutant-type α-synuclein protein might help to reduce the toxicity of the A30P mutant-type α-synuclein protein. PMID:23374072

Structures and free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins with dynamics.

PubMed

Wise-Scira, Olivia; Aloglu, Ahmet Kemal; Dunn, Aquila; Sakallioglu, Isin Tuna; Coskuner, Orkid

2013-03-20

The genetic missense A30P mutation of the wild-type α-synuclein protein results in the replacement of the 30th amino acid residue from alanine (Ala) to proline (Pro) and was initially found in the members of a German family who developed Parkinson's disease. Even though the structures of these proteins have been measured before, detailed understanding about the structures and their relationships with free energy landscapes is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson's disease. We report the secondary and tertiary structures and conformational free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins in an aqueous solution environment via extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations. In addition, we present the residual secondary structure component transition stabilities at the atomic level with dynamics in terms of free energy change calculations using a new strategy that we reported most recently. Our studies yield new interesting results; for instance, we find that the A30P mutation has local as well as long-range effects on the structural properties of the wild-type α-synuclein protein. The helical content at Ala18-Gly31 is less prominent in comparison to the wild-type α-synuclein protein. The β-sheet structure abundance decreases in the N-terminal region upon A30P mutation of the wild-type α-synuclein, whereas the NAC and C-terminal regions possess larger tendencies for β-sheet structure formation. Long-range intramolecular protein interactions are less abundant upon A30P mutation, especially between the NAC and C-terminal regions, which is linked to the less compact and less stable structures of the A30P mutant-type rather than the wild-type α-synuclein protein. Results including the usage of our new strategy for secondary structure transition stabilities show that the A30P mutant-type α-synuclein tendency toward aggregation is higher than the wild-type α-synuclein but we also find that the C-terminal and NAC regions of the A30P mutant-type α-synuclein are reactive toward fibrillzation and aggregation based on atomic level studies with dynamics in an aqueous solution environment. Therefore, we propose that small molecules or drugs blocking the specific residues, which we report herein, located in the NAC- and C-terminal regions of the A30P mutant-type α-synuclein protein might help to reduce the toxicity of the A30P mutant-type α-synuclein protein.

Impacts of structuring the electronic health record: Results of a systematic literature review from the perspective of secondary use of patient data.

PubMed

Vuokko, Riikka; Mäkelä-Bengs, Päivi; Hyppönen, Hannele; Lindqvist, Minna; Doupi, Persephone

2017-01-01

To explore the impacts that structuring of electronic health records (EHRs) has had from the perspective of secondary use of patient data as reflected in currently published literature. This paper presents the results of a systematic literature review aimed at answering the following questions; (1) what are the common methods of structuring patient data to serve secondary use purposes; (2) what are the common methods of evaluating patient data structuring in the secondary use context, and (3) what impacts or outcomes of EHR structuring have been reported from the secondary use perspective. The reported study forms part of a wider systematic literature review on the impacts of EHR structuring methods and evaluations of their impact. The review was based on a 12-step systematic review protocol adapted from the Cochrane methodology. Original articles included in the study were divided into three groups for analysis and reporting based on their use focus: nursing documentation, medical use and secondary use (presented in this paper). The analysis from the perspective of secondary use of data includes 85 original articles from 1975 to 2010 retrieved from 15 bibliographic databases. The implementation of structured EHRs can be roughly divided into applications for documenting patient data at the point of care and application for retrieval of patient data (post hoc structuring). Two thirds of the secondary use articles concern EHR structuring methods which were still under development or in the testing phase. of structuring patient data such as codes, terminologies, reference information models, forms or templates and documentation standards were usually applied in combination. Most of the identified benefits of utilizing structured EHR data for secondary use purposes concentrated on information content and quality or on technical quality and reliability, particularly in the case of Natural Language Processing (NLP) studies. A few individual articles evaluated impacts on care processes, productivity and costs, patient safety, care quality or other health impacts. In most articles these endpoints were usually discussed as goals of secondary use and less as evidence-supported impacts, resulting from the use of structured EHR data for secondary purposes. Further studies and more sound evaluation methods are needed for evidence on how EHRs are utilized for secondary purposes, and how structured documentation methods can serve different users' needs, e.g. administration, statistics and research and development, in parallel to medical use purposes. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Stable, concentrated solutions of high molecular weight polyaniline and articles therefrom

DOEpatents

Mattes, Benjamin R.; Wang, Hsing-Lin

1999-11-09

Stable, concentrated solutions of high molecular weight polyaniline. In order to process high quality fibers and other articles possessing good mechanical properties, it is known that solution concentrations of the chosen polymer should be in the range from 15-30% (w/w). Moreover, it is desirable to use the highest molecular weight consistent with the solubility properties of the polymer. However, such solutions are inherently unstable, forming gels before processing can be achieved. The present invention describes the addition gel inhibitors (GIs) to the polymer solution, thereby permitting high concentrations (between 15% and 30% (w/w)) of high molecular weight ((M.sub.w)>120,000, and (M.sub.n)>30,000) emeraldine base (EB) polyaniline to be dissolved. Secondary amines have been used for this purpose in concentrations which are small compared to those which might otherwise be used in a cosolvent role therefor. The resulting solutions are useful for generating excellent fibers, films, coatings and other objects, since the solutions are stable for significant time periods, and the GIs are present in too small concentrations to cause polymer deterioration. It is demonstrated that the GIs found to be useful do not act as cosolvents, and that gelation times of the solutions are directly proportional to the concentration of GI. In particular, there is a preferred concentration of GI, which if exceeded causes structural and electrical conductivity degradation of resulting articles. Heating of the solutions significantly improves solubility.

Physico-Chemical Evaluation of Rationally Designed Melanins as Novel Nature-Inspired Radioprotectors

PubMed Central

Schweitzer, Andrew D.; Howell, Robertha C.; Jiang, Zewei; Bryan, Ruth A.; Gerfen, Gary; Chen, Chin-Cheng; Mah, Dennis; Cahill, Sean

2009-01-01

Background Melanin, a high-molecular weight pigment that is ubiquitous in nature, protects melanized microorganisms against high doses of ionizing radiation. However, the physics of melanin interaction with ionizing radiation is unknown. Methodology/Principal Findings We rationally designed melanins from either 5-S-cysteinyl-DOPA, L-cysteine/L-DOPA, or L-DOPA with diverse structures as shown by elemental analysis and HPLC. Sulfur-containing melanins had higher predicted attenuation coefficients than non-sulfur-containing melanins. All synthetic melanins displayed strong electron paramagnetic resonance (2.14·1018, 7.09·1018, and 9.05·1017 spins/g, respectively), with sulfur-containing melanins demonstrating more complex spectra and higher numbers of stable free radicals. There was no change in the quality or quantity of the stable free radicals after high-dose (30,000 cGy), high-energy (137Cs, 661.6 keV) irradiation, indicating a high degree of radical stability as well as a robust resistance to the ionizing effects of gamma irradiation. The rationally designed melanins protected mammalian cells against ionizing radiation of different energies. Conclusions/Significance We propose that due to melanin's numerous aromatic oligomers containing multiple π-electron system, a generated Compton recoil electron gradually loses energy while passing through the pigment, until its energy is sufficiently low that it can be trapped by stable free radicals present in the pigment. Controlled dissipation of high-energy recoil electrons by melanin prevents secondary ionizations and the generation of damaging free radical species. PMID:19789711

Physico-chemical evaluation of rationally designed melanins as novel nature-inspired radioprotectors.

PubMed

Schweitzer, Andrew D; Howell, Robertha C; Jiang, Zewei; Bryan, Ruth A; Gerfen, Gary; Chen, Chin-Cheng; Mah, Dennis; Cahill, Sean; Casadevall, Arturo; Dadachova, Ekaterina

2009-09-30

Melanin, a high-molecular weight pigment that is ubiquitous in nature, protects melanized microorganisms against high doses of ionizing radiation. However, the physics of melanin interaction with ionizing radiation is unknown. We rationally designed melanins from either 5-S-cysteinyl-DOPA, L-cysteine/L-DOPA, or L-DOPA with diverse structures as shown by elemental analysis and HPLC. Sulfur-containing melanins had higher predicted attenuation coefficients than non-sulfur-containing melanins. All synthetic melanins displayed strong electron paramagnetic resonance (2.14.10(18), 7.09.10(18), and 9.05.10(17) spins/g, respectively), with sulfur-containing melanins demonstrating more complex spectra and higher numbers of stable free radicals. There was no change in the quality or quantity of the stable free radicals after high-dose (30,000 cGy), high-energy ((137)Cs, 661.6 keV) irradiation, indicating a high degree of radical stability as well as a robust resistance to the ionizing effects of gamma irradiation. The rationally designed melanins protected mammalian cells against ionizing radiation of different energies. We propose that due to melanin's numerous aromatic oligomers containing multiple pi-electron system, a generated Compton recoil electron gradually loses energy while passing through the pigment, until its energy is sufficiently low that it can be trapped by stable free radicals present in the pigment. Controlled dissipation of high-energy recoil electrons by melanin prevents secondary ionizations and the generation of damaging free radical species.

Teacher argumentation in the secondary science classroom: Images of two modes of scientific inquiry

NASA Astrophysics Data System (ADS)

Gray, Ron E.

The purpose of this exploratory study was to examine scientific arguments constructed by secondary science teachers during instruction. The analysis focused on how arguments constructed by teachers differed based on the mode of inquiry underlying the topic. Specifically, how did the structure and content of arguments differ between experimentally and historically based topics? In addition, what factors mediate these differences? Four highly experienced high school science teachers were observed daily during instructional units for both experimental and historical science topics. Data sources include classroom observations, field notes, reflective memos, classroom artifacts, a nature of science survey, and teacher interviews. The arguments were analyzed for structure and content using Toulmin's argumentation pattern and Walton's schemes for presumptive reasoning revealing specific patterns of use between the two modes of inquiry. Interview data was analyzed to determine possible factors mediating these patterns. The results of this study reveal that highly experienced teachers present arguments to their students that, while simple in structure, reveal authentic images of science based on experimental and historical modes of inquiry. Structural analysis of the data revealed a common trend toward a greater amount of scientific data used to evidence knowledge claims in the historical science units. The presumptive reasoning analysis revealed that, while some presumptive reasoning schemes remained stable across the two units (e.g. 'causal inferences' and 'sign' schemes), others revealed different patterns of use including the 'analogy', 'evidence to hypothesis', 'example', and 'expert opinion' schemes. Finally, examination of the interview and survey data revealed five specific factors mediating the arguments constructed by the teachers: view of the nature of science, nature of the topic, teacher personal factors, view of students, and pedagogical decisions. These factors influenced both the structure and use of presumptive reasoning in the arguments. The results have implications for classroom practice, teacher education, and further research.

Secondary Waste Form Down-Selection Data Package—Fluidized Bed Steam Reforming Waste Form

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qafoku, Nikolla; Westsik, Joseph H.; Strachan, Denis M.

2011-09-12

The Hanford Site in southeast Washington State has 56 million gallons of radioactive and chemically hazardous wastes stored in 177 underground tanks (ORP 2010). The U.S. Department of Energy (DOE), Office of River Protection (ORP), through its contractors, is constructing the Hanford Tank Waste Treatment and Immobilization Plant (WTP) to convert the radioactive and hazardous wastes into stable glass waste forms for disposal. Within the WTP, the pretreatment facility will receive the retrieved waste from the tank farms and separate it into two treated process streams. These waste streams will be vitrified, and the resulting waste canisters will be sentmore » to offsite (high-level waste [HLW]) and onsite (immobilized low-activity waste [ILAW]) repositories. As part of the pretreatment and ILAW processing, liquid secondary wastes will be generated that will be transferred to the Effluent Treatment Facility (ETF) on the Hanford Site for further treatment. These liquid secondary wastes will be converted to stable solid waste forms that will be disposed of in the Integrated Disposal Facility (IDF). To support the selection of a waste form for the liquid secondary wastes from WTP, Washington River Protection Solutions (WRPS) has initiated secondary waste form testing work at Pacific Northwest National Laboratory (PNNL). In anticipation of a down-selection process for a waste form for the Solidification Treatment Unit to be added to the ETF, PNNL is developing data packages to support that down-selection. The objective of the data packages is to identify, evaluate, and summarize the existing information on the four waste forms being considered for stabilizing and solidifying the liquid secondary wastes. At the Hanford Site, the FBSR process is being evaluated as a supplemental technology for treating and immobilizing Hanford LAW radioactive tank waste and for treating secondary wastes from the WTP pretreatment and LAW vitrification processes.« less

Preparation and Characterization of Stable α-Synuclein Lipoprotein Particles.

PubMed

Eichmann, Cédric; Campioni, Silvia; Kowal, Julia; Maslennikov, Innokentiy; Gerez, Juan; Liu, Xiaoxia; Verasdonck, Joeri; Nespovitaya, Nadezhda; Choe, Senyon; Meier, Beat H; Picotti, Paola; Rizo, Josep; Stahlberg, Henning; Riek, Roland

2016-04-15

Multiple neurodegenerative diseases are caused by the aggregation of the human α-Synuclein (α-Syn) protein. α-Syn possesses high structural plasticity and the capability of interacting with membranes. Both features are not only essential for its physiological function but also play a role in the aggregation process. Recently it has been proposed that α-Syn is able to form lipid-protein particles reminiscent of high-density lipoproteins. Here, we present a method to obtain a stable and homogeneous population of nanometer-sized particles composed of α-Syn and anionic phospholipids. These particles are called α-Syn lipoprotein (nano)particles to indicate their relationship to high-density lipoproteins formed by human apolipoproteins in vivo and of in vitro self-assembling phospholipid bilayer nanodiscs. Structural investigations of the α-Syn lipoprotein particles by circular dichroism (CD) and magic angle solid-state nuclear magnetic resonance (MAS SS-NMR) spectroscopy establish that α-Syn adopts a helical secondary structure within these particles. Based on cryo-electron microscopy (cryo-EM) and dynamic light scattering (DLS) α-Syn lipoprotein particles have a defined size with a diameter of ∼23 nm. Chemical cross-linking in combination with solution-state NMR and multiangle static light scattering (MALS) of α-Syn particles reveal a high-order protein-lipid entity composed of ∼8-10 α-Syn molecules. The close resemblance in size between cross-linked in vitro-derived α-Syn lipoprotein particles and a cross-linked species of endogenous α-Syn from SH-SY5Y human neuroblastoma cells indicates a potential functional relevance of α-Syn lipoprotein nanoparticles. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding

PubMed Central

Newcomer, Rebecca L.; Fraser, LaTasha C.R.; Teschke, Carolyn M.; Alexandrescu, Andrei T.

2015-01-01

The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining 3JNC’ couplings transmitted through H-bonds, the temperature and urea-concentration dependence of 1HN and 15N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and 3JNC’ H-bond couplings, are identified with an accuracy of 90% by 1HN temperature coefficients. The accuracy is improved to 95% when 15N temperature coefficients are also included. In contrast, the urea dependence of 1HN and 15N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility. PMID:26682823

Functional inclusion bodies produced in the yeast Pichia pastoris.

PubMed

Rueda, Fabián; Gasser, Brigitte; Sánchez-Chardi, Alejandro; Roldán, Mònica; Villegas, Sandra; Puxbaum, Verena; Ferrer-Miralles, Neus; Unzueta, Ugutz; Vázquez, Esther; Garcia-Fruitós, Elena; Mattanovich, Diethard; Villaverde, Antonio

2016-10-01

Bacterial inclusion bodies (IBs) are non-toxic protein aggregates commonly produced in recombinant bacteria. They are formed by a mixture of highly stable amyloid-like fibrils and releasable protein species with a significant extent of secondary structure, and are often functional. As nano structured materials, they are gaining biomedical interest because of the combination of submicron size, mechanical stability and biological activity, together with their ability to interact with mammalian cell membranes for subsequent cell penetration in absence of toxicity. Since essentially any protein species can be obtained as IBs, these entities, as well as related protein clusters (e.g., aggresomes), are being explored in biocatalysis and in biomedicine as mechanically stable sources of functional protein. One of the major bottlenecks for uses of IBs in biological interfaces is their potential contamination with endotoxins from producing bacteria. To overcome this hurdle, we have explored here the controlled production of functional IBs in the yeast Pichia pastoris (Komagataella spp.), an endotoxin-free host system for recombinant protein production, and determined the main physicochemical and biological traits of these materials. Quantitative and qualitative approaches clearly indicate the formation of IBs inside yeast, similar in morphology, size and biological activity to those produced in E. coli, that once purified, interact with mammalian cell membranes and penetrate cultured mammalian cells in absence of toxicity. Structurally and functionally similar from those produced in E. coli, the controlled production of IBs in P. pastoris demonstrates that yeasts can be used as convenient platforms for the biological fabrication of self-organizing protein materials in absence of potential endotoxin contamination and with additional advantages regarding, among others, post-translational modifications often required for protein functionality.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jung, Hyeyoung; Allan, Phoebe K.; Hu, Yan-Yan

Metallic germanium is a promising anode material in secondary lithium-ion batteries (LIBs) due to its high theoretical capacity (1623 mAh/g) and low operating voltage, coupled with the high lithium-ion diffusivity and electronic conductivity of lithiated Ge. Here, the lithiation mechanism of micron-sized Ge anodes has been investigated with X-ray diffraction (XRD), pair distribution function (PDF) analysis, and in-/ex-situ high-resolution Li-7 solid-state nuclear magnetic resonance (NMR), utilizing the structural information and spectroscopic fingerprints obtained by characterizing a series of relevant Li(x)Gey model compounds. In contrast to previous work, which postulated the formation of Li9Ge4 upon initial lithiation, we show that crystallinemore » Ge first reacts to form a mixture of amorphous and crystalline Li7Ge3 (space group P32(1)2). Although Li7Ge3 was proposed to be stable in a recent theoretical study of the Li-Ge phase diagram (Morris, A. J.; Grey, C. P.; Pickard, C. J. Phys. Rev. B: Condens. Matter Mater. Phys. 2014, 90, 054111), it had not been identified in prior experimental studies. Further lithiation results in the transformation of Li7Ge3, via a series of disordered phases with related structural motifs, to form a phase that locally resembles Li7Ge2, a process that involves the gradual breakage of the Ge-Ge bonds in the Ge-Ge dimers (dumbbells) on lithiation. Crystalline Li15Ge4 then grows, with an overlithiated phase, Li15+delta Ge4, being formed at the end of discharge. This study provides comprehensive experimental evidence, by using techniques that probe short-, medium-, and long-range order, for the structural transformations that occur on electrochemical lithiation of Ge; the results are consistent with corresponding theoretical studies regarding stable lithiated LixGey phases.« less

Effects of Relative Humidity on Ozone and Secondary Organic Aerosol Formation from the Photooxidation of Benzene and Ethylbenzene

NASA Astrophysics Data System (ADS)

Jia, L.; Xu, Y.

2012-12-01

The formation of ozone and secondary organic aerosol from benzene-NOx and ethylbenzene-NOx irradiations was investigated under different levels of relative humidity (RH) in a smog chamber. The results show that the increase in RH can greatly reduce the maximum O3 by the transformation of -NO2 and -ONO2-containing products into the particle phase. In benzene irradiations, the SOA number concentration increases over 26 times as RH rises from <5% to 80%, and the intensity of the bands of -OH, -C=O and C-OH from SOA samples also greatly increases with RH. In ethylbenzene irradiations, ethylglyoxal favors the formation of monohydrate, which limits the RH effects. During evaporating processes, the lost substances have similar structures for both benzene and ethylbenzene. This demonstrates that ethyl-containing substances are very stable and difficult to evaporate. For benzene some of glyoxal hydrates are left to form C-O-C and C=O-containing species like hemiacetal and acetal after evaporation, whereas for ethylbenzene, glyoxal favors cross reactions with ethylglyoxal during the evaporating process. It is concluded that the increase in RH can irreversibly enhance the yields of SOA from both benzene and ethylbenzene.

Ranibizumab for choroidal neovascularization secondary to pseudoxanthoma elasticum: 4-year results from the PIXEL study in France.

PubMed

Mimoun, Gérard; Ebran, Jean-Marc; Grenet, Typhaine; Donati, Alain; Cohen, Salomon-Yves; Ponthieux, Anne

2017-08-01

To evaluate the long-term effectiveness and safety of ranibizumab 0.5 mg in patients with choroidal neovascularization (CNV) secondary to pseudoxanthoma elasticum (PXE) in a real-world setting. A descriptive, observational, multicenter study in a retrospective and prospective cohort was conducted in France that included patients who had received at least one injection of ranibizumab 0.5 mg during the period October 2011 to October 2014, for CNV secondary to PXE. Eligible patients were identified by review of medical records or during routine consultations. The main objectives were to describe patient characteristics, assess changes in best-corrected visual acuity [VA, Early Treatment Diabetic Retinopathy Study (ETDRS) letters] over time, the number and reasons for ranibizumab treatment and overall safety. Of the 72 enrolled patients (98 eyes) from 23 centers, 39 (54.2%) were male and mean [±standard deviation (SD)] age was 59.6 (±8.3) years. The mean VA was 64.6 letters at the first ranibizumab injection, which was maintained at the 1-year follow-up (64.7 letters). Thereafter, the mean VA was stable until the 4-year follow-up. At 4 years, the proportion of eyes with VA gain of ≥15 letters was 3/19 (15.8%) and stable VA (change between -15 and +15 letters) was 10/19 (52.6%). Mean (±SD) annual number of ranibizumab injections was 4.1 (±4.0), lower in the second versus first year. The most common reason for ranibizumab treatment was progression of neovascular activity (42.9%). No deaths or new safety findings were reported. In patients with CNV secondary to PXE, ranibizumab 0.5 mg resulted in stable VA over 4 years with a limited number of injections. Safety findings were consistent with the established safety profile of ranibizumab.

An experimental study of secondary vortex structure in mixing layers

NASA Technical Reports Server (NTRS)

Bell, J. H.; Mehta, Rabindra D.

1990-01-01

This report covers the first eight months of an experimental research project on the secondary vortex structure in plane mixing layers. The aim of the project is to obtain quantitative data on the behavior of the secondary structure in a turbulent mixing layer at reasonable reynolds numbers (Re(sub delta(sub w)) approx. 50,000). In particular, we hope to resolve the questions of how the scale of the secondary vortex structure changes with the scale of the mixing layer, and whether the structures are fixed in space, or whether they 'meander' in the spanwise direction.

Convergence of an iterative procedure for large-scale static analysis of structural components

NASA Technical Reports Server (NTRS)

Austin, F.; Ojalvo, I. U.

1976-01-01

The paper proves convergence of an iterative procedure for calculating the deflections of built-up component structures which can be represented as consisting of a dominant, relatively stiff primary structure and a less stiff secondary structure, which may be composed of one or more substructures that are not connected to one another but are all connected to the primary structure. The iteration consists in estimating the deformation of the primary structure in the absence of the secondary structure on the assumption that all mechanical loads are applied directly to the primary structure. The j-th iterate primary structure deflections at the interface are imposed on the secondary structure, and the boundary loads required to produce these deflections are computed. The cycle is completed by applying the interface reaction to the primary structure and computing its updated deflections. It is shown that the mathematical condition for convergence of this procedure is that the maximum eigenvalue of the equation relating primary-structure deflection to imposed secondary-structure deflection be less than unity, which is shown to correspond with the physical requirement that the secondary structure be more flexible at the interface boundary.

Personal goals as predictors of intended classroom goals: comparing elementary and secondary school pre-service teachers.

PubMed

Daniels, Lia M; Frenzel, Anne C; Stupnisky, Robert H; Stewart, Tara L; Perry, Raymond P

2013-09-01

The literature documents fewer classroom mastery goal structures in secondary school compared to elementary. However, little is known about how personal achievement goals may influence classroom goal structures. This is especially true at the level of pre-service teachers. Our objective was to investigate if pre-service teachers' personal goals predicted their intended classroom goal structures. Participants were 125 elementary and 175 secondary school pre-service teachers from two Western Canadian universities. Structural equation modelling was used to examine if the structural relationships and latent means of personal and intended classroom goal structures differed for elementary and secondary school pre-service teachers. The results revealed that personal goals predicted the goal structures that pre-service teachers intended to establish; however, the relationships and means differed between elementary and secondary school pre-service teachers. Specifically, personal mastery-approach goals positively predicted classroom mastery goals much more strongly at the elementary than the secondary level. Furthermore, elementary pre-service teachers had significantly higher latent mean scores on personal mastery-approach goals than their secondary counterparts. It seems possible that the currently documented differences between classroom goal structures noted for elementary compared to secondary school may be based on the personal goals endorsed as pre-service teachers. The results are further discussed in terms of alignment with research on practising teachers' personal and classroom goals and implications for teacher education. © 2012 The British Psychological Society.

The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment

PubMed Central

Condic-Jurkic, Karmen; Subramanian, Nandhitha; Mark, Alan E.

2018-01-01

Despite decades of research, the mechanism of action of the ABC multidrug transporter P-glycoprotein (P-gp) remains elusive. Due to experimental limitations, many researchers have turned to molecular dynamics simulation studies in order to investigate different aspects of P-gp function. However, such studies are challenging and caution is required when interpreting the results. P-gp is highly flexible and the time scale on which it can be simulated is limited. There is also uncertainty regarding the accuracy of the various crystal structures available, let alone the structure of the protein in a physiologically relevant environment. In this study, three alternative structural models of mouse P-gp (3G5U, 4KSB, 4M1M), all resolved to 3.8 Å, were used to initiate sets of simulations of P-gp in a membrane environment in order to determine: a) the sensitivity of the results to differences in the starting configuration; and b) the extent to which converged results could be expected on the times scales commonly simulated for this system. The simulations suggest that the arrangement of the nucleotide binding domains (NBDs) observed in the crystal structures is not stable in a membrane environment. In all simulations, the NBDs rapidly associated (within 10 ns) and changes within the transmembrane helices were observed. The secondary structure within the transmembrane domain was best preserved in the 4M1M model under the simulation conditions used. However, the extent to which replicate simulations diverged on a 100 to 200 ns timescale meant that it was not possible to draw definitive conclusions as to which structure overall was most stable, or to obtain converged and reliable results for any of the properties examined. The work brings into question the reliability of conclusions made in regard to the nature of specific interactions inferred from previous simulation studies on this system involving similar sampling times. It also highlights the need to demonstrate the statistical significance of any results obtained in simulations of large flexible proteins, especially where the initial structure is uncertain. PMID:29370310

The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment.

PubMed

Condic-Jurkic, Karmen; Subramanian, Nandhitha; Mark, Alan E; O'Mara, Megan L

2018-01-01

Despite decades of research, the mechanism of action of the ABC multidrug transporter P-glycoprotein (P-gp) remains elusive. Due to experimental limitations, many researchers have turned to molecular dynamics simulation studies in order to investigate different aspects of P-gp function. However, such studies are challenging and caution is required when interpreting the results. P-gp is highly flexible and the time scale on which it can be simulated is limited. There is also uncertainty regarding the accuracy of the various crystal structures available, let alone the structure of the protein in a physiologically relevant environment. In this study, three alternative structural models of mouse P-gp (3G5U, 4KSB, 4M1M), all resolved to 3.8 Å, were used to initiate sets of simulations of P-gp in a membrane environment in order to determine: a) the sensitivity of the results to differences in the starting configuration; and b) the extent to which converged results could be expected on the times scales commonly simulated for this system. The simulations suggest that the arrangement of the nucleotide binding domains (NBDs) observed in the crystal structures is not stable in a membrane environment. In all simulations, the NBDs rapidly associated (within 10 ns) and changes within the transmembrane helices were observed. The secondary structure within the transmembrane domain was best preserved in the 4M1M model under the simulation conditions used. However, the extent to which replicate simulations diverged on a 100 to 200 ns timescale meant that it was not possible to draw definitive conclusions as to which structure overall was most stable, or to obtain converged and reliable results for any of the properties examined. The work brings into question the reliability of conclusions made in regard to the nature of specific interactions inferred from previous simulation studies on this system involving similar sampling times. It also highlights the need to demonstrate the statistical significance of any results obtained in simulations of large flexible proteins, especially where the initial structure is uncertain.

Metastable ripple phase of fully hydrated dipalmitoylphosphatidylcholine as studied by small angle x-ray scattering

PubMed Central

Yao, Haruhiko; Matuoka, Sinzi; Tenchov, Boris; Hatta, Ichiro

1991-01-01

Fully hydrated dipalmitoylphosphatidylcholine (DPPC) undergoes liquid crystalline to metastable Pβ, phase transition in cooling. A small angle x-ray scattering study has been performed for obtaining further evidence about the structure of this phase. From a high-resolution observation of x-ray diffraction profiles, a distinct multipeak pattern has become obvious. Among them the (01) reflection in the secondary ripple structure is identified clearly. There are peaks assigned straightforwardly to (10) and (20) reflections in the primary ripple structure and peaks assigned to (10) and (20) reflections in the secondary ripple structure. Therefore the multipeak pattern is due to superposition of the reflections cause by the primary and secondary ripple structures. The lattice parameters are estimated as follows: for the primary ripple structure a = 7.09 nm, b = 13.64 nm, and γ = 95°, and for the secondary ripple structure a = 8.2 nm, b = 26.6 nm, and γ = 90°. The lattice parameters thus obtained for the secondary ripple structure are not conclusive, however. The hydrocarbon chains in the primary ripple structure have been reported as being tilted against the bilayer plane and, on the other hand, the hydrocarbon chains in the secondary ripple structure are likely to be perpendicular to the bilayer plane. This fact seems to be related to a sequential mechanism of phase transitions. On heating from the Lβ, phase where the hydrocarbon chains are tilted the primary ripple structure having tilted hydrocarbon chains takes place and on cooling from the Lα phase where the hydrocarbon chains are not tilted the secondary ripple structure with untilted chains tends to be stabilized. It appears that the truly metastable ripple phase is expressed by the second ripple structure although in the course of the actual cooling transition both the secondary and primary ripple structures form and coexist. PMID:19431787

Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA

PubMed Central

Seligmann, Hervé; Raoult, Didier

2018-01-01

We examine the hypothesis that de novo template-free RNAs still form spontaneously, as they did at the origins of life, invade modern genomes, contribute new genetic material. Previously, analyses of RNA secondary structures suggested that some RNAs resembling ancestral (t)RNAs formed recently de novo, other parasitic sequences cluster with rRNAs. Here positive control analyses of additional RNA secondary structures confirm ancestral and de novo statuses of RNA grouped according to secondary structure. Viroids with branched stems resemble de novo RNAs, rod-shaped viroids resemble rRNA secondary structures, independently of GC contents. 5′ UTR leading regions of West Nile and Dengue flavivirid viruses resemble de novo and rRNA structures, respectively. An RNA homologous with Megavirus, Dengue and West Nile genomes, copperhead snake microsatellites and levant cotton repeats, not templated by Mimivirus' genome, persists throughout Mimivirus' infection. Its secondary structure clusters with candidate de novo RNAs. The saltatory phyletic distribution and secondary structure of Mimivirus' peculiar RNA suggest occasional template-free polymerization of this sequence, rather than noncanonical transcriptions (swinger polymerization, posttranscriptional editing). PMID:29449833

The characterization of Cr secondary oxide phases in ZnO films studied by X-ray spectroscopy and photoemission spectroscopy

NASA Astrophysics Data System (ADS)

Chiou, J. W.; Chang, S. Y.; Huang, W. H.; Chen, Y. T.; Hsu, C. W.; Hu, Y. M.; Chen, J. M.; Chen, C.-H.; Kumar, K.; Guo, J.-H.

2011-03-01

X-ray absorption near-edge structure (XANES), X-ray emission spectroscopy (XES), and X-ray photoemission spectroscopy (XPS) were used to characterize the Cr secondary oxide phases in ZnO films that had been prepared using a co-sputtering method. Analysis of the Cr L3,2-edge XANES spectra reveals that the intensity of white-line features decreases subtly as the sputtering power increases, indicating that the occupation of Cr 3 d orbitals increases with Cr concentration in (Zn, Cr)O films. The O K-edge spectra show that the intensity of XANES features of (Zn, Cr)O films is lower than those of ZnO film, suggesting enhanced occupation of O 2 p-derived states through O 2 p-Cr 3 d hybridization. The XES and XPS spectra indicate that the line shapes in the valence band of (Zn, Cr)O films are quite different from those of ZnO and that the Cr 2O 3 phase dominates the spinel structure of (Zn, Cr)O films increasingly as the Cr sputtering power is increased. Over all results suggest that the non-ferromagnetic behavior of (Zn, Cr)O films can be attributed to the dominant presence of Cr 2O 3, whereas the bulk comprise phase segregations of Cr 2O 3 and/or ZnCr 2O 4, which results them the most stable TM-doped ZnO material against etching.

Time-domain analysis of planar microstrip devices using a generalized Yee-algorithm based on unstructured grids

NASA Technical Reports Server (NTRS)

Gedney, Stephen D.; Lansing, Faiza

1993-01-01

The generalized Yee-algorithm is presented for the temporal full-wave analysis of planar microstrip devices. This algorithm has the significant advantage over the traditional Yee-algorithm in that it is based on unstructured and irregular grids. The robustness of the generalized Yee-algorithm is that structures that contain curved conductors or complex three-dimensional geometries can be more accurately, and much more conveniently modeled using standard automatic grid generation techniques. This generalized Yee-algorithm is based on the the time-marching solution of the discrete form of Maxwell's equations in their integral form. To this end, the electric and magnetic fields are discretized over a dual, irregular, and unstructured grid. The primary grid is assumed to be composed of general fitted polyhedra distributed throughout the volume. The secondary grid (or dual grid) is built up of the closed polyhedra whose edges connect the centroid's of adjacent primary cells, penetrating shared faces. Faraday's law and Ampere's law are used to update the fields normal to the primary and secondary grid faces, respectively. Subsequently, a correction scheme is introduced to project the normal fields onto the grid edges. It is shown that this scheme is stable, maintains second-order accuracy, and preserves the divergenceless nature of the flux densities. Finally, for computational efficiency the algorithm is structured as a series of sparse matrix-vector multiplications. Based on this scheme, the generalized Yee-algorithm has been implemented on vector and parallel high performance computers in a highly efficient manner.

RNAstructure: software for RNA secondary structure prediction and analysis.

PubMed

Reuter, Jessica S; Mathews, David H

2010-03-15

To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.

Study on the Effect of Secondary Banded Structure on the Fatigue Property of Non-Quenched and Tempered Micro Alloyed Steel

NASA Astrophysics Data System (ADS)

Yajie, Cheng; Qingliang, Liao; Yue, Zhang

Due to composition segregation and cooling speed, streamline or banded structure were often obtained in the thermal forming parts along the direction of parts forming. Generally speaking, banded structure doesn't decrease the longitudinal mechanical properties, so the secondary banded structure can't get enough attention. The effect of secondary banded structure on the fatigue properties of micro alloyed DG20Mn and 35CrMo steel was investigated using the axial tensile fatigue test of stress ratio of 0.1. The result shows that secondary banded structure was obtained in the center of the steel parts, because of the composition segregation and the lower cooling rate in center part of steel. Secondary banded structure has no significant effect on axial tensile properties of both DG20Mn and 35CrMo, but decreases the axial tensile fatigue performance of DG20Mn steel. This study suggests that under the high cyclic tensile stress, multi-source damage cracks in steel initiated by large strain of pearlite of secondary banded structure, which is larger than damage strain, is the major factor of the decrease of fatigue life of steel.

Secondary Instability of Stationary Crossflow Vortices in Mach 6 Boundary Layer Over a Circular Cone

NASA Technical Reports Server (NTRS)

Li, Fei; Choudhari, Meelan M.; Paredes-Gonzalez, Pedro; Duan, Lian

2015-01-01

Hypersonic boundary layer flows over a circular cone at moderate incidence can support strong crossflow instability. Due to more efficient excitation of stationary crossflow vortices by surface roughness, such boundary layer flows may transition to turbulence via rapid amplification of the high-frequency secondary instabilities of finite amplitude stationary crossflow vortices. The amplification characteristics of these secondary instabilities are investigated for crossflow vortices generated by an azimuthally periodic array of roughness elements over a 7-degree half-angle circular cone in a Mach 6 free stream. Depending on the local amplitude of the stationary crossflow mode, the most unstable secondary disturbances either originate from the second (i.e., Mack) mode instabilities of the unperturbed boundary layer or correspond to genuine secondary instabilities that reduce to stable disturbances at sufficiently small amplitudes of the stationary crossflow vortex. The predicted frequencies of dominant secondary disturbances are similar to those measured during wind tunnel experiments at Purdue University and the Technical University of Braunschweig, Germany.

DNA Secondary Structure at Chromosomal Fragile Sites in Human Disease

PubMed Central

Thys, Ryan G; Lehman, Christine E; Pierce, Levi C. T; Wang, Yuh-Hwa

2015-01-01

DNA has the ability to form a variety of secondary structures that can interfere with normal cellular processes, and many of these structures have been associated with neurological diseases and cancer. Secondary structure-forming sequences are often found at chromosomal fragile sites, which are hotspots for sister chromatid exchange, chromosomal translocations, and deletions. Structures formed at fragile sites can lead to instability by disrupting normal cellular processes such as DNA replication and transcription. The instability caused by disruption of replication and transcription can lead to DNA breakage, resulting in gene rearrangements and deletions that cause disease. In this review, we discuss the role of DNA secondary structure at fragile sites in human disease. PMID:25937814

Comparative analysis of thermal unfolding simulations of RNA recognition motifs (RRMs) of TAR DNA-binding protein 43 (TDP-43).

PubMed

Prakash, Amresh; Kumar, Vijay; Meena, Naveen Kumar; Hassan, Md Imtaiyaz; Lynn, Andrew M

2018-01-10

TAR DNA-binding protein 43 (TDP-43) inclusions have been found in Amyotrophic lateral sclerosis (ALS) and several other neurodegenerative diseases. Many studies suggest the involvement of RNA recognition motifs (RRMs) in TDP-43 proteinopathy. To elucidate the structural stability and the unfolding dynamics of RRMs, we have carried out atomistic molecular dynamics simulations at two different temperatures (300 and 500 K). The simulations results indicate that there are distinct structural differences in the unfolding pathway between the two domains and RRM1 unfolds faster than RRM2 in accordance with the lower thermal stability found experimentally. The unfolding behaviors of secondary structures showed that the α-helix was more stable than β-sheet and structural rearrangements of β-sheets results in formation of additional α-helices. At higher temperature, RRM1 exhibit increased overall flexibility and unfolding than RRM2. The temperature-dependent free energy landscapes consist of multiple metastable states stabilized by non-native contacts and hydrogen bonds in RRM2, thus rendering the RRM2 more prone to misfolding. The structural rearrangements of RRM2 could lead to aberrant protein-protein interactions that may account for enhanced aggregation and toxicity of TDP-43. Our analysis, thus identify the structural and thermodynamic characteristics of the RRMs of TDP-43, which will serve to uncover molecular mechanisms and driving forces in TDP-43 misfolding and aggregation.

Single-Molecule Microscopy and Force Spectroscopy of Membrane Proteins

NASA Astrophysics Data System (ADS)

Engel, Andreas; Janovjak, Harald; Fotiadis, Dimtrios; Kedrov, Alexej; Cisneros, David; Müller, Daniel J.

Single-molecule atomic force microscopy (AFM) provides novel ways to characterize the structure-function relationship of native membrane proteins. High-resolution AFM topographs allow observing the structure of single proteins at sub-nanometer resolution as well as their conformational changes, oligomeric state, molecular dynamics and assembly. We will review these feasibilities illustrating examples of membrane proteins in native and reconstituted membranes. Classification of individual topographs of single proteins allows understanding the principles of motions of their extrinsic domains, to learn about their local structural flexibilities and to find the entropy minima of certain conformations. Combined with the visualization of functionally related conformational changes these insights allow understanding why certain flexibilities are required for the protein to function and how structurally flexible regions allow certain conformational changes. Complementary to AFM imaging, single-molecule force spectroscopy (SMFS) experiments detect molecular interactions established within and between membrane proteins. The sensitivity of this method makes it possible to measure interactions that stabilize secondary structures such as transmembrane α-helices, polypeptide loops and segments within. Changes in temperature or protein-protein assembly do not change the locations of stable structural segments, but influence their stability established by collective molecular interactions. Such changes alter the probability of proteins to choose a certain unfolding pathway. Recent examples have elucidated unfolding and refolding pathways of membrane proteins as well as their energy landscapes.

Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.

PubMed

Reddy, Jithender G; Kumar, Dinesh; Hosur, Ramakrishna V

2015-02-01

Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH – which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins. Copyright © 2014 John Wiley & Sons, Ltd.

Antimicrobial function of the GAPDH-related antimicrobial peptide in the skin of skipjack tuna, Katsuwonus pelamis.

PubMed

Seo, Jung-Kil; Lee, Min Jeong; Go, Hye-Jin; Kim, Yeon Jun; Park, Nam Gyu

2014-02-01

A 3.4 kDa of antimicrobial peptide was purified from an acidified skin extract of skipjack tuna, Katsuwonus pelamis, by preparative acid-urea-polyacrylamide gel electrophoresis and C18 reversed-phase HPLC. A comparison of the N-terminal amino acid sequence of the purified peptide with that of other known polypeptides revealed high sequence homology with the YFGAP (Yellowfin tuna Glyceraldehyde-3-phosphate dehydrogenase-related Antimicrobial Peptide); thus, this peptide was identified as the skipjack tuna GAPDH-related antimicrobial peptide (SJGAP). SJGAP showed potent antimicrobial activity against Gram-positive bacteria, such as Bacillus subtilis, Micrococcus luteus, Staphylococcus aureus, and Streptococcus iniae (minimal effective concentrations [MECs], 1.2-17.0 μg/mL), Gram-negative bacteria, such as Aeromonas hydrophila, Escherichia coli D31, and Vibrio parahaemolyticus (MECs, 3.1-12.0 μg/mL), and against Candida albicans (MEC, 16.0 μg/mL) without significant hemolytic activity. Antimicrobial activity of this peptide is heat-stable but salt-sensitive. According to the secondary structural prediction and the homology modeling, this peptide consists of three secondary structural motifs, including one α-helix and two parallel β-strands, and forms an amphipathic structure. This peptide showed neither membrane permeabilization ability nor killing ability, but did display a small degree of leakage ability. These results suggest that SJGAP acts through a bacteriostatic process rather than bactericidal one. SJGAP is another GAPDH-related antimicrobial peptide isolated from skipjack tuna and likely plays an important role for GAPDH in the innate immune defense of tuna fish. Copyright © 2014 Elsevier Ltd. All rights reserved.

External-Cavity Quantum Cascade Laser Spectroscopy for Mid-IR Transmission Measurements of Proteins in Aqueous Solution.

PubMed

Alcaráz, Mirta R; Schwaighofer, Andreas; Kristament, Christian; Ramer, Georg; Brandstetter, Markus; Goicoechea, Héctor; Lendl, Bernhard

2015-07-07

In this work, we report mid-IR transmission measurements of the protein amide I band in aqueous solution at large optical paths. A tunable external-cavity quantum cascade laser (EC-QCL) operated in pulsed mode at room temperature allowed one to apply a path length of up to 38 μm, which is four times larger than that applicable with conventional FT-IR spectrometers. To minimize temperature-induced variations caused by background absorption of the ν2-vibration of water (HOH-bending) overlapping with the amide I region, a highly stable temperature control unit with relative temperature stability within 0.005 °C was developed. An advanced data processing protocol was established to overcome fluctuations in the fine structure of the emission curve that are inherent to the employed EC-QCL due to its mechanical instabilities. To allow for wavenumber accuracy, a spectral calibration method has been elaborated to reference the acquired IR spectra to the absolute positions of the water vapor absorption bands. Employing this setup, characteristic spectral features of five well-studied proteins exhibiting different secondary structures could be measured at concentrations as low as 2.5 mg mL(-1). This concentration range could previously only be accessed by IR measurements in D2O. Mathematical evaluation of the spectral overlap and comparison of second derivative spectra confirm excellent agreement of the QCL transmission measurements with protein spectra acquired by FT-IR spectroscopy. This proves the potential of the applied setup to monitor secondary structure changes of proteins in aqueous solution at extended optical path lengths, which allow experiments in flow through configuration.

miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets

PubMed Central

Paicu, Claudia; Mohorianu, Irina; Stocks, Matthew; Xu, Ping; Coince, Aurore; Billmeier, Martina; Dalmay, Tamas; Moulton, Vincent; Moxon, Simon

2017-01-01

Abstract Motivation MicroRNAs are a class of ∼21–22 nt small RNAs which are excised from a stable hairpin-like secondary structure. They have important gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in eukaryotes. There are several computational tools for miRNA detection from next-generation sequencing datasets. However, many of these tools suffer from high false positive and false negative rates. Here we present a novel miRNA prediction algorithm, miRCat2. miRCat2 incorporates a new entropy-based approach to detect miRNA loci, which is designed to cope with the high sequencing depth of current next-generation sequencing datasets. It has a user-friendly interface and produces graphical representations of the hairpin structure and plots depicting the alignment of sequences on the secondary structure. Results We test miRCat2 on a number of animal and plant datasets and present a comparative analysis with miRCat, miRDeep2, miRPlant and miReap. We also use mutants in the miRNA biogenesis pathway to evaluate the predictions of these tools. Results indicate that miRCat2 has an improved accuracy compared with other methods tested. Moreover, miRCat2 predicts several new miRNAs that are differentially expressed in wild-type versus mutants in the miRNA biogenesis pathway. Availability and Implementation miRCat2 is part of the UEA small RNA Workbench and is freely available from http://srna-workbench.cmp.uea.ac.uk/. Contact v.moulton@uea.ac.uk or s.moxon@uea.ac.uk Supplementary information Supplementary data are available at Bioinformatics online. PMID:28407097

Bioinformatics analysis of single and multi-hybrid epitopes of GRA-1, GRA-4, GRA-6 and GRA-7 proteins to improve DNA vaccine design against Toxoplasma gondii.

PubMed

Shaddel, Minoo; Ebrahimi, Mansour; Tabandeh, Mohammad Reza

2018-06-01

Toxoplasma gondii , is a causative agent of morbidity and mortality in immunocompromised and congenitally-infected individuals. Attempts to construct DNA vaccines against T. gondii using surface proteins are increasing. The dense granule antigens are highly expressed in the acute and chronic phases of T. gondii infection and considered as suitable DNA vaccine candidates to control toxoplasmosis. In the present study, bioinformatics tools and online software were used to predict, analyze and compare the structural, physical and chemical characters and immunogenicity of the GRA-1, GRA-4, GRA-6 and GRA-7 proteins. Sequence alignment results indicated that the GRA-1, GRA-4, GRA-6 and GRA-7 proteins had low similarity. The secondary structure prediction demonstrated that among the four proteins, GRA-1 and GRA-6 had similar secondary structure except for a little discrepancy. Hydrophilicity/hydrophobicity analysis showed multiple hydrophilic regions and some classical high hydrophilic domains for each protein sequence. Immunogenic epitope prediction results demonstrated that the GRA-1 and GRA-4 epitopes were stable and GRA-4 showed the highest degree of antigenicity. Although the GRA-7 epitope had the highest score of immunogenicity, this epitope was instable and had the lowest degree of antigenicity and half-time in eukaryotic cell. Also, the results indicated that GRA4-GRA7 epitope and GRA6-GRA7 had the highest degree of antigenicity and immunogenicity among multi-hybrid epitopes, respectively. Totally, in the present study, single epitopes showed the highest degree of antigenicity compared with multi-hybrid epitopes. Given the results, it can be concluded that GRA-4 and GRA-7 can be powerful DNA vaccine candidates against T. gondii .

PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies.

PubMed

Jeon, Jouhyun; Arnold, Roland; Singh, Fateh; Teyra, Joan; Braun, Tatjana; Kim, Philip M

2016-04-01

The identification of structured units in a protein sequence is an important first step for most biochemical studies. Importantly for this study, the identification of stable structured region is a crucial first step to generate novel synthetic antibodies. While many approaches to find domains or predict structured regions exist, important limitations remain, such as the optimization of domain boundaries and the lack of identification of non-domain structured units. Moreover, no integrated tool exists to find and optimize structural domains within protein sequences. Here, we describe a new tool, PAT ( http://www.kimlab.org/software/pat ) that can efficiently identify both domains (with optimized boundaries) and non-domain putative structured units. PAT automatically analyzes various structural properties, evaluates the folding stability, and reports possible structural domains in a given protein sequence. For reliability evaluation of PAT, we applied PAT to identify antibody target molecules based on the notion that soluble and well-defined protein secondary and tertiary structures are appropriate target molecules for synthetic antibodies. PAT is an efficient and sensitive tool to identify structured units. A performance analysis shows that PAT can characterize structurally well-defined regions in a given sequence and outperforms other efforts to define reliable boundaries of domains. Specially, PAT successfully identifies experimentally confirmed target molecules for antibody generation. PAT also offers the pre-calculated results of 20,210 human proteins to accelerate common queries. PAT can therefore help to investigate large-scale structured domains and improve the success rate for synthetic antibody generation.

Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks.

PubMed

Babaei, Sepideh; Geranmayeh, Amir; Seyyedsalehi, Seyyed Ali

2010-12-01

The supervised learning of recurrent neural networks well-suited for prediction of protein secondary structures from the underlying amino acids sequence is studied. Modular reciprocal recurrent neural networks (MRR-NN) are proposed to model the strong correlations between adjacent secondary structure elements. Besides, a multilayer bidirectional recurrent neural network (MBR-NN) is introduced to capture the long-range intramolecular interactions between amino acids in formation of the secondary structure. The final modular prediction system is devised based on the interactive integration of the MRR-NN and the MBR-NN structures to arbitrarily engage the neighboring effects of the secondary structure types concurrent with memorizing the sequential dependencies of amino acids along the protein chain. The advanced combined network augments the percentage accuracy (Q₃) to 79.36% and boosts the segment overlap (SOV) up to 70.09% when tested on the PSIPRED dataset in three-fold cross-validation. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

New insights from cluster analysis methods for RNA secondary structure prediction

PubMed Central

Rogers, Emily; Heitsch, Christine

2016-01-01

A widening gap exists between the best practices for RNA secondary structure prediction developed by computational researchers and the methods used in practice by experimentalists. Minimum free energy (MFE) predictions, although broadly used, are outperformed by methods which sample from the Boltzmann distribution and data mine the results. In particular, moving beyond the single structure prediction paradigm yields substantial gains in accuracy. Furthermore, the largest improvements in accuracy and precision come from viewing secondary structures not at the base pair level but at lower granularity/higher abstraction. This suggests that random errors affecting precision and systematic ones affecting accuracy are both reduced by this “fuzzier” view of secondary structures. Thus experimentalists who are willing to adopt a more rigorous, multilayered approach to secondary structure prediction by iterating through these levels of granularity will be much better able to capture fundamental aspects of RNA base pairing. PMID:26971529

Low pressure-induced secondary structure transitions of regenerated silk fibroin in its wet film studied by time-resolved infrared spectroscopy.

PubMed

He, Zhipeng; Liu, Zhao; Zhou, Xiaofeng; Huang, He

2018-06-01

The secondary structure transitions of regenerated silk fibroin (RSF) under different external perturbations have been studied extensively, except for pressure. In this work, time-resolved infrared spectroscopy with the attenuated total reflectance (ATR) accessory was employed to follow the secondary structure transitions of RSF in its wet film under low pressure. It has been found that pressure alone is favorable only to the formation of β-sheet structure. Under constant pressure there is an optimum amount of D 2 O in the wet film (D 2 O : film = 2:1) so as to provide the optimal condition for the reorganization of the secondary structure and to have the largest formation of β-sheet structure. Under constant amount of D 2 O and constant pressure, the secondary structure transitions of RSF in its wet film can be divided into three stages along with time. In the first stage, random coil, α-helix, and β-turn were quickly transformed into β-sheet. In the second stage, random coil and β-turn were relatively slowly transformed into β-sheet and α-helix, and the content of α-helix was recovered to the value prior to the application of pressure. In the third and final stage, no measurable changes can be found for each secondary structure. This study may be helpful to understand the secondary structure changes of silk fibroin in silkworm's glands under hydrostatic pressure. © 2018 Wiley Periodicals, Inc.

Neighborhood Characteristics and Expectations of Racially Discriminatory Experiences Among African American Adolescents.

PubMed

Witherspoon, Dawn P; Seaton, Eleanor K; Rivas-Drake, Deborah

2016-09-01

This study examined how youth's neighborhood characteristics informed their expectations of racial discrimination concurrently and longitudinally. Secondary analyses were conducted on data from Waves 1, 3, 4, 5, and 6 of the Maryland Adolescent Development in Context Study, which permitted the examination of neighborhood influences among a socioeconomically diverse sample of African American parents and adolescents (n = 863; Mage  = 12.29). Youth exposed to more neighborhood disadvantage in seventh grade reported more negative concurrent neighborhood perceptions, which, in turn, predicted greater expectations of racial discrimination in eighth grade; youth's expectations remained stable into adulthood. Thus, support was found for the mediating role of youth's subjective neighborhood perceptions in the longitudinal relation between neighborhood structure and expectations of racial discrimination. © 2016 The Authors. Child Development © 2016 Society for Research in Child Development, Inc.

Bigfoot. a new family of MITE elements characterized from the Medicago genus.

PubMed

Charrier, B; Foucher, F; Kondorosi, E; d'Aubenton-Carafa, Y; Thermes, C; Kondorosi, A; Ratet, P

1999-05-01

We have characterized from the legume plant Medicago a new family of miniature inverted-repeat transposable elements (MITE), called the Bigfoot transposable elements. Two of these insertion elements are present only in a single allele of two different M. sativa genes. Using a PCR strategy we have isolated 19 other Bigfoot elements from the M. sativa and M. truncatula genomes. They differ from the previously characterized MITEs by their sequence, a target site of 9 bp and a partially clustered genomic distribution. In addition, we show that they exhibit a significantly stable secondary structure. These elements may represent up to 0.1% of the genome of the outcrossing Medicago sativa but are present at a reduced copy number in the genome of the autogamous M. truncatula plant, revealing major differences in the genome organization of these two plants.

Molecular interaction of (ethanol)2-water heterotrimers.

PubMed

Mejía, Sol M; Espinal, Juan F; Restrepo, Albeiro; Mondragón, Fanor

2007-08-23

The potential energy surface of the (ethanol)2-water heterotrimers for the trans and gauche conformers of ethanol was studied using density functional theory. The same approximation was used for characterizing representative clusters of (ethanol)3, (methanol)3, and (methanol)2-water. Trimerization energies and enthalpies as well as the analysis of geometric parameters suggest that the structures with a cyclic pattern in the three hydrogen bonds of the type O-H---O (primary hydrogen bonds), where all molecules are proton donor-acceptor at the same time, are more stable than those with just two primary hydrogen bonds. Additionally, we propose the formation of "secondary hydrogen bonds" between hydrogen atoms of the methyl group of ethanol and the oxygen atom of water or other ethanol molecule (C-H---O), which were found to be weaker than the primary hydrogen bonds.

Tunable stability of monodisperse secondary O/W nano-emulsions

NASA Astrophysics Data System (ADS)

Vecchione, R.; Ciotola, U.; Sagliano, A.; Bianchini, P.; Diaspro, A.; Netti, P. A.

2014-07-01

Stable and biodegradable oil in water (O/W) nano-emulsions can have a huge impact on a wide range of bio-applications, from food to cosmetics and pharmaceuticals. Emulsions, however, are immiscible systems unstable over time; polymer coatings are known to be helpful, but an effective procedure to stabilize monodisperse and biodegradable O/W nano-emulsions is yet to be designed. Here, we coat biodegradable O/W nano-emulsions with a molecular layer of biodegradable polyelectrolytes such as polysaccharides - like chitosan - and polypeptides - like polylysine - and effectively re-disperse and densify the polymer coating at high pressure, thus obtaining monodisperse and stable systems. In particular, focusing on chitosan, our tests show that it is possible to obtain unprecedented ultra-stable O/W secondary nano-emulsions (diameter sizes tunable from ~80 to 160 nm and polydispersion indices below 0.1) by combining this process with high concentrations of polymers. Depending on the polymer concentration, it is possible to control the level of coating that results in a tunable stability ranging from a few weeks to several months. The above range of concentrations has been investigated using a fluorescence-based approach with new insights into the coating evolution.Stable and biodegradable oil in water (O/W) nano-emulsions can have a huge impact on a wide range of bio-applications, from food to cosmetics and pharmaceuticals. Emulsions, however, are immiscible systems unstable over time; polymer coatings are known to be helpful, but an effective procedure to stabilize monodisperse and biodegradable O/W nano-emulsions is yet to be designed. Here, we coat biodegradable O/W nano-emulsions with a molecular layer of biodegradable polyelectrolytes such as polysaccharides - like chitosan - and polypeptides - like polylysine - and effectively re-disperse and densify the polymer coating at high pressure, thus obtaining monodisperse and stable systems. In particular, focusing on chitosan, our tests show that it is possible to obtain unprecedented ultra-stable O/W secondary nano-emulsions (diameter sizes tunable from ~80 to 160 nm and polydispersion indices below 0.1) by combining this process with high concentrations of polymers. Depending on the polymer concentration, it is possible to control the level of coating that results in a tunable stability ranging from a few weeks to several months. The above range of concentrations has been investigated using a fluorescence-based approach with new insights into the coating evolution. Electronic supplementary information (ESI) available: Experimental section, Fig. S1-S3, and Tables S1-S6. See DOI: 10.1039/c4nr02273d

Role of TAR RNA splicing in translational regulation of simian immunodeficiency virus from rhesus macaques.

PubMed Central

Viglianti, G A; Rubinstein, E P; Graves, K L

1992-01-01

The untranslated leader sequences of rhesus macaque simian immunodeficiency virus mRNAs form a stable secondary structure, TAR. This structure can be modified by RNA splicing. In this study, the role of TAR splicing in virus replication was investigated. The proportion of viral RNAs containing a spliced TAR structure is high early after infection and decreases at later times. Moreover, proviruses containing mutations which prevent TAR splicing are significantly delayed in replication. These mutant viruses require approximately 20 days to achieve half-maximal virus production, in contrast to wild-type viruses, which require approximately 8 days. We attribute this delay to the inefficient translation of unspliced-TAR-containing mRNAs. The molecular basis for this translational effect was examined in in vitro assays. We found that spliced-TAR-containing mRNAs were translated up to 8.5 times more efficiently than were similar mRNAs containing an unspliced TAR leader. Furthermore, these spliced-TAR-containing mRNAs were more efficiently associated with ribosomes. We postulate that the level of TAR splicing provides a balance for the optimal expression of both viral proteins and genomic RNA and therefore ultimately controls the production of infectious virions. Images PMID:1629957

Coarse-grained, foldable, physical model of the polypeptide chain.

PubMed

Chakraborty, Promita; Zuckermann, Ronald N

2013-08-13

Although nonflexible, scaled molecular models like Pauling-Corey's and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report here the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees of freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and α-carbon units, connected by mechanical bonds (corresponding to ϕ and ψ) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to readily fold into stable secondary structures. The model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure. Furthermore, this physical model can serve as the basis for linking tangible biomacromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human-computer interface.

Thermoelectric and Structural Properties of Zr-/Hf-Based Half-Heusler Compounds Produced at a Large Scale

NASA Astrophysics Data System (ADS)

Zillmann, D.; Waag, A.; Peiner, E.; Feyand, M.-H.; Wolyniec, A.

2018-02-01

The half-Heusler (HH) systems are promising candidates for thermoelectric (TE) applications since they have shown high figures of merit ( zT) of ˜ 1, which are directly related to the energy conversion efficiency. To use HH compounds for TE devices, the materials must be phase-stable at operating temperatures up to 600°C. Currently, only a few HH compositions are available in large quantities. Hence, we focus on the TE and structural properties of three commercially available Zr-/Hf-based HH compounds in this publication. In particular, we evaluate the thermal conductivities and the figures of merit and critically discuss uncertainties and propagation error in the measurements. We find thermal conductivities of less than 6.0 W K^{-1}m^{-1} for all investigated materials and notably high figures of merit of 0.93 and 0.60 for n- and p-type compounds, respectively, at 600°C. Additionally, our investigations reveal that the grain structures of all materials also contain secondary phases like HfO2, Sn-Ni and Ti-Zr-Sn rich phases while an additional SnO_2 phase was found following several hours of harsh heat treatment at 800°C.

Latent Hardeners for the Assembly of Epoxy Composites

NASA Technical Reports Server (NTRS)

Palmieri, Frank; Wohl, Christopher J.; Connell, John W.; Mercado, Zoar; Galloway, Jordan

2016-01-01

Large-scale composite structures are commonly joined by secondary bonding of molded-and-cured thermoset components. This approach may result in unpredictable joint strengths. In contrast, assemblies made by co-curing, although limited in size by the mold, result in stable structures, and are certifiable for commercial aviation because of structural continuity through the joints. Multifunctional epoxy resins were prepared that should produce fully-cured subcomponents with uncured joining surfaces, enabling them to be assembled by co-curing in a subsequent out-of-autoclave process. Aromatic diamines were protected by condensation with a ketone or aldehyde to form imines. Properties of the amine-cured epoxy were compared with those of commercially available thermosetting epoxy resins and rheology and thermal analysis were used to demonstrate the efficacy of imine protection. Optimum conditions to reverse the protecting chemistry in the solid state using moisture and acid catalysis were determined. Alternative chemistries were also investigated. For example, chain reaction depolymerization and photoinitiated catalysts would be expected to minimize liberation of volatile organic content upon deprotection and avoid residual reactive species that could damage the resin. Results from the analysis of protected and deprotected resins will be presented.

A PSD (position sensing device) to map the shift and tilt of the SRT secondary mirror

NASA Astrophysics Data System (ADS)

Pisanu, Tonino; Buffa, Franco; Concu, Raimondo; Marongiu, Pasqualino; Pili, Mauro; Poppi, Sergio; Serra, Giampaolo; Urru, Enrico; Vargiu, Gianpaolo

2014-07-01

The Sardinia Radio Telescope (SRT) Metrology team has started to install the initial group of devices on the new 64 meters radio-telescope. These devices will be devoted for the realization of the antenna deformation control system: an electronic inclinometer able to monitor the alidade deformations and a Position Sensing Device (PSD) able to map the secondary mirror (M2) displacements and tilts. The inclinometer is used to map the rail conditions, the azimuthal axis inclination and the thermal effects on the alidade structure. The PSD will be used to measure the secondary mirror displacements induced by the gravity and by the thermal deformations that produce shifts and tilts with respect to it s ideal optical alignment. The PSD will be traced by a laser diode installed on a mechanically stable position inside the vertex room. Preliminarly we decided to characterize excursion range of M2, in order to know if the PSD measuring range of about +/- 10 mm is enough for our purposes. We designed, built and tested an optical measuring device, based on commercial CMOS with a wider measurement range of +/- 40 mm and with a resolution of around 0.1 mm. After a laboratory characterization at the 23 meters real distance, the PSD and the laser have been installed in the antenna. In this paper we show the results of the measurements performed by moving the antenna in elevation.

Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques

PubMed Central

Wang, Hsin-Wei; Hsu, Yen-Chu; Hwang, Jenn-Kang; Lyu, Ping-Chiang; Pai, Tun-Wen; Tang, Chuan Yi

2010-01-01

This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had “opened” their “closed” structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge loop determination is comparable to that of manual inspection. This method has been implemented as a web-based tool, which requires two protein structures as the input and then the type and/or existence of DS relationships between the input structures are determined according to the A-D image-based structural alignments and the DS score. The proposed method is expected to trigger large-scale studies of this interesting structural phenomenon and facilitate related applications. PMID:20976204

Entropy-theory-based study on the relationship between land use structure and industry system: a case study of the eastern Hubei metropolitan area

NASA Astrophysics Data System (ADS)

Su, Lilan; Liu, Yanfang; Gao, Xiaoyong

2009-10-01

During the process of economic growth, the industry structure transforms at different developing sections and that industrial composition as well as each department interior demand for land resources would reflect on land-use structure reform. This paper takes Hubei as the research zone, through a consecutive time sequence of 10 years period (1996-2005) just before and after the 1 plus 8 Eastern Hubei Metropolitan Area project, a quantitative study of the correlation between the industry structure and land-use structure is made based on the entropy theory. According to the classification of industrial composition, the land-use structure here is also redefined into four types as Land Use for Primary Industry, Land Use for Secondary Industry, Land Use for Tertiary Industry, and Land Use for Potential Reserve, in the aim that it should model new methods for researching the relationship of industry structure and land-use structure, and the instinct driving force would be presented more evidently at the same time. The outcomes indicate that the change of land-use structure has close relationship with the structure of industry composition; the trend of information entropy in Hubei mostly keeps increasing during the past 10 years which predicating the symmetrical degree of land-use structure is gradually built; and Eastern Hubei Metropolitan Area is of favorable power far superiority other units within province in promoting regional development, yet land-use structure adjustments are still not stable and a optimal mode of land use needs further approach.

Structural variations of single and tandem mismatches in RNA duplexes: a joint MD simulation and crystal structure database analysis.

PubMed

Halder, Sukanya; Bhattacharyya, Dhananjay

2012-10-04

Internal loops within RNA duplex regions are formed by single or tandem basepairing mismatches with flanking canonical Watson-Crick basepairs on both sides. They are the most common motif observed in RNA secondary structures and play integral functional and structural roles. In this report, we have studied the structural features of 1 × 1, 2 × 2, and 3 × 3 internal loops using all-atom molecular dynamics (MD) simulation technique with explicit solvent model. As MD simulation is intricately dependent on the choice of force-field and these are often rather approximate, we have used both the most popular force-fields for nucleic acids-CHARMM27 and AMBER94-for a comparative analysis. We find that tandem noncanonical basepairs forming 2 × 2 and 3 × 3 internal loops are considerably more stable than the single mismatches forming 1 × 1 internal loops, irrespective of the force field. We have also analyzed crystal structure database to study the conservation of these helical fragments in the corresponding sets of RNA structures. We observe that the nature of stability in MD simulations mimic their fluctuating natures in crystal data sets also, probably indicating reliable natures of both the force fields to reproduce experimental results. We also notice significant structural changes in the wobble G:U basepairs present in these double helical stretches, leading to a biphasic stability for these wobble pairs to release the deformational strains introduced by internal loops within duplex regions.

Probing the hammerhead ribozyme structure with ribonucleases.

PubMed Central

Hodgson, R A; Shirley, N J; Symons, R H

1994-01-01

Susceptibility to RNase digestion has been used to probe the conformation of the hammerhead ribozyme structure prepared from chemically synthesised RNAs. Less than about 1.5% of the total sample was digested to obtain a profile of RNase digestion sites. The observed digestion profiles confirmed the predicted base-paired secondary structure for the hammerhead. Digestion profiles of both cis and trans hammerhead structures were nearly identical which indicated that the structural interactions leading to self-cleavage were similar for both systems. Furthermore, the presence or absence of Mg2+ did not affect the RNase digestion profiles, thus indicating that Mg2+ did not modify the hammerhead structure significantly to induce self-cleavage. The base-paired stems I and II in the hammerhead structure were stable whereas stem III, which was susceptible to digestion, appeared to be an unstable region. The single strand domains separating the stems were susceptible to digestion with the exception of sites adjacent to guanosines; GL2.1 in the stem II loop and G12 in the conserved GAAAC sequence, which separates stems II and III. The absence of digestion at GL2.1 in the stem II hairpin loop of the hammerhead complex was maintained in uncomplexed ribozyme and in short oligonucleotides containing only the stem II hairpin region. In contrast, the G12 site became susceptible when the ribozyme was not complexed with its substrate. Overall the results are consistent with the role of Mg2+ in the hammerhead self-cleavage reaction being catalytic and not structural. Images PMID:8202361

The Ramachandran Number: An Order Parameter for Protein Geometry

DOE PAGES

Mannige, Ranjan V.; Kundu, Joyjit; Whitelam, Stephen; ...

2016-08-04

Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as α-helices and β-sheets. Secondary structure is characterized by the local rotational state of the protein backbone, quantified by two dihedral angles called Øand Ψ. Particular types of secondary structure can generally be described by a single (diffuse) location on a two-dimensional plot drawn in the space of the angles Ø andΨ, called a Ramachandran plot. By contrast, a recently-discovered nanomaterial made from peptoids, structural isomers of peptides, displays a secondary-structure motif corresponding to two regions on the Ramachandran plot [Mannige et al., Nature 526, 415 (2015)].more » In order to describe such 'higher-order' secondary structure in a compact way we introduce here a means of describing regions on the Ramachandran plot in terms of a single Ramachandran number, R, which is a structurally meaningful combination of Ø andΨ. We show that the potential applications of R are numerous: it can be used to describe the geometric content of protein structures, and can be used to draw diagrams that reveal, at a glance, the frequency of occurrence of regular secondary structures and disordered regions in large protein datasets. We propose that R might be used as an order parameter for protein geometry for a wide range of applications.« less

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

PubMed Central

Yang, Yuedong; Gao, Jianzhao; Wang, Jihua; Heffernan, Rhys; Hanson, Jack; Paliwal, Kuldip; Zhou, Yaoqi

2018-01-01

Abstract Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new methods breathe new life into this field. The highest three-state accuracy without relying on structure templates is now at 82–84%, a number unthinkable just a few years ago. These improvements came from increasingly larger databases of protein sequences and structures for training, the use of template secondary structure information and more powerful deep learning techniques. As we are approaching to the theoretical limit of three-state prediction (88–90%), alternative to secondary structure prediction (prediction of backbone torsion angles and Cα-atom-based angles and torsion angles) not only has more room for further improvement but also allows direct prediction of three-dimensional fragment structures with constantly improved accuracy. About 20% of all 40-residue fragments in a database of 1199 non-redundant proteins have <6 Å root-mean-squared distance from the native conformations by SPIDER2. More powerful deep learning methods with improved capability of capturing long-range interactions begin to emerge as the next generation of techniques for secondary structure prediction. The time has come to finish off the final stretch of the long march towards protein secondary structure prediction. PMID:28040746

Soft actuators and soft actuating devices

DOEpatents

Yang, Dian; Whitesides, George M.

2017-10-17

A soft buckling linear actuator is described, including: a plurality of substantially parallel bucklable, elastic structural components each having its longest dimension along a first axis; and a plurality of secondary structural components each disposed between and bridging two adjacent bucklable, elastic structural components; wherein every two adjacent bucklable, elastic structural components and the secondary structural components in-between define a layer comprising a plurality of cells each capable of being connected with a fluid inflation or deflation source; the secondary structural components from two adjacent layers are not aligned along a second axis perpendicular to the first axis; and the secondary structural components are configured not to buckle, the bucklable, elastic structural components are configured to buckle along the second axis to generate a linear force, upon the inflation or deflation of the cells. Methods of actuation using the same are also described.

An updated version of NPIDB includes new classifications of DNA–protein complexes and their families

PubMed Central

Zanegina, Olga; Kirsanov, Dmitriy; Baulin, Eugene; Karyagina, Anna; Alexeevski, Andrei; Spirin, Sergey

2016-01-01

The recent upgrade of nucleic acid–protein interaction database (NPIDB, http://npidb.belozersky.msu.ru/) includes a newly elaborated classification of complexes of protein domains with double-stranded DNA and a classification of families of related complexes. Our classifications are based on contacting structural elements of both DNA: the major groove, the minor groove and the backbone; and protein: helices, beta-strands and unstructured segments. We took into account both hydrogen bonds and hydrophobic interaction. The analyzed material contains 1942 structures of protein domains from 748 PDB entries. We have identified 97 interaction modes of individual protein domain–DNA complexes and 17 DNA–protein interaction classes of protein domain families. We analyzed the sources of diversity of DNA–protein interaction modes in different complexes of one protein domain family. The observed interaction mode is sometimes influenced by artifacts of crystallization or diversity in secondary structure assignment. The interaction classes of domain families are more stable and thus possess more biological sense than a classification of single complexes. Integration of the classification into NPIDB allows the user to browse the database according to the interacting structural elements of DNA and protein molecules. For each family, we present average DNA shape parameters in contact zones with domains of the family. PMID:26656949

A Novel Protein Interaction between Nucleotide Binding Domain of Hsp70 and p53 Motif

PubMed Central

Elengoe, Asita; Naser, Mohammed Abu; Hamdan, Salehhuddin

2015-01-01

Currently, protein interaction of Homo sapiens nucleotide binding domain (NBD) of heat shock 70 kDa protein (PDB: 1HJO) with p53 motif remains to be elucidated. The NBD-p53 motif complex enhances the p53 stabilization, thereby increasing the tumor suppression activity in cancer treatment. Therefore, we identified the interaction between NBD and p53 using STRING version 9.1 program. Then, we modeled the three-dimensional structure of p53 motif through homology modeling and determined the binding affinity and stability of NBD-p53 motif complex structure via molecular docking and dynamics (MD) simulation. Human DNA binding domain of p53 motif (SCMGGMNR) retrieved from UniProt (UniProtKB: P04637) was docked with the NBD protein, using the Autodock version 4.2 program. The binding energy and intermolecular energy for the NBD-p53 motif complex were −0.44 Kcal/mol and −9.90 Kcal/mol, respectively. Moreover, RMSD, RMSF, hydrogen bonds, salt bridge, and secondary structure analyses revealed that the NBD protein had a strong bond with p53 motif and the protein-ligand complex was stable. Thus, the current data would be highly encouraging for designing Hsp70 structure based drug in cancer therapy. PMID:26098630

A Novel Protein Interaction between Nucleotide Binding Domain of Hsp70 and p53 Motif.

PubMed

Elengoe, Asita; Naser, Mohammed Abu; Hamdan, Salehhuddin

2015-01-01

Currently, protein interaction of Homo sapiens nucleotide binding domain (NBD) of heat shock 70 kDa protein (PDB: 1HJO) with p53 motif remains to be elucidated. The NBD-p53 motif complex enhances the p53 stabilization, thereby increasing the tumor suppression activity in cancer treatment. Therefore, we identified the interaction between NBD and p53 using STRING version 9.1 program. Then, we modeled the three-dimensional structure of p53 motif through homology modeling and determined the binding affinity and stability of NBD-p53 motif complex structure via molecular docking and dynamics (MD) simulation. Human DNA binding domain of p53 motif (SCMGGMNR) retrieved from UniProt (UniProtKB: P04637) was docked with the NBD protein, using the Autodock version 4.2 program. The binding energy and intermolecular energy for the NBD-p53 motif complex were -0.44 Kcal/mol and -9.90 Kcal/mol, respectively. Moreover, RMSD, RMSF, hydrogen bonds, salt bridge, and secondary structure analyses revealed that the NBD protein had a strong bond with p53 motif and the protein-ligand complex was stable. Thus, the current data would be highly encouraging for designing Hsp70 structure based drug in cancer therapy.

Characterization of folding intermediates during urea-induced denaturation of human carbonic anhydrase II.

PubMed

Wahiduzzaman; Dar, Mohammad Aasif; Haque, Md Anzarul; Idrees, Danish; Hassan, Md Imtaiyaz; Islam, Asimul; Ahmad, Faizan

2017-02-01

Knowledge of folding/unfolding pathway is fundamental basis to study protein structure and stability. Human carbonic anhydrase II (HCAII) is a ∼29kDa, β-sheet dominated monomeric protein of 259 amino acid residues. In the present study, the urea-induced denaturation of HCAII was carried out which was a tri-phasic process, i.e., N (native) ↔ X I ↔ X II ↔ D (denatured) with stable intermediates X I and X II populated around 2 and 4M urea, respectively. The far-UV CD was used to characterize the intermediate states (X I and X II ) for secondary structural content, near-UV CD for tertiary structure, dynamic light scattering for hydrodynamic radius and ANS fluorescence spectroscopy for the presence of exposed hydrophobic patches. Based on these experiments, we concluded that urea-induced X I state has characteristics of molten globule state while X II state bears characteristics features of pre-molten globule state. Characterization of the intermediates on the folding pathway will contribute to a deeper understanding of the structure-function relationship of HCAII. Furthermore, this system may provide an excellent model to study urea stress and the strategies adopted by the organisms to combat such a stress. Copyright © 2016 Elsevier B.V. All rights reserved.

Structure-Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis

NASA Astrophysics Data System (ADS)

Anwar, Muhammad Ayaz; Choi, Sangdun

2017-03-01

Toll-like receptor 4 (TLR4), a vital innate immune receptor present on cell surfaces, initiates a signaling cascade during danger and bacterial intrusion. TLR4 needs to form a stable hexamer complex, which is necessary to dimerize the cytoplasmic domain. However, D299G and T399I polymorphism may abrogate the stability of the complex, leading to compromised TLR4 signaling. Crystallography provides valuable insights into the structural aspects of the TLR4 ectodomain; however, the dynamic behavior of polymorphic TLR4 is still unclear. Here, we employed molecular dynamics simulations (MDS), as well as principal component and residue network analyses, to decipher the structural aspects and signaling propagation associated with mutations in TLR4. The mutated complexes were less cohesive, displayed local and global variation in the secondary structure, and anomalous decay in rotational correlation function. Principal component analysis indicated that the mutated complexes also exhibited distinct low-frequency motions, which may be correlated to the differential behaviors of these TLR4 variants. Moreover, residue interaction networks (RIN) revealed that the mutated TLR4/myeloid differentiation factor (MD) 2 complex may perpetuate abnormal signaling pathways. Cumulatively, the MDS and RIN analyses elucidated the mutant-specific conformational alterations, which may help in deciphering the mechanism of loss-of-function mutations.

Free energy minimization to predict RNA secondary structures and computational RNA design.

PubMed

Churkin, Alexander; Weinbrand, Lina; Barash, Danny

2015-01-01

Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

Effect of centrifugal forces on formation of secondary flow structures in a 180-degree curved artery model under pulsatile inflow conditions

NASA Astrophysics Data System (ADS)

Callahan, Shannon; Sajjad, Roshan; Bulusu, Kartik V.; Plesniak, Michael W.

2013-11-01

An experimental investigation of secondary flow structures within a 180-degree bent tube model of a curved artery was performed using phase-averaged, two-component, two-dimensional, particle image velocimetry (2C-2D PIV) under pulsatile inflow conditions. Pulsatile waveforms ranging from simple sinusoidal to physiological inflows were supplied. We developed a novel continuous wavelet transform algorithm (PIVlet 1.2) and applied it to vorticity fields for coherent secondary flow structure detection. Regime maps of secondary flow structures revealed new, deceleration-phase-dependent flow morphologies. The temporal instances where streamwise centrifugal forces dominated were associated with large-scale coherent structures, such as deformed Dean-, Lyne- and Wall-type (D-L-W) vortical structures. Magnitudes of streamwise and cross-stream centrifugal forces tend to balance during deceleration phases. Deceleration events were also associated with spatial reorganization and asymmetry in large-scale D-L-W secondary flow structures. Hence, the interaction between streamwise and cross-stream centrifugal forces that affects secondary flow morphologies is explained using a ``residual force'' parameter i.e., the difference in magnitudes of these forces. Supported by the NSF Grant No. CBET- 0828903 and GW Center for Biomimetics and Bioinspired Engineering.

NMR studies of the backbone flexibility and structure of human growth hormone: a comparison of high and low pH conformations.

PubMed

Kasimova, Marina R; Kristensen, Søren M; Howe, Peter W A; Christensen, Thorkild; Matthiesen, Finn; Petersen, Jørgen; Sørensen, Hans H; Led, Jens J

2002-05-03

(15)N NMR relaxation parameters and amide (1)H/(2)H-exchange rates have been used to characterize the structural flexibility of human growth hormone (rhGH) at neutral and acidic pH. Our results show that the rigidity of the molecule is strongly affected by the solution conditions. At pH 7.0 the backbone dynamics parameters of rhGH are uniform along the polypeptide chain and their values are similar to those of other folded proteins. In contrast, at pH 2.7 the overall backbone flexibility increases substantially compared to neutral pH and the average order parameter approaches the lower limit expected for a folded protein. However, a significant variation of the backbone dynamics through the molecule indicates that under acidic conditions the mobility of the residues becomes more dependent on their location within the secondary structure units. In particular, the order parameters of certain loop regions decrease dramatically and become comparable to those found in unfolded proteins. Furthermore, the HN-exchange rates at low pH reveal that the residues most protected from exchange are clustered at one end of the helical bundle, forming a stable nucleus. We suggest that this nucleus maintains the overall fold of the protein under destabilizing conditions. We therefore conclude that the acid state of rhGH consists of a structurally conserved, but dynamically more flexible helical core surrounded by an aura of highly mobile, unstructured loops. However, in spite of its prominent flexibility the acid state of rhGH cannot be considered a "molten globule" state because of its high stability. It appears from our work that under certain conditions, a protein can tolerate a considerable increase in flexibility of its backbone, along with an increased penetration of water into its core, while still maintaining a stable folded conformation.

Control of secondary instability of the crossflow and Görtler-like vortices (Success and problems)

NASA Astrophysics Data System (ADS)

Kozlov, Viktor V.; Grek, Genrich R.

The secondary instability on a group of crossflow vortices developing in a swept wing boundary layer is described. It is shown that, for travelling waves, there is a region of linear development, and the growth rate of disturbances appreciably depends on the separation between the vortices. Methods of controlling the secondary instability of the vortices by a controlled wave and local suction are proposed and substantiated. The stability of a flat plate boundary layer modulated by G&ou ml;rtler-like stationary vortices is described. Vortices were generated inside the boundary layer by means of roughness elements arranged in a regular array along the spanwise (z) direction. Transition is not caused directly by these structures, but by the growth of small amplitude travelling waves riding on top of the steady vortices. This situation is analogous to the transition process in Görtler and cross-flows. The waves were found to amplify up to a stage where higher harmonics are gener ated, leading to turbulent breakdown and disintegration of the spanwise boundary layer structure. For strong modulations, the observed instability is quite powerful, and can be excited "naturally" by small uncontrollable background disturbances. Controlled oscillations were then introduced by means of a vibrating ribbon, allowing a detailed investigation of the wave characteristics. The instability seems to be associated with the spanwise gradients of the mean flow, , and at all z-positions, the maximum wave amplitude was found at a wall-normal position where the mean velocity is equal to the phase velocity of the wave, U(y)=c, i.e., at the local critical layer. Unstable waves were observed at frequency well above those for which Tollmien-Schlichting (TS) waves amplify in the Blasius boundary layer. Excitation at lower frequencies and milder basic flow modulation showed that TS-type waves may a lso develop. Study of the transition control in that flow by means of riblets shows that the effect of the riblets is to suppress longitudinal vortex structures in a boundary layer. The boundary layer becomes stable with respect to high-frequency travelling waves, which cause the transition in the absence of the riblets.

PreSSAPro: a software for the prediction of secondary structure by amino acid properties.

PubMed

Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

2007-10-01

PreSSAPro is a software, available to the scientific community as a free web service designed to provide predictions of secondary structures starting from the amino acid sequence of a given protein. Predictions are based on our recently published work on the amino acid propensities for secondary structures in either large but not homogeneous protein data sets, as well as in smaller but homogeneous data sets corresponding to protein structural classes, i.e. all-alpha, all-beta, or alpha-beta proteins. Predictions result improved by the use of propensities evaluated for the right protein class. PreSSAPro predicts the secondary structure according to the right protein class, if known, or gives a multiple prediction with reference to the different structural classes. The comparison of these predictions represents a novel tool to evaluate what sequence regions can assume different secondary structures depending on the structural class assignment, in the perspective of identifying proteins able to fold in different conformations. The service is available at the URL http://bioinformatica.isa.cnr.it/PRESSAPRO/.

Finding the target sites of RNA-binding proteins

PubMed Central

Li, Xiao; Kazan, Hilal; Lipshitz, Howard D; Morris, Quaid D

2014-01-01

RNA–protein interactions differ from DNA–protein interactions because of the central role of RNA secondary structure. Some RNA-binding domains (RBDs) recognize their target sites mainly by their shape and geometry and others are sequence-specific but are sensitive to secondary structure context. A number of small- and large-scale experimental approaches have been developed to measure RNAs associated in vitro and in vivo with RNA-binding proteins (RBPs). Generalizing outside of the experimental conditions tested by these assays requires computational motif finding. Often RBP motif finding is done by adapting DNA motif finding methods; but modeling secondary structure context leads to better recovery of RBP-binding preferences. Genome-wide assessment of mRNA secondary structure has recently become possible, but these data must be combined with computational predictions of secondary structure before they add value in predicting in vivo binding. There are two main approaches to incorporating structural information into motif models: supplementing primary sequence motif models with preferred secondary structure contexts (e.g., MEMERIS and RNAcontext) and directly modeling secondary structure recognized by the RBP using stochastic context-free grammars (e.g., CMfinder and RNApromo). The former better reconstruct known binding preferences for sequence-specific RBPs but are not suitable for modeling RBPs that recognize shape and geometry of RNAs. Future work in RBP motif finding should incorporate interactions between multiple RBDs and multiple RBPs in binding to RNA. WIREs RNA 2014, 5:111–130. doi: 10.1002/wrna.1201 PMID:24217996

Remanent magnetization stratigraphy of lunar cores

NASA Technical Reports Server (NTRS)

Banerjee, S. K.; Gingrich, D.; Marvin, J. A.

1977-01-01

Depth dependent fluctuations have been observed in the natural remanent magnetizations (NRM) of drive cores and drill strings from Apollo 16 and 17 missions. Partial demagnetization of unstable secondary magnetizations and identification of characteristic error signals from a core which is known to have been recently disturbed allow us to identify and isolate the stable NRM stratigraphy in double drive core 60010/60009 and drill strings 60002-60004. The observed magnetization fluctuations persist after normalization to take into account depth dependent variations in the carriers of stable NRM. We tentatively ascribe the stable NRM stratigraphy to instantaneous records of past magnetic fields at the lunar surface and suggest that the stable NRM stratigraphy technique could develop as a new relative time-stratigraphic tool, to be used with other physical measurements such as relative intensity of ferromagnetic resonance and charged particle track density to study the evolution of the lunar regolith.

Structural diversity of domain superfamilies in the CATH database.

PubMed

Reeves, Gabrielle A; Dallman, Timothy J; Redfern, Oliver C; Akpor, Adrian; Orengo, Christine A

2006-07-14

The CATH database of domain structures has been used to explore the structural variation of homologous domains in 294 well populated domain structure superfamilies, each containing at least three sequence diverse relatives. Our analyses confirm some previously detected trends relating sequence divergence to structural variation but for a much larger dataset and in some superfamilies the new data reveal exceptional structural variation. Use of a new algorithm (2DSEC) to analyse variability in secondary structure compositions across a superfamily sheds new light on how structures evolve. 2DSEC detects inserted secondary structures that embellish the core of conserved secondary structures found throughout the superfamily. Analysis showed that for 56% of highly populated superfamilies (>9 sequence diverse relatives), there are twofold or more increases in the numbers of secondary structures in some relatives. In some families fivefold increases occur, sometimes modifying the fold of the domain. Manual inspection of secondary structure insertions or embellishments in 48 particularly variable superfamilies revealed that although these insertions were usually discontiguous in the sequence they were often co-located in 3D resulting in a larger structural motif that often modified the geometry of the active site or the surface conformation promoting diverse domain partnerships and protein interactions. These observations, supported by automatic analysis of all well populated CATH families, suggest that accretion of small secondary structure insertions may provide a simple mechanism for evolving new functions in diverse relatives. Some layered domain architectures (e.g. mainly-beta and alpha-beta sandwiches) that recur highly in the genomes more frequently exploit these types of embellishments to modify function. In these architectures, aggregation occurs most often at the edges, top or bottom of the beta-sheets. Information on structural variability across domain superfamilies has been made available through the CATH Dictionary of Homologous Structures (DHS).

RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model.

PubMed

Jabbari, Hosna; Wark, Ian; Montemagno, Carlo

2018-01-01

RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design. Since experimental structure determination is time-consuming and expensive, accurate computational prediction of RNA structure is of great importance. Prediction of RNA secondary structure is relatively simpler than its tertiary structure and provides information about its tertiary structure, therefore, RNA secondary structure prediction has received attention in the past decades. Numerous methods with different folding approaches have been developed for RNA secondary structure prediction. While methods for prediction of RNA pseudoknot-free structure (structures with no crossing base pairs) have greatly improved in terms of their accuracy, methods for prediction of RNA pseudoknotted secondary structure (structures with crossing base pairs) still have room for improvement. A long-standing question for improving the prediction accuracy of RNA pseudoknotted secondary structure is whether to focus on the prediction algorithm or the underlying energy model, as there is a trade-off on computational cost of the prediction algorithm versus the generality of the method. The aim of this work is to argue when comparing different methods for RNA pseudoknotted structure prediction, the combination of algorithm and energy model should be considered and a method should not be considered superior or inferior to others if they do not use the same scoring model. We demonstrate that while the folding approach is important in structure prediction, it is not the only important factor in prediction accuracy of a given method as the underlying energy model is also as of great value. Therefore we encourage researchers to pay particular attention in comparing methods with different energy models.

Self-Efficacy, School Resources, Job Stressors and Burnout among Spanish Primary and Secondary School Teachers: A Structural Equation Approach

ERIC Educational Resources Information Center

Betoret, Fernando Domenech

2009-01-01

This study examines the relationship between school resources, teacher self-efficacy, potential multi-level stressors and teacher burnout using structural equation modelling. The causal structure for primary and secondary school teachers was also examined. The sample was composed of 724 primary and secondary Spanish school teachers. The changes…

Study on lithium/air secondary batteries-Stability of NASICON-type lithium ion conducting glass-ceramics with water

NASA Astrophysics Data System (ADS)

Hasegawa, Satoshi; Imanishi, Nobuyuki; Zhang, Tao; Xie, Jian; Hirano, Atsushi; Takeda, Yasuo; Yamamoto, Osamu

The water stability of the fast lithium ion conducting glass-ceramic electrolyte, Li 1+ x+ yAl xTi 2- xSi yP 3- yO 12 (LATP), has been examined in distilled water, and aqueous solutions of LiNO 3, LiCl, LiOH, and HCl. This glass-ceramics are stable in aqueous LiNO 3 and aqueous LiCl, and unstable in aqueous 0.1 M HCl and 1 M LiOH. In distilled water, the electrical conductivity slightly increases as a function of immersion time in water. The Li-Al/Li 3- xPO 4- yN y/LATP/aqueous 1 M LiCl/Pt cell, where lithium phosphors oxynitrides Li 3- xPO 4- yN y (LiPON) are used to protect the direct reaction of Li and LATP, shows a stable open circuit voltage (OCV) of 3.64 V at 25 °C, and no cell resistance change for 1 week. Lithium phosphors oxynitride is effectively used as a protective layer to suppress the reaction between the LATP and Li metal. The water-stable Li/LiPON/LATP system can be used in Li/air secondary batteries with the air electrode containing water.

RNApdbee 2.0: multifunctional tool for RNA structure annotation.

PubMed

Zok, Tomasz; Antczak, Maciej; Zurkowski, Michal; Popenda, Mariusz; Blazewicz, Jacek; Adamiak, Ryszard W; Szachniuk, Marta

2018-04-30

In the field of RNA structural biology and bioinformatics, an access to correctly annotated RNA structure is of crucial importance, especially in the secondary and 3D structure predictions. RNApdbee webserver, introduced in 2014, primarily aimed to address the problem of RNA secondary structure extraction from the PDB files. Its new version, RNApdbee 2.0, is a highly advanced multifunctional tool for RNA structure annotation, revealing the relationship between RNA secondary and 3D structure given in the PDB or PDBx/mmCIF format. The upgraded version incorporates new algorithms for recognition and classification of high-ordered pseudoknots in large RNA structures. It allows analysis of isolated base pairs impact on RNA structure. It can visualize RNA secondary structures-including that of quadruplexes-with depiction of non-canonical interactions. It also annotates motifs to ease identification of stems, loops and single-stranded fragments in the input RNA structure. RNApdbee 2.0 is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/.

Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce.

PubMed

Yehdego, Daniel T; Zhang, Boyu; Kodimala, Vikram K R; Johnson, Kyle L; Taufer, Michela; Leung, Ming-Ying

2013-05-01

Secondary structures of ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Experimental observations and computing limitations suggest that we can approach the secondary structure prediction problem for long RNA sequences by segmenting them into shorter chunks, predicting the secondary structures of each chunk individually using existing prediction programs, and then assembling the results to give the structure of the original sequence. The selection of cutting points is a crucial component of the segmenting step. Noting that stem-loops and pseudoknots always contain an inversion, i.e., a stretch of nucleotides followed closely by its inverse complementary sequence, we developed two cutting methods for segmenting long RNA sequences based on inversion excursions: the centered and optimized method. Each step of searching for inversions, chunking, and predictions can be performed in parallel. In this paper we use a MapReduce framework, i.e., Hadoop, to extensively explore meaningful inversion stem lengths and gap sizes for the segmentation and identify correlations between chunking methods and prediction accuracy. We show that for a set of long RNA sequences in the RFAM database, whose secondary structures are known to contain pseudoknots, our approach predicts secondary structures more accurately than methods that do not segment the sequence, when the latter predictions are possible computationally. We also show that, as sequences exceed certain lengths, some programs cannot computationally predict pseudoknots while our chunking methods can. Overall, our predicted structures still retain the accuracy level of the original prediction programs when compared with known experimental secondary structure.

Density functional study of molecular interactions in secondary structures of proteins.

PubMed

Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

2016-01-01

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

Pairwise amino acid secondary structural propensities

NASA Astrophysics Data System (ADS)

Chemmama, Ilan E.; Chapagain, Prem P.; Gerstman, Bernard S.

2015-04-01

We investigate the propensities for amino acids to form a specific secondary structure when they are paired with other amino acids. Our investigations use molecular dynamics (MD) computer simulations, and we compare the results to those from the Protein Data Bank (PDB). Proper comparison requires weighting of the MD results in a manner consistent with the relative frequency of appearance in the PDB of each possible pair of amino acids. We find that the propensity for an amino acid to assume a secondary structure varies dramatically depending on the amino acid that is before or after it in the primary sequence. This cooperative effect means that when selecting amino acids to facilitate the formation of a secondary structure in peptide engineering experiments, the adjacent amino acids must be considered. We also examine the preference for a secondary structure in bacterial proteins and compare the results to those of human proteins.

Dimensionally stable composite structures and composite mirrors for spaceborne optical instruments

NASA Astrophysics Data System (ADS)

Sippel, Rudolf; Stute, Thomas; Erdl, Günther

2018-04-01

This paper, "Dimensionally stable composite structures and composite mirrors for spaceborne optical instruments," was presented as part of International Conference on Space Optics—ICSO 1997, held in Toulouse, France.

Study of structural stability and damaging effect on membrane for four Aβ42 dimers

PubMed Central

Feng, Wei; Lei, Huimin; Si, Jiarui; Zhang, Tao

2017-01-01

Increasing evidence shows that Aβ oligomers are key pathogenic molecules in Alzheimer’s disease. Among Aβ oligomers, dimer is the smallest aggregate and toxic unit. Therefore, understanding its structural and dynamic properties is quite useful to prevent the formation and toxicity of the Aβ oligomers. In this study, we performed molecular dynamic simulations on four Aβ42 dimers, 2NCb, CNNC, NCNC and NCCN, within the hydrated DPPC membrane. Four Aβ42 dimers differ in the arrangements of two Aβ42 peptides. This study aims to investigate the impact of aggregation pattern of two Aβ peptides on the structural stability of the Aβ42 dimer and its disruption to the biological membrane. The MD results demonstrate that the NCCN, CNNC and NCNC have the larger structural fluctuation at the N-terminus of Aβ42 peptide, where the β-strand structure converts into the coil structure. The loss of the N-terminal β-strand further impairs the aggregate ability of Aβ42 dimer. In addition, inserting Aβ42 dimer into the membrane can considerably decrease the average APL of DPPC membrane. Moreover this decrease effect is largely dependent on the distance to the location of Aβ42 dimer and its secondary structure forms. Based on the results, the 2NCb is considered as a stable dimeric unit for aggregating the larger Aβ42 oligomer, and has a potent ability to disrupt the membrane. PMID:28594887

Structural alterations in rat liver proteins due to streptozotocin-induced diabetes and the recovery effect of selenium: Fourier transform infrared microspectroscopy and neural network study

NASA Astrophysics Data System (ADS)

Bozkurt, Ozlem; Haman Bayari, Sevgi; Severcan, Mete; Krafft, Christoph; Popp, Jürgen; Severcan, Feride

2012-07-01

The relation between protein structural alterations and tissue dysfunction is a major concern as protein fibrillation and/or aggregation due to structural alterations has been reported in many disease states. In the current study, Fourier transform infrared microspectroscopic imaging has been used to investigate diabetes-induced changes on protein secondary structure and macromolecular content in streptozotocin-induced diabetic rat liver. Protein secondary structural alterations were predicted using neural network approach utilizing the amide I region. Moreover, the role of selenium in the recovery of diabetes-induced alterations on macromolecular content and protein secondary structure was also studied. The results revealed that diabetes induced a decrease in lipid to protein and glycogen to protein ratios in diabetic livers. Significant alterations in protein secondary structure were observed with a decrease in α-helical and an increase in β-sheet content. Both doses of selenium restored diabetes-induced changes in lipid to protein and glycogen to protein ratios. However, low-dose selenium supplementation was not sufficient to recover the effects of diabetes on protein secondary structure, while a higher dose of selenium fully restored diabetes-induced alterations in protein structure.

Adsorption of fibrinogen on a biomedical-grade stainless steel 316LVM surface: a PM-IRRAS study of the adsorption thermodynamics, kinetics and secondary structure changes.

PubMed

Desroches, Marie-Josee; Omanovic, Sasha

2008-05-14

Polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS) was employed to investigate the interaction of serum protein fibrinogen with a biomedical-grade 316LVM stainless steel surface, in terms of the adsorption thermodynamics, kinetics and secondary structure changes of the protein. Apparent Gibbs energy of adsorption values indicated a highly spontaneous and strong adsorption of fibrinogen onto the surface. The kinetics of fibrinogen adsorption were successfully modeled using a pseudo first-order kinetic model. Deconvolution of the amide I bands indicated that the adsorption of fibrinogen on 316LVM results in significant changes in the protein's secondary structure that occur predominantly within the first minute of adsorption. Among the investigated structures, the alpha-helix structure undergoes the smallest changes, while the beta-sheet and beta-turns structures undergo significant changes. It was shown that lateral interactions between the adsorbed molecules do not play a role in controlling the secondary structure changes. An increase in temperature induced changes in the secondary structure of the protein, characterized by a loss of the alpha-helical content and its transformation into the beta-turns structure.

Synthesis of core-shell structured FAU/SBA-15 composite molecular sieves and their performance in catalytic cracking of polystyrene

NASA Astrophysics Data System (ADS)

Du, Jinlong; Shi, Chunwei; Wu, Wenyuan; Bian, Xue; Chen, Ping; Cui, Qingzhu; Cui, Zhixuan

2017-12-01

Composite molecular sieves, FAU/SBA-15, having core-shell structure were synthesized. The synthesized composite sieves were characterized by X-ray diffractometry (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDS), pyrolysis fourier transform infrared (Py-FTIR) spectroscopy, temperature programmed desorption spectra (NH3-TPD), UV Raman spectroscopy, nuclear magnetic resonance (NMR) and other techniques. XRD, SEM, TEM, N2 adsorption-desorption, mass spectrometry, NMR and EDS results showed that the composite molecular sieve contained two pore channels. Py-FTIR results showed that the addition of HY molecular sieves improved the acidity of the composite zeolite. The crystallization mechanism during the growth of FAU/SBA-15 shell was deduced from the influence of crystallization time on the synthesis of FAU/SBA-15 core-shell structured composite molecular sieve. HY dissociated partially in H2SO4 solution, and consisted of secondary structural units. This framework structure was more stable than its presence in the isolated form on the same ring or in the absence of Al. Thus it played a guiding role and connected with SBA-15 closely through the Si-O bond. This resulted in the gradual covering of the exterior surface of FAU phase by SBA-15 molecular sieves. The presence of SBA-15 restricted the formation of the other high mass components and increased the selectivity towards ethylbenzene.

pH Dependence of a 310-Helix versus a Turn in the M-Loop Region of PDE4: Observations on PDB Entries and an Electronic Structure Study.

PubMed

Usharani, Dandamudi; Srivani, Palakuri; Sastry, G Narahari; Jemmis, Eluvathingal D

2008-06-01

Available X-ray crystal structures of phosphodiesterase 4 (PDE 4) are classified into two groups based on a secondary structure difference of a 310-helix versus a turn in the M-loop region. The only variable that was discernible between these two sets is the pH at the crystallization conditions. Assuming that at lower pH there is a possibility of protonation, thermodynamics of protonation and deprotonation of the aspartic acid, cysteine side chains, and amide bonds are calculated. The models in the gas phase and in the explicit solvent using the ONIOM method are calculated at the B3LYP/6-31+G* and B3LYP/6-31+G*:UFF levels of theory, respectively. The molecular dynamics (MD) simulations are also performed on the M-loop region of a 310-helix and a turn with explicit water for 10 ns under NPT conditions. The isodesmic equations of the various protonation states show that the turn containing structure is thermodynamically more stable when proline or cysteine is protonated. The preference for the turn structure on protonation (pH = 6.5-7.5) is due to an increase in the number of the hydrogen bonding and electrostatic interactions gained by the surrounding environment such as adjacent residues and solvent molecules.

Crystal Structure of the Minimalist Max-E47 Protein Chimera

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmadpour, Faraz; Ghirlando, Rodolfo; De Jong, Antonia T.

Max-E47 is a protein chimera generated from the fusion of the DNA-binding basic region of Max and the dimerization region of E47, both members of the basic region/helix-loop-helix (bHLH) superfamily of transcription factors. Like native Max, Max-E47 binds with high affinity and specificity to the E-box site, 5'-CACGTG, both in vivo and in vitro. We have determined the crystal structure of Max-E47 at 1.7 Å resolution, and found that it associates to form a well-structured dimer even in the absence of its cognate DNA. Analytical ultracentrifugation confirms that Max-E47 is dimeric even at low micromolar concentrations, indicating that the Max-E47more » dimer is stable in the absence of DNA. Circular dichroism analysis demonstrates that both non-specific DNA and the E-box site induce similar levels of helical secondary structure in Max-E47. These results suggest that Max-E47 may bind to the E-box following the two-step mechanism proposed for other bHLH proteins. In this mechanism, a rapid step where protein binds to DNA without sequence specificity is followed by a slow step where specific protein:DNA interactions are fine-tuned, leading to sequence-specific recognition. Collectively, these results show that the designed Max-E47 protein chimera behaves both structurally and functionally like its native counterparts.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manikandan, M.; Santhosh, M.; Rajeswarapalanichamy, R., E-mail: rrpalanichamy@gmail.com

Ab initio calculations are performed to investigate the structural stability, electronic structure and mechanical properties of actinide carbides AnC (An=U, Np) for three different crystal structures, namely NaCl, CsCl and ZnS. Among the considered structures, NaCl structure is found to be the most stable structure for these carbides at normal pressure. A pressure induced structural phase transition from NaCl to ZnS is observed. The electronic structure reveals that these carbides are metals. The calculated elastic constants indicate that these carbides are mechanically stable at normal pressure.

Comparative Study of Ultrasonication-Induced and Naturally Self-Assembled Silk Fibroin-Wool Keratin Hydrogel Biomaterials

PubMed Central

Vu, Trang; Xue, Ye; Vuong, Trinh; Erbe, Matthew; Bennet, Christopher; Palazzo, Ben; Popielski, Lucas; Rodriguez, Nelson; Hu, Xiao

2016-01-01

This study reports the formation of biocompatible hydrogels using protein polymers from natural silk cocoon fibroins and sheep wool keratins. Silk fibroin protein contains β-sheet secondary structures, allowing for the formation of physical cross-linkers in the hydrogels. Comparative studies were performed on two groups of samples. In the first group, ultrasonication was used to induce a quick gelation of a protein aqueous solution, enhancing the ability of Bombyx mori silk fibroin chains to quickly entrap the wool keratin protein molecules homogenously. In the second group, silk/keratin mixtures were left at room temperature for days, resulting in naturally-assembled gelled solutions. It was found that silk/wool blended solutions can form hydrogels at different mixing ratios, with perfectly interconnected gel structure when the wool content was less than 30 weight percent (wt %) for the first group (ultrasonication), and 10 wt % for the second group (natural gel). Differential scanning calorimetry (DSC) and temperature modulated DSC (TMDSC) were used to confirm that the fibroin/keratin hydrogel system was well-blended without phase separation. Fourier transform infrared spectroscopy (FTIR) was used to investigate the secondary structures of blended protein gels. It was found that intermolecular β-sheet contents significantly increase as the system contains more silk for both groups of samples, resulting in stable crystalline cross-linkers in the blended hydrogel structures. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) were used to analyze the samples’ characteristic morphology on both micro- and nanoscales, which showed that ultrasonic waves can significantly enhance the cross-linker formation and avoid phase separation between silk and keratin molecules in the blended systems. With the ability to form cross-linkages non-chemically, these silk/wool hydrogels may be economically useful for various biomedical applications, thanks to the good biocompatibility of protein molecules and the various characteristics of hydrogel systems. PMID:27618011

Uptake and selective partitioning of dietary lipids to ovarian and muscle tissue of maturing female coho salmon, Oncorhynchus kisutch, during secondary oocyte growth.

PubMed

Johnson, Ronald B; Kroeger, Eric L; Reichert, William L; Carter, Cameron S; Rust, Michael B

2017-06-01

Female coho salmon, Oncorhynchus kisutch, were fed one of two experimental feeds containing lipids with markedly different stable 13 C isotope signatures during the late cortical alveolus, lipid droplet, and vitellogenesis stages of secondary oocyte growth. Ovarian and muscle lipids fatty acid concentrations were significantly affected by treatment during all three stages of development. Stable 13 C isotope analyses confirmed that dietary lipids were incorporated into both ovarian and muscle lipids during all three stages and revealed that ovarian lipids were more affected than muscle lipids during vitellogenesis. Arachidonic acid (ARA) was incorporated into ovarian lipids at the highest rate of all fatty acids examined with the greatest uptake observed during the cortical alveolus and lipid droplet stages of development. Docosahexaenoic acid (DHA) was incorporated into ovarian lipids at the next highest rate with the greatest uptake observed during the lipid droplet stage of development. The presence of an ovary specific, fatty acid transfer mechanism is proposed. Results from this study demonstrate the ability to greatly alter the fatty acid composition of ovarian lipids through a dietary change during secondary oocyte growth and may be of great interest to producers of farmed salmon and salmon broodstock programs. Published by Elsevier Inc.

Fast prediction of RNA-RNA interaction using heuristic algorithm.

PubMed

Montaseri, Soheila

2015-01-01

Interaction between two RNA molecules plays a crucial role in many medical and biological processes such as gene expression regulation. In this process, an RNA molecule prohibits the translation of another RNA molecule by establishing stable interactions with it. Some algorithms have been formed to predict the structure of the RNA-RNA interaction. High computational time is a common challenge in most of the presented algorithms. In this context, a heuristic method is introduced to accurately predict the interaction between two RNAs based on minimum free energy (MFE). This algorithm uses a few dot matrices for finding the secondary structure of each RNA and binding sites between two RNAs. Furthermore, a parallel version of this method is presented. We describe the algorithm's concurrency and parallelism for a multicore chip. The proposed algorithm has been performed on some datasets including CopA-CopT, R1inv-R2inv, Tar-Tar*, DIS-DIS, and IncRNA54-RepZ in Escherichia coli bacteria. The method has high validity and efficiency, and it is run in low computational time in comparison to other approaches.

Lactobacillus reuteri 2′-Deoxyribosyltransferase, a Novel Biocatalyst for Tailoring of Nucleosides▿ † ‡

PubMed Central

Fernández-Lucas, Jesús; Acebal, Carmen; Sinisterra, José V.; Arroyo, Miguel; de la Mata, Isabel

2010-01-01

A novel type II nucleoside 2′-deoxyribosyltransferase from Lactobacillus reuteri (LrNDT) has been cloned and overexpressed in Escherichia coli. The recombinant LrNDT has been structural and functionally characterized. Sedimentation equilibrium analysis revealed a homohexameric molecule of 114 kDa. Circular dichroism studies have showed a secondary structure containing 55% α-helix, 10% β-strand, 16% β-sheet, and 19% random coil. LrNDT was thermostable with a melting temperature (Tm) of 64°C determined by fluorescence, circular dichroism, and differential scanning calorimetric studies. The enzyme showed high activity in a broad pH range (4.6 to 7.9) and was also very stable between pH 4 and 7.9. The optimal temperature for activity was 40°C. The recombinant LrNDT was able to synthesize natural and nonnatural nucleoside analogues, improving activities described in the literature, and remarkably, exhibited unexpected new arabinosyltransferase activity, which had not been described so far in this kind of enzyme. Furthermore, synthesis of new arabinonucleosides and 2′-fluorodeoxyribonucleosides was carried out. PMID:20048065

Intrinsic and extrinsic dielectric responses of CaCu3Ti4O12 thin films

NASA Astrophysics Data System (ADS)

Rubinger, C. P. L.; Moreira, R. L.; Ribeiro, G. M.; Matinaga, F. M.; Autier Laurent, S.; Mercey, B.; Lobo, R. P. S. M.

2011-10-01

CaCu3Ti4O12 thin films were epitaxially grown on (001) LaAlO3 substrates by pulsed laser deposition under optimized growth conditions. The crystal structure and sample morphology were characterized by x-ray diffraction, AFM, TEM, ellipsometry, and Raman spectroscopy. The dielectric responses of the films were investigated in a large temperature range (5 to 375 K) by infrared reflectivity and impedance spectroscopies. The films exhibited a colossal dielectric response, with the dielectric permittivity reaching 104 at 100 Hz. The results obtained in a broad frequency range allowed us to investigate the behavior of intrinsic and extrinsic dielectric responses of this material. The room temperature centrosymmetrical cubic structure remains stable down to 5 K, though softening of the lower frequency infrared phonon modes indicates an incipient ferroelectric character. The radio frequency dielectric response reveals two relaxations of extrinsic origin, a primary higher frequency relaxation responsible for the colossal dielectric behavior and a secondary one of lower frequency. The activation energies of these processes are compatible with the presence of shallow defect levels created by oxygen vacancies.

High pressure-temperature polymorphism of 1,1-diamino-2,2-dinitroethylene

NASA Astrophysics Data System (ADS)

Bishop, M. M.; Chellappa, R. S.; Liu, Z.; Preston, D. N.; Sandstrom, M. M.; Dattelbaum, D. M.; Vohra, Y. K.; Velisavljevic, N.

2014-05-01

1,1-diamino-2,2-dinitroethylene (FOX-7) is a low sensitivity energetic material with performance comparable to commonly used secondary explosives such as RDX and HMX. At ambient pressure, FOX-7 exhibits complex polymorphism with at least three structurally distinct phases (α, β, and γ). In this study, we have investigated the high pressure-temperature stability of FOX-7 polymorphs using synchrotron mid-infrared (MIR) spectroscopy. At ambient pressure, our MIR spectra and corresponding differential scanning calorimetry (DSC) measurements confirmed the known α → β (~110 °C) and α → β (~160 °C) structural phase transitions; as well as, indicated an additional transition γ → (~210 °C), with the δ phase being stable up to ~251 °C prior to decomposition. In situ MIR spectra obtained during isobaric heating at 0.9 GPa, revealed a potential α → β transition that could occur as early as 180 °C, while β → β+δ phase transition shifted to ~300 °C with suppression of γ phase. Decomposition was observed slightly above 325 °C at 0.9 GPa.

Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation.

PubMed

Velazquez Camacho, Oscar; Galan, Carmen; Swist-Rosowska, Kalina; Ching, Reagan; Gamalinda, Michael; Karabiber, Fethullah; De La Rosa-Velazquez, Inti; Engist, Bettina; Koschorz, Birgit; Shukeir, Nicholas; Onishi-Seebacher, Megumi; van de Nobelen, Suzanne; Jenuwein, Thomas

2017-08-01

The Suv39h1 and Suv39h2 histone lysine methyltransferases are hallmark enzymes at mammalian heterochromatin. We show here that the mouse Suv39h2 enzyme differs from Suv39h1 by containing an N-terminal basic domain that facilitates retention at mitotic chromatin and provides an additional affinity for major satellite repeat RNA. To analyze an RNA-dependent interaction with chromatin, we purified native nucleosomes from mouse ES cells and detect that Suv39h1 and Suv39h2 exclusively associate with poly-nucleosomes. This association was attenuated upon RNaseH incubation and entirely lost upon RNaseA digestion of native chromatin. Major satellite repeat transcripts remain chromatin-associated and have a secondary structure that favors RNA:DNA hybrid formation. Together, these data reveal an RNA-mediated mechanism for the stable chromatin interaction of the Suv39h KMT and suggest a function for major satellite non-coding RNA in the organization of an RNA-nucleosome scaffold as the underlying structure of mouse heterochromatin.

Biomagnification profiles of polycyclic aromatic hydrocarbons, alkylphenols and polychlorinated biphenyls in Tokyo Bay elucidated by delta13C and delta15N isotope ratios as guides to trophic web structure.

PubMed

Takeuchi, Ichiro; Miyoshi, Noriko; Mizukawa, Kaoruko; Takada, Hideshige; Ikemoto, Tokutaka; Omori, Koji; Tsuchiya, Kotaro

2009-05-01

Biomagnification profiles of polycyclic aromatic hydrocarbons (PAHs), alkylphenols, and polychlorinated biphenyls (PCBs) from the innermost part of Tokyo Bay, Japan were analyzed using stable carbon (delta(13)C) and nitrogen (delta(15)N) isotope ratios as guides to trophic web structure. delta(15)N analysis indicated that all species of mollusks tested were primary consumers, while decapods and fish were secondary consumers. Higher concentrations of PCBs occurred in decapods and fish than in mollusks. In contrast, concentrations of PAHs and alkylphenols were lower in decapods and fish than in mollusks. Unlike PCBs, whose concentrations largely increased with increasing delta(15)N (i.e. increasing trophic level), all PAHs and alkylphenols analyzed followed a reverse trend. Molecular weights of PAHs are lower than those of PCBs, therefore low membrane permeability caused by large molecular size is an unlikely factor in the "biodilution" of PAHs. Organisms at higher trophic levels may rapidly metabolize PAHs or they may assimilate less of them.

Macroporous Silica with Thick Framework for Steam-Stable and High-Performance Poly(ethyleneimine)/Silica CO2 Adsorbent.

PubMed

Min, Kyungmin; Choi, Woosung; Choi, Minkee

2017-06-09

Poly(ethyleneimine) (PEI)/silica has been widely studied as a solid adsorbent for post-combustion CO 2 capture. In this work, a highly macroporous silica (MacS), synthesized by secondary sintering of fumed silica, is compared with various mesoporous silicas with different pore structures as a support for PEI. The silicas with large pore diameter and volume enabled high CO 2 adsorption kinetics and capacity, because pore occlusion by the supported PEI was minimized. The steam stability of the silica structures increased with the silica wall thickness owing to suppressed framework ripening. The silicas with low steam stability showed rapid leaching of PEI, which indicated that the PEI squeezed out of the collapsed silica pores leached more readily. Consequently, MacS that had an extra-large pore volume (1.80 cm 3  g -1 ) and pore diameter (56.0 nm), and a thick wall (>10 nm), showed the most promising CO 2 adsorption kinetics and capacity as well as steam stability. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Long-Term Study of the Microbial Community Structure in a ...

EPA Pesticide Factsheets

Many US water treatment facilities use chloramination to limit regulated disinfectant by-product formation. However, chloramination has been shown to promote nitrifying bacteria, and 30 to 63% of water utilities using secondary chloramine disinfection experience nitrification episodes. In this study, we examined the Bacterial population in a simulated chloraminated drinking water distribution system (DWDS). After six months of continuous operation, coupons were incubated in CDC reactors receiving water from the simulated DWDS to study biofilm development. The DWDS was then subjected to episodes of nitrification, followed by a ‘chlorine burn’ by switching disinfectant from chloramine to chlorine, a common nitrification control strategy. The study was organized into five distinct operational schemes: (1) PRE-MODIFIED; system stabilization, (2) STANDARD I; stable chloramine residual, (3) FAILURE; complete nitrification and minimal chloramine residual, (4) RESTORE; chlorine burn, and (5) STANDARD II; stable chloramine residual. Bulk water and biofilm samples were collected and analyzed for water quality parameters and microbial composition. No change in microbial biomass (ATP) in bulk water and biofilm samples was detected during the STANDARD I scheme, while an increase in biofilms was detected after 80 days (FAILURE, i.e. nitrification) followed by a decrease after a chlorine burn with a final increase to previous values (STANDARD I) during the STANDARD I

On the bistable zone of milling processes

PubMed Central

Dombovari, Zoltan; Stepan, Gabor

2015-01-01

A modal-based model of milling machine tools subjected to time-periodic nonlinear cutting forces is introduced. The model describes the phenomenon of bistability for certain cutting parameters. In engineering, these parameter domains are referred to as unsafe zones, where steady-state milling may switch to chatter for certain perturbations. In mathematical terms, these are the parameter domains where the periodic solution of the corresponding nonlinear, time-periodic delay differential equation is linearly stable, but its domain of attraction is limited due to the existence of an unstable quasi-periodic solution emerging from a secondary Hopf bifurcation. A semi-numerical method is presented to identify the borders of these bistable zones by tracking the motion of the milling tool edges as they might leave the surface of the workpiece during the cutting operation. This requires the tracking of unstable quasi-periodic solutions and the checking of their grazing to a time-periodic switching surface in the infinite-dimensional phase space. As the parameters of the linear structural behaviour of the tool/machine tool system can be obtained by means of standard modal testing, the developed numerical algorithm provides efficient support for the design of milling processes with quick estimates of those parameter domains where chatter can still appear in spite of setting the parameters into linearly stable domains. PMID:26303918

Secondary flow structures in a 180∘ elastic curved vessel with torsion under steady and pulsatile inflow conditions

NASA Astrophysics Data System (ADS)

Najjari, Mohammad Reza; Plesniak, Michael W.

2017-11-01

Secondary flow vortical structures were investigated in an elastic 180° curved pipe with and without torsion under steady and pulsatile flow using particle image velocimetry (PIV). The elastic thin-walled curved pipes were constructed using Sylgard 184, and inserted into a bath of refractive index matched fluid to perform PIV. A vortex identification method was employed to identify various vortical structures in the flow. The secondary flow structures in the planar compliant model with dilatation of 0.61%-3.23% under pulsatile flow rate were compared with the rigid vessel model results, and it was found that local vessel compliance has a negligible effect on secondary flow morphology. The secondary flow structures were found to be more sensitive to out of plane curvature (torsion) than to vessel compliance. Torsion distorts the symmetry of secondary flow and results in more complex vortical structures in both steady and pulsatile flows. In high Re number steady flow with torsion, a single dominant vortical structure can be detected at the middle of the 90° cross section. In pulsatile flow with torsion, the split-Dean and Lyne-type vortices with same rotation direction originating from opposite sides of the cross section tend to merge together. supported by GW Center for Biomimetics and Bioinspired Engineering.

A parallel strategy for predicting the secondary structure of polycistronic microRNAs.

PubMed

Han, Dianwei; Tang, Guiliang; Zhang, Jun

2013-01-01

The biogenesis of a functional microRNA is largely dependent on the secondary structure of the microRNA precursor (pre-miRNA). Recently, it has been shown that microRNAs are present in the genome as the form of polycistronic transcriptional units in plants and animals. It will be important to design efficient computational methods to predict such structures for microRNA discovery and its applications in gene silencing. In this paper, we propose a parallel algorithm based on the master-slave architecture to predict the secondary structure from an input sequence. We conducted some experiments to verify the effectiveness of our parallel algorithm. The experimental results show that our algorithm is able to produce the optimal secondary structure of polycistronic microRNAs.

The Globular State of the Single-Stranded RNA: Effect of the Secondary Structure Rearrangements

PubMed Central

Grigoryan, Zareh A.; Karapetian, Armen T.

2015-01-01

The mutual influence of the slow rearrangements of secondary structure and fast collapse of the long single-stranded RNA (ssRNA) in approximation of coarse-grained model is studied with analytic calculations. It is assumed that the characteristic time of the secondary structure rearrangement is much longer than that for the formation of the tertiary structure. A nonequilibrium phase transition of the 2nd order has been observed. PMID:26345143

Principles for Predicting RNA Secondary Structure Design Difficulty.

PubMed

Anderson-Lee, Jeff; Fisker, Eli; Kosaraju, Vineet; Wu, Michelle; Kong, Justin; Lee, Jeehyung; Lee, Minjae; Zada, Mathew; Treuille, Adrien; Das, Rhiju

2016-02-27

Designing RNAs that form specific secondary structures is enabling better understanding and control of living systems through RNA-guided silencing, genome editing and protein organization. Little is known, however, about which RNA secondary structures might be tractable for downstream sequence design, increasing the time and expense of design efforts due to inefficient secondary structure choices. Here, we present insights into specific structural features that increase the difficulty of finding sequences that fold into a target RNA secondary structure, summarizing the design efforts of tens of thousands of human participants and three automated algorithms (RNAInverse, INFO-RNA and RNA-SSD) in the Eterna massive open laboratory. Subsequent tests through three independent RNA design algorithms (NUPACK, DSS-Opt and MODENA) confirmed the hypothesized importance of several features in determining design difficulty, including sequence length, mean stem length, symmetry and specific difficult-to-design motifs such as zigzags. Based on these results, we have compiled an Eterna100 benchmark of 100 secondary structure design challenges that span a large range in design difficulty to help test future efforts. Our in silico results suggest new routes for improving computational RNA design methods and for extending these insights to assess "designability" of single RNA structures, as well as of switches for in vitro and in vivo applications. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Determination of secondary flow morphologies by wavelet analysis in a curved artery model with physiological inflow

NASA Astrophysics Data System (ADS)

Bulusu, Kartik V.; Hussain, Shadman; Plesniak, Michael W.

2014-11-01

Secondary flow vortical patterns in arterial curvatures have the potential to affect several cardiovascular phenomena, e.g., progression of atherosclerosis by altering wall shear stresses, carotid atheromatous disease, thoracic aortic aneurysms and Marfan's syndrome. Temporal characteristics of secondary flow structures vis-à-vis physiological (pulsatile) inflow waveform were explored by continuous wavelet transform (CWT) analysis of phase-locked, two-component, two-dimensional particle image velocimeter data. Measurements were made in a 180° curved artery test section upstream of the curvature and at the 90° cross-sectional plane. Streamwise, upstream flow rate measurements were analyzed using a one-dimensional antisymmetric wavelet. Cross-stream measurements at the 90° location of the curved artery revealed interesting multi-scale, multi-strength coherent secondary flow structures. An automated process for coherent structure detection and vortical feature quantification was applied to large ensembles of PIV data. Metrics such as the number of secondary flow structures, their sizes and strengths were generated at every discrete time instance of the physiological inflow waveform. An autonomous data post-processing method incorporating two-dimensional CWT for coherent structure detection was implemented. Loss of coherence in secondary flow structures during the systolic deceleration phase is observed in accordance with previous research. The algorithmic approach presented herein further elucidated the sensitivity and dependence of morphological changes in secondary flow structures on quasiperiodicity and magnitude of temporal gradients in physiological inflow conditions.

Decision-making under risk conditions is susceptible to interference by a secondary executive task.

PubMed

Starcke, Katrin; Pawlikowski, Mirko; Wolf, Oliver T; Altstötter-Gleich, Christine; Brand, Matthias

2011-05-01

Recent research suggests two ways of making decisions: an intuitive and an analytical one. The current study examines whether a secondary executive task interferes with advantageous decision-making in the Game of Dice Task (GDT), a decision-making task with explicit and stable rules that taps executive functioning. One group of participants performed the original GDT solely, two groups performed either the GDT and a 1-back or a 2-back working memory task as a secondary task simultaneously. Results show that the group which performed the GDT and the secondary task with high executive load (2-back) decided less advantageously than the group which did not perform a secondary executive task. These findings give further evidence for the view that decision-making under risky conditions taps into the rational-analytical system which acts in a serial and not parallel way as performance on the GDT is disturbed by a parallel task that also requires executive resources.

Hot spot of structural ambivalence in prion protein revealed by secondary structure principal component analysis.

PubMed

Yamamoto, Norifumi

2014-08-21

The conformational conversion of proteins into an aggregation-prone form is a common feature of various neurodegenerative disorders including Alzheimer's, Huntington's, Parkinson's, and prion diseases. In the early stage of prion diseases, secondary structure conversion in prion protein (PrP) causing β-sheet expansion facilitates the formation of a pathogenic isoform with a high content of β-sheets and strong aggregation tendency to form amyloid fibrils. Herein, we propose a straightforward method to extract essential information regarding the secondary structure conversion of proteins from molecular simulations, named secondary structure principal component analysis (SSPCA). The definite existence of a PrP isoform with an increased β-sheet structure was confirmed in a free-energy landscape constructed by mapping protein structural data into a reduced space according to the principal components determined by the SSPCA. We suggest a "spot" of structural ambivalence in PrP-the C-terminal part of helix 2-that lacks a strong intrinsic secondary structure, thus promoting a partial α-helix-to-β-sheet conversion. This result is important to understand how the pathogenic conformational conversion of PrP is initiated in prion diseases. The SSPCA has great potential to solve various challenges in studying highly flexible molecular systems, such as intrinsically disordered proteins, structurally ambivalent peptides, and chameleon sequences.

Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.

PubMed

Eddy, Sean R

2014-01-01

Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a focus on detecting signatures of conserved RNA secondary structure. An interesting new front is the application of chemical and enzymatic experiments that probe RNA structure on a transcriptome-wide scale. I review several proposed approaches for incorporating structure probing data into the computational prediction of RNA secondary structure. Using probabilistic inference formalisms, I show how all these approaches can be unified in a well-principled framework, which in turn allows RNA probing data to be easily integrated into a wide range of analyses that depend on RNA secondary structure inference. Such analyses include homology search and genome-wide detection of new structural RNAs.

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

PubMed Central

Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H.

2008-01-01

A novel method is presented for joint prediction of alignment and common secondary structures of two RNA sequences. The joint consideration of common secondary structures and alignment is accomplished by structural alignment over a search space defined by the newly introduced motif called matched helical regions. The matched helical region formulation generalizes previously employed constraints for structural alignment and thereby better accommodates the structural variability within RNA families. A probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities is utilized for scoring structural alignments. Maximum a posteriori (MAP) common secondary structures, sequence alignment and joint posterior probabilities of base pairing are obtained from the model via a dynamic programming algorithm called PARTS. The advantage of the more general structural alignment of PARTS is seen in secondary structure predictions for the RNase P family. For this family, the PARTS MAP predictions of secondary structures and alignment perform significantly better than prior methods that utilize a more restrictive structural alignment model. For the tRNA and 5S rRNA families, the richer structural alignment model of PARTS does not offer a benefit and the method therefore performs comparably with existing alternatives. For all RNA families studied, the posterior probability estimates obtained from PARTS offer an improvement over posterior probability estimates from a single sequence prediction. When considering the base pairings predicted over a threshold value of confidence, the combination of sensitivity and positive predictive value is superior for PARTS than for the single sequence prediction. PARTS source code is available for download under the GNU public license at http://rna.urmc.rochester.edu. PMID:18304945

Secondary Moments due to Prestressing with Different Bond at the Ultimate Limit State

NASA Astrophysics Data System (ADS)

Halvoník, Jaroslav; Pažma, Peter; Vida, Radoslav

2018-03-01

Secondary effects of prestressing develop in statically indeterminate structures (e.g., continuous beams) due to the restraint of deformations imposed by hyperstatic restraints. These effects may significantly influence internal forces and stresses in prestressed structures. Secondary effects are influenced by the redundancy of a structural system, which raises the question of whether they will remain constant after a change in the structural system, e.g., due to the development of plastic hinge(s) in a critical cross-section(s) or after the development of a kinematic mechanism, or if they will disappear when the structure changes into a sequence of simply supported beams. The paper deals with an investigation of the behavior of continuous post-tensioned beams subjected to an ultimate load with significant secondary effects from prestressing. A total of 6 two-span beams prestressed by tendons with different bonds were tested in a laboratory with a load that changed their structural system into a kinematic mechanism. The internal forces and secondary effects of the prestressing were controlled through measurements of the reactions in all the supports. The results revealed that the secondary effects remained as a permanent part of the action on the experimental beams, even after the development of the kinematic mechanism. The results obtained confirmed that secondary effects should be included in all combinations of actions for verifications of ultimate limit states (ULS).

New Convex and Spherical Structures of Bare Boron Clusters

NASA Astrophysics Data System (ADS)

Boustani, Ihsan

1997-10-01

New stable structures of bare boron clusters can easily be obtained and constructed with the help of an "Aufbau Principle" suggested by a systematicab initioHF-SCF and direct CI study. It is concluded that boron cluster formation can be established by elemental units of pentagonal and hexagonal pyramids. New convex and small spherical clusters different from the classical known forms of boron crystal structures are obtained by a combination of both basic units. Convex structures simulate boron surfaces which can be considered as segments of open or closed spheres. Both convex clusters B16and B46have energies close to those of their conjugate quasi-planar clusters, which are relatively stable and can be considered to act as a calibration mark. The closed spherical clusters B12, B22, B32, and B42are less stable than the corresponding conjugated quasi-planar structures. As a consequence, highly stable spherical boron clusters can systematically be predicted when their conjugate quasi-planar clusters are determined and energies are compared.

Materials and structures

NASA Astrophysics Data System (ADS)

Saito, Theodore T.; Langenbeck, Sharon L.; Al-Jamily, Ghanim; Arnold, Joe; Barbee, Troy; Coulter, Dan; Dolgin, Ben; Fichter, Buck; George, Patricia; Gorenstein, Paul

1992-08-01

Materials and structures technology covers a wide range of technical areas. Some of the most pertinent issues for the Astrotech 21 missions include dimensionally stable structural materials, advanced composites, dielectric coatings, optical metallic coatings for low scattered light applications, low scattered light surfaces, deployable and inflatable structures (including optical), support structures in 0-g and 1-g environments, cryogenic optics, optical blacks, contamination hardened surfaces, radiation hardened glasses and crystals, mono-metallic telescopes and instruments, and materials characterization. Some specific examples include low coefficients of thermal expansion (CTE) structures (0.01 ppm/K), lightweight thermally stable mirror materials, thermally stable optical assemblies, high reliability/accuracy (1 micron) deployable structures, and characterization of nanometer level behavior of materials/structures for interferometry concepts. Large filled-aperture concepts will require materials with CTE's of 10(exp 9) at 80 K, anti-contamination coatings, deployable and erectable structures, composite materials with CTE's less than 0.01 ppm/K and thermal hysteresis, 0.001 ppm/K. Gravitational detection systems such as LAGOS will require rigid/deployable structures, dimensionally stable components, lightweight materials with low conductivity, and high stability optics. The Materials and Structures panel addressed these issues and the relevance of the Astrotech 21 mission requirements by dividing materials and structures technology into five categories. These categories, the necessary development, and applicable mission/program development phasing are summarized. For each of these areas, technology assessments were made and development plans were defined.

Lithium-ion batteries with intrinsic pulse overcharge protection

DOEpatents

Chen, Zonghai; Amine, Khalil

2013-02-05

The present invention relates in general to the field of lithium rechargeable batteries, and more particularly relates to the positive electrode design of lithium-ion batteries with improved high-rate pulse overcharge protection. Thus the present invention provides electrochemical devices containing a cathode comprising at least one primary positive material and at least one secondary positive material; an anode; and a non-aqueous electrolyte comprising a redox shuttle additive; wherein the redox potential of the redox shuttle additive is greater than the redox potential of the primary positive material; the redox potential of the redox shuttle additive is lower than the redox potential of the secondary positive material; and the redox shuttle additive is stable at least up to the redox potential of the secondary positive material.

[Changes in the secondary and tertiary structure of serum albumin in interactions with ligands of various structures].

PubMed

Trinus, F P; Braver-Chernobul'skaia, B S; Luĭk, A I; Boldeskul, A E; Velichko, A N

1984-01-01

High affinity interactions between blood serum albumin and five substances of various chemical structure, exhibiting distinct physiological activity, were accompanied by alterations in the protein tertiary structure, while the albumin secondary structure was involved in conformational transformation after less effective affinity binding.

Gender Stereotypes and Gendered Vocational Aspirations among Swiss Secondary School Students

ERIC Educational Resources Information Center

Hadjar, Andreas; Aeschlimann, Belinda

2015-01-01

Background: Horizontal gender inequalities appear to be rather stable, with girls more often choosing "female" service professions, and boys choosing career paths related to science, technology, engineering or Mathematics. Purpose: Non-egalitarian patriarchal gender-role orientations and gender associations (perceived femininity) of the…

Energetic costs and implications of the intake of plant secondary metabolites on digestive and renal morphology in two austral passerines.

PubMed

Barceló, Gonzalo; Ríos, Juan Manuel; Maldonado, Karin; Sabat, Pablo

2016-07-01

Seed-eating birds have a diet of high nutritional value; however, they must cope with plant secondary metabolites (PSM). We postulated that the detoxification capacity of birds is associated with a metabolic cost, given that the organs responsible for detoxification significantly contribute to energetic metabolism. We used an experimental approach to assess the effects of phenol-enriched diets on two passerines with different feeding habits: the omnivorous rufous-collared sparrow (Zonotrichia capensis) and the granivorous common diuca-finch (Diuca diuca). The birds were fed with one of three diets: control diet, supplemented with tannic acid, or supplemented with Opuntia ficus-indica phenolic extract (a common food of the sparrow but not the finch). After 5 weeks of exposure to the diets, we measured basal metabolic rates (BMR), energy intake, glucuronic acid output and digestive and kidney structure. In both species, detoxification capacity expressed as glucuronic acid output was higher in individuals consuming phenol-enriched diets compared to the control diet. However, whereas sparrows increase energy intake and intestinal mass when feeding on phenol-enriched diets, finches had lower intestinal mass and energy intake remains stable. Furthermore, sparrows had higher BMR on phenol-enriched diets compared to the control group, whereas in the finches BMR remains unchanged. Interspecific differences in response to phenols intake may be determined by the dietary habits of these species. While both species can feed on moderate phenolic diets for 5 weeks, energy costs may differ due to different responses in food intake and organ structure to counteract the effects of PSM intake.

Residue-residue contacts: application to analysis of secondary structure interactions.

PubMed

Potapov, Vladimir; Edelman, Marvin; Sobolev, Vladimir

2013-01-01

Protein structures and their complexes are formed and stabilized by interactions, both inside and outside of the protein. Analysis of such interactions helps in understanding different levels of structures (secondary, super-secondary, and oligomeric states). It can also assist molecular biologists in understanding structural consequences of modifying proteins and/or ligands. In this chapter, our definition of atom-atom and residue-residue contacts is described and applied to analysis of protein-protein interactions in dimeric β-sandwich proteins.

Rotational spectra of tetracyclic quinolizidine alkaloids: does a water molecule flip sparteine?

PubMed

Lesarri, Alberto; Pinacho, Ruth; Enríquez, Lourdes; Rubio, José E; Jaraíz, Martín; Abad, José L; Gigosos, Marco A

2017-07-21

Sparteine is a quinolizidine alkaloid used as a chiral auxiliary in asymmetric synthesis. We examine whether hydration by a single molecule can flip sparteine from the most stable trans conformation to the bidentate cis arrangement observed in catalytic complexation to a metal center. Sparteine and the sparteine-water dimer were generated in a supersonic jet expansion with H 2 16 O and H 2 18 O, and characterized by broadband chirped-pulse microwave spectroscopy. Even though the bidentate water dimer was predicted with larger binding energy, a single isomer was observed for the monohydrated cluster, with sparteine retaining the trans conformation observed for the free molecule. The absence of the bidentate dimer is attributed to the kinetic control of cluster formation, favoring the pre-expansion most abundant monomer. The structural properties of the O-HN hydrogen bond in the dimer are compared with those of complexes of other secondary and tertiary amines.

β-δ phase transition during dropweight impact on cyclotetramethylene-tetranitroamine

NASA Astrophysics Data System (ADS)

Czerski, H.; Greenaway, M. W.; Proud, W. G.; Field, J. E.

2004-10-01

The secondary explosive cyclotetramethylene-tetranitroamine (HMX) exists in a variety of crystal structures; the most widely used being the β-phase which is stable at room temperature and pressure. On heating, a more impact sensitive form (δ phase) is produced. The nonlinear optical technique of second harmonic generation (SHG) can be used as a probe of phase since δ-phase HMX generates a second harmonic at 532nm when 1064nm laser light is incident upon it. We present high-speed photography of SHG in HMX samples during dropweight impact and show that this technique can provide good spatial information and time resolution. We find evidence for small areas of δ-phase HMX appearing in the period from 13μs before ignition to 10μs afterwards, demonstrating that the heating on impact is sufficient to overcome the loading conditions and cause the phase change.

Preparing and Restoring Composite Resin Restorations. The Advantage of High Magnification Loupes or the Dental Surgical Operating Microscope.

PubMed

Mamoun, John

2015-01-01

Use of magnification, such as 6x to 8x binocular surgical loupes or the surgical operating microscope, combined with co-axial illumination, may facilitate the creation of stable composite resin restorations that are less likely to develop caries, cracks or margin stains over years of service. Microscopes facilitate observation of clinically relevant microscopic visual details, such as microscopic amounts of demineralization or caries at preparation margins; microscopic areas of soft, decayed tooth structure; microscopic amounts of moisture contamination of the preparation during bonding; or microscopic marginal gaps in the composite. Preventing microscope-level errors in composite fabrication can result in a composite restoration that, at initial placement, appears perfect when viewed under 6x to 8x magnification and which also is free of secondary caries, marginal staining or cracks at multi-year follow-up visits.

A study to investigate the chemical stability of gallium phosphate oxide/gallium arsenide phosphide

NASA Technical Reports Server (NTRS)

Kuhlman, G. J.

1979-01-01

The elemental composition with depth into the oxide films was examined using secondary ion mass spectrometry. Results indicate that the layers are arsenic-deficient through the bulk of the oxide and arsenic-rich near both the oxide surface and the oxide-semiconductor interface region. Phosphorus is incorporated into the oxide in an approximately uniform manner. The MIS capacitor structures exhibited deep-depletion characteristics and hysteresis indicative of electron trapping at the oxide-semiconductor interface. Post-oxidation annealing of the films in argon or nitrogen generally results in slightly increased dielectric leakage currents and decreased C-V hysteresis effects, and is associated with arsenic loss at the oxide surface. The results of bias-temperature stress experiments indicate that the major instability effects are due to changes in the electron trapping behavior. No changes were observed in the elemental profiles following electrical stressing, indicating that the grown films are chemically stable under device operating conditions.

Streamwise-Localized Solutions with natural 1-fold symmetry

NASA Astrophysics Data System (ADS)

Altmeyer, Sebastian; Willis, Ashley; Hof, Björn

2014-11-01

It has been proposed in recent years that turbulence is organized around unstable invariant solutions, which provide the building blocks of the chaotic dynamics. In direct numerical simulations of pipe flow we show that when imposing a minimal symmetry constraint (reflection in an axial plane only) the formation of turbulence can indeed be explained by dynamical systems concepts. The hypersurface separating laminar from turbulent motion, the edge of turbulence, is spanned by the stable manifolds of an exact invariant solution, a periodic orbit of a spatially localized structure. The turbulent states themselves (turbulent puffs in this case) are shown to arise in a bifurcation sequence from a related localized solution (the upper branch orbit). The rather complex bifurcation sequence involves secondary Hopf bifurcations, frequency locking and a period doubling cascade until eventually turbulent puffs arise. In addition we report preliminary results of the transition sequence for pipe flow without symmetry constraints.

Research on fast ecological restoration technology of high and steep rocky slope of highway

NASA Astrophysics Data System (ADS)

Qin, Xin

2017-08-01

Along with the development of the western region, the traffic construction in mountainous areas is booming. In the infrastructure, it produced a large number of secondary bare land. Soil erosion is serious. Based on the literature search and analysis of the domestic and international slope ecological restoration technology, this paper proposes a fast and efficient adaptive highway high steep rock slope ecological restoration technology (it has been authorized by the national patent). And it states the systemic structure, working principle and key construction technology. The ecological restoration technique combines the growth characteristics of the vegetation and the characteristics of the rock mass, which not only improves the survival rate of plants, but also stable slope. The results of this study make up for the shortcomings of the existing ecological restoration technology of slope. Compared with the prior art, which have obvious advantages and suitable for the ecological restoration of high steep rock slope.

Re-evaluating reaction rates relevant to nova nucleosynthesis from a nuclear structure perspective

NASA Astrophysics Data System (ADS)

Jenkins, D. G.; Lister, C. J.; Janssens, R. V. F.; Khoo, T. L.; Moore, E. F.; Rehm, K. E.; Seweryniak, D.; Wuosmaa, A. H.; Davinson, T.; Woods, P. J.; Jokinen, A.; Penttila, H.; Martınez-Pinedo, G.; Jose, J.

2006-03-01

Conventionally, reaction rates relevant to nova nucleosynthesis are determined by performing the relevant proton capture reactions directly for stable species, or as has become possible more recently in inverse kinematics using short-lived accelerated radioactive beams with recoil separators. A secondary approach is to compile information on the properties of levels in the Gamow window using transfer reactions. We present a complementary technique where the states of interest are populated in a heavy-ion fusion reaction and their gamma decay studied with a state-of-the-art array of high-purity germanium detectors. The advantages of this approach, including the ability to determine resonance energies with high precision and the possibility of determining spins and parities from gamma-ray angular distributions are discussed. Two specific examples related to the 22Na(p,γ) and 30P(p,γ) reactions are presented.

Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou Fengfeng; Tran Thao; Xu Ying

2008-01-25

Miniature inverted-repeat transposable elements (MITEs) were first identified in plants and exerted extensive proliferations throughout eukaryotic and archaeal genomes. But very few MITEs have been characterized in bacteria. We identified a novel MITE, called Nezha, in cyanobacteria Anabaena variabilis ATCC 29413 and Nostoc sp. PCC 7120. Nezha, like most previously known MITEs in other organisms, is small in size, non-coding, carrying TIR and DR signals, and of potential to form a stable RNA secondary structure, and it tends to insert into A+T-rich regions. Recent transpositions of Nezha were observed in A. variabilis ATCC 29413 and Nostoc sp. PCC 7120, respectively.more » Nezha might have proliferated recently with aid from the transposase encoded by ISNpu3-like elements. A possible horizontal transfer event of Nezha from cyanobacteria to Polaromonas JS666 is also observed.« less

Passivation and electrochemical behavior of 316L stainless steel in chlorinated simulated concrete pore solution

NASA Astrophysics Data System (ADS)

Luo, Hong; Su, Huaizhi; Dong, Chaofang; Li, Xiaogang

2017-04-01

In this paper, the passivation and electrochemical behavior of 316L stainless steel in chlorinated simulated concrete pore solutions at different pH was evaluated by potentiodynamic measurements, electrochemical impedance spectroscopy. The composition of the passive film and surface morphology were investigated by X-ray photoelectron spectroscopy (XPS), secondary ion mass spectrometry (SIMS), and scanning electron microscopy, respectively. The results reveal that metastable pitting susceptibility, stable pitting corrosion, and composition of the passive film are influenced by pH value. After long time immersion, a bilayer structure passive film can be formed in this environment. The appearance of molybdates on the outermost surface layer, further enhancing the stability of the passive film. Moreover, the good pitting corrosion resistance of 316L stainless steel in simulated concrete pore solution without carbonated is mainly due to the presence of high Cr/Fe ratio and molybdates ions within the passive film.

Carbide/nitride grain refined rare earth-iron-boron permanent magnet and method of making

DOEpatents

McCallum, R.W.; Branagan, D.J.

1996-01-23

A method of making a permanent magnet is disclosed wherein (1) a melt is formed having a base alloy composition comprising RE, Fe and/or Co, and B (where RE is one or more rare earth elements) and (2) TR (where TR is a transition metal selected from at least one of Ti, Zr, Hf, V, Nb, Ta, Cr, Mo, W, and Al) and at least one of C and N are provided in the base alloy composition melt in substantially stoichiometric amounts to form a thermodynamically stable compound (e.g. TR carbide, nitride or carbonitride). The melt is rapidly solidified in a manner to form particulates having a substantially amorphous (metallic glass) structure and a dispersion of primary TRC, TRN and/or TRC/N precipitates. The amorphous particulates are heated above the crystallization temperature of the base alloy composition to nucleate and grow a hard magnetic phase to an optimum grain size and to form secondary TRC, TRN and/or TRC/N precipitates dispersed at grain boundaries. The crystallized particulates are consolidated at an elevated temperature to form a shape. During elevated temperature consolidation, the primary and secondary precipitates act to pin the grain boundaries and minimize deleterious grain growth that is harmful to magnetic properties. 33 figs.

On the interplay of point defects and Cd in non-polar ZnCdO films

NASA Astrophysics Data System (ADS)

Zubiaga, A.; Reurings, F.; Tuomisto, F.; Plazaola, F.; García, J. A.; Kuznetsov, A. Yu.; Egger, W.; Zúñiga-Pérez, J.; Muñoz-Sanjosé, V.

2013-01-01

Non-polar ZnCdO films, grown over m- and r-sapphire with a Cd concentration ranging between 0.8% and 5%, have been studied by means of slow positron annihilation spectroscopy (PAS) combined with chemical depth profiling by secondary ion mass spectroscopy and Rutherford back-scattering. Vacancy clusters and Zn vacancies with concentrations up to 1017 cm-3 and 1018 cm-3, respectively, have been measured inside the films. Secondary ion mass spectroscopy results show that most Cd stays inside the ZnCdO film but the diffused atoms can penetrate up to 1.3 μm inside the ZnO buffer. PAS results give an insight to the structure of the meta-stable ZnCdO above the thermodynamical solubility limit of 2%. A correlation between the concentration of vacancy clusters and Cd has been measured. The concentration of Zn vacancies is one order of magnitude larger than in as-grown non-polar ZnO films and the vacancy cluster are, at least partly, created by the aggregation of smaller Zn vacancy related defects. The Zn vacancy related defects and the vacancy clusters accumulate around the Cd atoms as a way to release the strain induced by the substitutional CdZn in the ZnO crystal.

Carbide/nitride grain refined rare earth-iron-boron permanent magnet and method of making

DOEpatents

McCallum, R. William; Branagan, Daniel J.

1996-01-23

A method of making a permanent magnet wherein 1) a melt is formed having a base alloy composition comprising RE, Fe and/or Co, and B (where RE is one or more rare earth elements) and 2) TR (where TR is a transition metal selected from at least one of Ti, Zr, Hf, V, Nb, Ta, Cr, Mo, W, and Al) and at least one of C and N are provided in the base alloy composition melt in substantially stoichiometric amounts to form a thermodynamically stable compound (e.g. TR carbide, nitride or carbonitride). The melt is rapidly solidified in a manner to form particulates having a substantially amorphous (metallic glass) structure and a dispersion of primary TRC, TRN and/or TRC/N precipitates. The amorphous particulates are heated above the crystallization temperature of the base alloy composition to nucleate and grow a hard magnetic phase to an optimum grain size and to form secondary TRC, TRN and/or TRC/N precipitates dispersed at grain boundaries. The crystallized particulates are consolidated at an elevated temperature to form a shape. During elevated temperature consolidation, the primary and secondary precipitates act to pin the grain boundaries and minimize deleterious grain growth that is harmful to magnetic properties.

Capillary suspensions as beneficial formulation concept for high energy density Li-ion battery electrodes

NASA Astrophysics Data System (ADS)

Bitsch, Boris; Gallasch, Tobias; Schroeder, Melanie; Börner, Markus; Winter, Martin; Willenbacher, Norbert

2016-10-01

We introduce a novel formulation concept to prepare high capacity graphite electrodes for lithium ion batteries. The concept is based on the capillary suspension phenomenon: graphite and conductive agent are dispersed in an aqueous binder solution and the organic solvent octanol is added as immiscible, secondary fluid providing the formation of a sample-spanning network resulting in unique stability and coating properties. No additional processing steps compared to conventional slurry preparation are required. The resulting ultra-thick electrodes comprise mass loadings of about 16.5 mg cm-2, uniform layer thickness, and superior edge contours. The adjustment of mechanical energy input ensures uniform distribution of the conductive agent and sufficient electronic conductivity of the final dry composite electrode. The resulting pore structure is due to the stable network provided by the secondary fluid which evaporates residue-free during drying. Constant current-constant potential (CC-CP) cycling clearly indicates that the corresponding microstructure significantly improves the kinetics of reversible Li+ (de-) intercalation. A double layer electrode combining a conventionally prepared layer coated directly onto the Cu current collector with an upper layer stabilized with octanol was prepared applying wet-on-wet coating. CC-CP cycling data confirms that staged porosity within the electrode cross section results in superior electrochemical performance.

Linear regression techniques for use in the EC tracer method of secondary organic aerosol estimation

NASA Astrophysics Data System (ADS)

Saylor, Rick D.; Edgerton, Eric S.; Hartsell, Benjamin E.

A variety of linear regression techniques and simple slope estimators are evaluated for use in the elemental carbon (EC) tracer method of secondary organic carbon (OC) estimation. Linear regression techniques based on ordinary least squares are not suitable for situations where measurement uncertainties exist in both regressed variables. In the past, regression based on the method of Deming [1943. Statistical Adjustment of Data. Wiley, London] has been the preferred choice for EC tracer method parameter estimation. In agreement with Chu [2005. Stable estimate of primary OC/EC ratios in the EC tracer method. Atmospheric Environment 39, 1383-1392], we find that in the limited case where primary non-combustion OC (OC non-comb) is assumed to be zero, the ratio of averages (ROA) approach provides a stable and reliable estimate of the primary OC-EC ratio, (OC/EC) pri. In contrast with Chu [2005. Stable estimate of primary OC/EC ratios in the EC tracer method. Atmospheric Environment 39, 1383-1392], however, we find that the optimal use of Deming regression (and the more general York et al. [2004. Unified equations for the slope, intercept, and standard errors of the best straight line. American Journal of Physics 72, 367-375] regression) provides excellent results as well. For the more typical case where OC non-comb is allowed to obtain a non-zero value, we find that regression based on the method of York is the preferred choice for EC tracer method parameter estimation. In the York regression technique, detailed information on uncertainties in the measurement of OC and EC is used to improve the linear best fit to the given data. If only limited information is available on the relative uncertainties of OC and EC, then Deming regression should be used. On the other hand, use of ROA in the estimation of secondary OC, and thus the assumption of a zero OC non-comb value, generally leads to an overestimation of the contribution of secondary OC to total measured OC.

Ionic modulation of QPX stability as a nano-switch regulating gene expression in neurons

NASA Astrophysics Data System (ADS)

Baghaee Ravari, Soodeh

G-quadruplexes (G-QPX) have been the subject of intense research due to their unique structural configuration and potential applications, particularly their functionality in biological process as a novel type of nano--switch. They have been found in critical regions of the human genome such as telomeres, promoter regions, and untranslated regions of RNA. About 50% of human DNA in promoters has G-rich regions with the potential to form G-QPX structures. A G-QPX might act mechanistically as an ON/OFF switch, regulating gene expression, meaning that the formation of G-QPX in a single strand of DNA disrupts double stranded DNA, prevents the binding of transcription factors (TF) to their recognition sites, resulting in gene down-regulation. Although there are numerous studies on biological roles of G-QPXs in oncogenes, their potential formation in neuronal cells, in particular upstream of transcription start sites, is poorly investigated. The main focus of this research is to identify stable G-QPXs in the 97bp active promoter region of the choline acetyltransferase (ChAT) gene, the terminal enzyme involved in synthesis of the neurotransmitter acetylcholine, and to clarify ionic modulation of G-QPX nanostructures through the mechanism of neural action potentials. Different bioinformatics analyses (in silico), including the QGRS, quadparser and G4-Calculator programs, have been used to predict stable G-QPX in the active promoter region of the human ChAT gene, located 1000bp upstream from the TATA box. The results of computational studies (using those three different algorithms) led to the identification of three consecutive intramolecular G-QPX structures in the negative strand (ChAT G17-2, ChAT G17, and ChAT G29) and one intramolecular G-QPX structure in the positive strand (ChAT G30). Also, the results suggest the possibility that nearby G-runs in opposed DNA strands with a short distance of each other may be able to form a stable intermolecular G-QPX involving two DNA complementary strands (ds ChAT G21). Formation of G-QPX structures, by blocking the availability of the transcription factor binding site (TFBS) on double stranded DNA, can interfere with transcriptional activation. This suggests that there is competition between TFBS binding to dsDNA and the conversion to high order non-B form secondary structures (G-QPXs) in the active promoter region. TFBS mapping analysis of the active promoter region of the human ChAT gene revealed that it contains multiple consensus AP-2alpha and Sp1 binding sites and consensus sites for other TF, including multiple sites for GR-alpha, Pax-5, p53 and GC box proteins. (Abstract shortened by ProQuest.).

Polarization-dependent two-photon absorption for the determination of protein secondary structure: A theoretical study

NASA Astrophysics Data System (ADS)

Wanapun, Duangporn; Wampler, Ronald D.; Begue, Nathan J.; Simpson, Garth J.

2008-03-01

A new method for sensitive determination of protein secondary structure via multi-photon absorption is considered theoretically. Perturbation theory is developed to describe the polarization-dependent two-photon absorption (TPA) of α-helix and β-sheet protein secondary structures. The exciton coupling interactions responsible for relatively weak electronic circular dichroism in one-photon absorption are predicted to give rise to large changes in the TPA cross-section (>200%) for circular versus linear incident polarizations, defined as CLD. The CLD effect in TPA is electric dipole-allowed, which explains the much greater sensitivity. These predictions suggest TPA should be a viable means of sensitively probing protein secondary structure.

Belongingness in Early Secondary School: Key Factors that Primary and Secondary Schools Need to Consider.

PubMed

Vaz, Sharmila; Falkmer, Marita; Ciccarelli, Marina; Passmore, Anne; Parsons, Richard; Black, Melissa; Cuomo, Belinda; Tan, Tele; Falkmer, Torbjörn

2015-01-01

It is unknown if, and how, students redefine their sense of school belongingness after negotiating the transition to secondary school. The current study used longitudinal data from 266 students with, and without, disabilities who negotiated the transition from 52 primary schools to 152 secondary schools. The study presents the 13 most significant personal student and contextual factors associated with belongingness in the first year of secondary school. Student perception of school belongingness was found to be stable across the transition. No variability in school belongingness due to gender, disability or household-socio-economic status (SES) was noted. Primary school belongingness accounted for 22% of the variability in secondary school belongingness. Several personal student factors (competence, coping skills) and school factors (low-level classroom task-goal orientation), which influenced belongingness in primary school, continued to influence belongingness in secondary school. In secondary school, effort-goal orientation of the student and perception of their school's tolerance to disability were each associated with perception of school belongingness. Family factors did not influence belongingness in secondary school. Findings of the current study highlight the need for primary schools to foster belongingness among their students at an early age, and transfer students' belongingness profiles as part of the hand-over documentation. Most of the factors that influenced school belongingness before and after the transition to secondary are amenable to change.

Belongingness in Early Secondary School: Key Factors that Primary and Secondary Schools Need to Consider

PubMed Central

Vaz, Sharmila; Falkmer, Marita; Ciccarelli, Marina; Passmore, Anne; Parsons, Richard; Black, Melissa; Cuomo, Belinda; Tan, Tele; Falkmer, Torbjörn

2015-01-01

It is unknown if, and how, students redefine their sense of school belongingness after negotiating the transition to secondary school. The current study used longitudinal data from 266 students with, and without, disabilities who negotiated the transition from 52 primary schools to 152 secondary schools. The study presents the 13 most significant personal student and contextual factors associated with belongingness in the first year of secondary school. Student perception of school belongingness was found to be stable across the transition. No variability in school belongingness due to gender, disability or household-socio-economic status (SES) was noted. Primary school belongingness accounted for 22% of the variability in secondary school belongingness. Several personal student factors (competence, coping skills) and school factors (low-level classroom task-goal orientation), which influenced belongingness in primary school, continued to influence belongingness in secondary school. In secondary school, effort-goal orientation of the student and perception of their school’s tolerance to disability were each associated with perception of school belongingness. Family factors did not influence belongingness in secondary school. Findings of the current study highlight the need for primary schools to foster belongingness among their students at an early age, and transfer students’ belongingness profiles as part of the hand-over documentation. Most of the factors that influenced school belongingness before and after the transition to secondary are amenable to change. PMID:26372554

Landuse legacies of old-field succession and soil structure at the Calhoun Criticl Zone Observatory in SC, USA.

NASA Astrophysics Data System (ADS)

Brecheisen, Z. S.; Richter, D. D., Jr.; Callaham, M.; Carrera-Martinez, R.; Heine, P.

2017-12-01

The pre-colonial Southern Piedmont was an incredibly stable CZ with erosion rates between 0.35-3m/Myr on a 4th order interfluve. With soils and saprolite weathered up to 30m in total depth bedrock with multi-million year residence times under continual forest cover prior to widespread agricultural disturbance. With this biogeomorphic stability came time for soil macroporosity and soil structure to be established and maintained by the activities of soil fauna, plant root growth and death, and tree-fall tip-up events serving to continually mix and aerate the soil. Greatly accelerated surficial agricultural erosion (ca. 1750-1930) has fundamentally altered the Calhoun Critical Zone Observatory forest community dynamics aboveground and the soil structure, hydrology, and biogeochemistry belowground. The arrival of the plow to the Southern Piedmont marked the destruction of soil structure, macropore networks, and many of the macroinvertebrate soil engineers. This transformation came via forest clearing, soil tilling, compaction, and wholesale soil erosion, with the region having lost an estimated average of 18cm of soil across the landscape. In the temporal LULC progression from hardwood forests, to cultivated farms, to reforestation, secondary forest soil structure is expected to remain altered compared to the reference hardwood ecosystems. The research presented herein seeks to quantify CZ soil structure regeneration in old-field pine soil profiles' Ksat, aggregation, texture, macro-invertebrates, and direct measurements of topsoil porosity using X-ray computed tomography analysis on 15cm soil cores.

In Vivo Stable Transduction of Humanized Liver Tissue in Chimeric Mice via High-Capacity Adenovirus–Lentivirus Hybrid Vector

PubMed Central

Kataoka, Miho; Tateno, Chise; Yoshizato, Katsutoshi; Kawasaki, Yoshiko; Kimura, Takahiro; Faure-Kumar, Emmanuelle; Palmer, Donna J.; Ng, Philip; Okamura, Haruki; Kasahara, Noriyuki

2010-01-01

Abstract We developed hybrid vectors employing high-capacity adenovirus as a first-stage carrier encoding all the components required for in situ production of a second-stage lentivirus, thereby achieving stable transgene expression in secondary target cells. Such vectors have never previously been tested in normal tissues, because of the scarcity of suitable in vivo systems permissive for second-stage lentivirus assembly. Here we employed a novel murine model in which endogenous liver tissue is extensively reconstituted with engrafted human hepatocytes, and successfully achieved stable transduction by the second-stage lentivirus produced in situ from first-stage adenovirus. This represents the first demonstration of the functionality of adenoviral-lentiviral hybrid vectors in a normal parenchymal organ in vivo. PMID:19725756

In silico ribozyme evolution in a metabolically coupled RNA population.

PubMed

Könnyű, Balázs; Szilágyi, András; Czárán, Tamás

2015-05-27

The RNA World hypothesis offers a plausible bridge from no-life to life on prebiotic Earth, by assuming that RNA, the only known molecule type capable of playing genetic and catalytic roles at the same time, could have been the first evolvable entity on the evolutionary path to the first living cell. We have developed the Metabolically Coupled Replicator System (MCRS), a spatially explicit simulation modelling approach to prebiotic RNA-World evolution on mineral surfaces, in which we incorporate the most important experimental facts and theoretical considerations to comply with recent knowledge on RNA and prebiotic evolution. In this paper the MCRS model framework has been extended in order to investigate the dynamical and evolutionary consequences of adding an important physico-chemical detail, namely explicit replicator structure - nucleotide sequence and 2D folding calculated from thermodynamical criteria - and their possible mutational changes, to the assumptions of a previously less detailed toy model. For each mutable nucleotide sequence the corresponding 2D folded structure with minimum free energy is calculated, which in turn is used to determine the fitness components (degradation rate, replicability and metabolic enzyme activity) of the replicator. We show that the community of such replicators providing the monomer supply for their own replication by evolving metabolic enzyme activities features an improved propensity for stable coexistence and structural adaptation. These evolutionary advantages are due to the emergent uniformity of metabolic replicator fitnesses imposed on the community by local group selection and attained through replicator trait convergence, i.e., the tendency of replicator lengths, ribozyme activities and population sizes to become similar between the coevolving replicator species that are otherwise both structurally and functionally different. In the most general terms it is the surprisingly high extra viability of the metabolic replicator system that the present model adds to the MCRS concept of the origin of life. Surface-bound, metabolically coupled RNA replicators tend to evolve different, enzymatically active sites within thermodynamically stable secondary structures, and the system as a whole evolves towards the robust coexistence of a complete set of such ribozymes driving the metabolism producing monomers for their own replication.

On the Possibility of using Alluminium-Magnesium Alloys with Improved Mechanical Characteristics for Body Elements of Zenit-2S Launch Vehicle Propellant Tanks

NASA Astrophysics Data System (ADS)

Sitalo, V.; Lytvyshko, T.

2002-01-01

Yuzhnoye SDO developed several generations of launch vehicles and spacecraft that are characterized by weight perfection, optimal cost, accuracy of output geometrical characteristics, stable strength characteristics, high tightness. The main structural material of launch vehicles are thermally welded non-strengthened aluminium- magnesium alloys. The aluminium-magnesium alloys in the annealed state have insufficiently high strength characteristics. Considerable increase of yield strength of sheets and plates can be reached by cold working but in this case, plasticity reduces. An effective way to improve strength of aluminium-magnesium alloys is their alloying with scandium. The alloying with scandium leads to modification of the structure of ingots (size reduction of cast grain) and formation of supersaturated solid solutions of scandium and aluminium during crystallization. During subsequent heatings (annealing of the ingots, heating for deformation) the solid solution disintegrates with the formation of disperse particles of Al3Sc type, that cause great strengthening of the alloy. High degree of dispersion and density of distribution in the matrix of secondary Al3Sc particles contribute to the considerable increase of the temperature of recrystallization of deformed intermediate products and to the formation of stable non-recrystallized structure. The alloying of alluminium-magnesium alloys with scandium increases their strength and operational characteristics, preserves their technological and corrosion properties, improves weldability. The alloys can be used within the temperature limits ­196-/+150 0C. The experimental structures of propellant tanks made of alluminium-magnesium alloys with scandium have been manufactured and tested. It was ascertained that the propellant tanks have higher margin of safety during loading with internal pressure and higher stability factor of the shrouds during loading with axial compression force which is caused by higher value of yield strength. The analysis of the performed work showed good prospects of using the alluminium-magnesium alloys with increased mechanical characteristics for making body elements of propellant tanks of the Zenit -2S launch vehicles. The use of these alloys can give the increase of structural strength by 20-30% and considerable increase of payload weight.

DNA secondary structures: stability and function of G-quadruplex structures

PubMed Central

Bochman, Matthew L.; Paeschke, Katrin; Zakian, Virginia A.

2013-01-01

In addition to the canonical double helix, DNA can fold into various other inter- and intramolecular secondary structures. Although many such structures were long thought to be in vitro artefacts, bioinformatics demonstrates that DNA sequences capable of forming these structures are conserved throughout evolution, suggesting the existence of non-B-form DNA in vivo. In addition, genes whose products promote formation or resolution of these structures are found in diverse organisms, and a growing body of work suggests that the resolution of DNA secondary structures is critical for genome integrity. This Review focuses on emerging evidence relating to the characteristics of G-quadruplex structures and the possible influence of such structures on genomic stability and cellular processes, such as transcription. PMID:23032257

Bioinformatics approaches for structural and functional analysis of proteins in secondary metabolism in Withania somnifera.

PubMed

Sanchita; Singh, Swati; Sharma, Ashok

2014-11-01

Withania somnifera (Ashwagandha) is an affluent storehouse of large number of pharmacologically active secondary metabolites known as withanolides. These secondary metabolites are produced by withanolide biosynthetic pathway. Very less information is available on structural and functional aspects of enzymes involved in withanolides biosynthetic pathways of Withiana somnifera. We therefore performed a bioinformatics analysis to look at functional and structural properties of these important enzymes. The pathway enzymes taken for this study were 3-Hydroxy-3-methylglutaryl coenzyme A reductase, 1-Deoxy-D-xylulose-5-phosphate synthase, 1-Deoxy-D-xylulose-5-phosphate reductase, farnesyl pyrophosphate synthase, squalene synthase, squalene epoxidase, and cycloartenol synthase. The prediction of secondary structure was performed for basic structural information. Three-dimensional structures for these enzymes were predicted. The physico-chemical properties such as pI, AI, GRAVY and instability index were also studied. The current information will provide a platform to know the structural attributes responsible for the function of these protein until experimental structures become available.

DSSPcont: continuous secondary structure assignments for proteins

PubMed Central

Carter, Phil; Andersen, Claus A. F.; Rost, Burkhard

2003-01-01

The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.columbia.edu/services/DSSPcont) introduces a continuous assignment of secondary structure that replaces ‘static’ by ‘dynamic’ states. Technically, the continuum results from calculating weighted averages over 10 discrete DSSP assignments with different hydrogen bond thresholds. A DSSPcont assignment for a particular residue is a percentage likelihood of eight secondary structure states, derived from a weighted average of the ten DSSP assignments. The continuous assignments have two important features: (i) they reflect the structural variations due to thermal fluctuations as detected by NMR spectroscopy; and (ii) they reproduce the structural variation between many NMR models from one single model. Therefore, functionally important variation can be extracted from a single X-ray structure using the continuous assignment procedure. PMID:12824310

Tracking Radionuclide Fractionation in the First Atomic Explosion Using Stable Elements

DOE PAGES

Bonamici, Chloë E.; Hervig, Richard L.; Kinman, William S.

2017-08-25

Compositional analysis of postdetonation fallout is a tool for forensic identification of nuclear devices. However, the relationship between device composition and fallout composition is difficult to interpret because of the complex combination of physical mixing, nuclear reactions, and chemical fractionations that occur in the chaotic nuclear fireball. By using a combination of in situ microanalytical techniques (electron microprobe analysis and secondary ion mass spectrometry), we show that some heavy stable elements (Rb, Sr, Zr, Ba, Cs, Ba, La, Ce, Nd, Sm, Dy, Lu, U, Th) in glassy fallout from the first nuclear test, Trinity, are reliable chemical proxies for radionuclidesmore » generated during the explosion. Stable-element proxies show that radionuclides from the Trinity device were chemically, but not isotopically, fractionated by condensation. Moreover, stable-element proxies delineate chemical fractionation trends that can be used to connect present-day fallout composition to past fireball composition. Stable-element proxies therefore offer a novel approach for elucidating the phenomenology of the nuclear fireball as it relates to the formation of debris and the fixation of device materials within debris.« less

Tracking Radionuclide Fractionation in the First Atomic Explosion Using Stable Elements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bonamici, Chloë E.; Hervig, Richard L.; Kinman, William S.

Compositional analysis of postdetonation fallout is a tool for forensic identification of nuclear devices. However, the relationship between device composition and fallout composition is difficult to interpret because of the complex combination of physical mixing, nuclear reactions, and chemical fractionations that occur in the chaotic nuclear fireball. By using a combination of in situ microanalytical techniques (electron microprobe analysis and secondary ion mass spectrometry), we show that some heavy stable elements (Rb, Sr, Zr, Ba, Cs, Ba, La, Ce, Nd, Sm, Dy, Lu, U, Th) in glassy fallout from the first nuclear test, Trinity, are reliable chemical proxies for radionuclidesmore » generated during the explosion. Stable-element proxies show that radionuclides from the Trinity device were chemically, but not isotopically, fractionated by condensation. Moreover, stable-element proxies delineate chemical fractionation trends that can be used to connect present-day fallout composition to past fireball composition. Stable-element proxies therefore offer a novel approach for elucidating the phenomenology of the nuclear fireball as it relates to the formation of debris and the fixation of device materials within debris.« less

Tracking Radionuclide Fractionation in the First Atomic Explosion Using Stable Elements.

PubMed

Bonamici, Chloë E; Hervig, Richard L; Kinman, William S

2017-09-19

Compositional analysis of postdetonation fallout is a tool for forensic identification of nuclear devices. However, the relationship between device composition and fallout composition is difficult to interpret because of the complex combination of physical mixing, nuclear reactions, and chemical fractionations that occur in the chaotic nuclear fireball. Using a combination of in situ microanalytical techniques (electron microprobe analysis and secondary ion mass spectrometry), we show that some heavy stable elements (Rb, Sr, Zr, Ba, Cs, Ba, La, Ce, Nd, Sm, Dy, Lu, U, Th) in glassy fallout from the first nuclear test, Trinity, are reliable chemical proxies for radionuclides generated during the explosion. Stable-element proxies show that radionuclides from the Trinity device were chemically, but not isotopically, fractionated by condensation. Furthermore, stable-element proxies delineate chemical fractionation trends that can be used to connect present-day fallout composition to past fireball composition. Stable-element proxies therefore offer a novel approach for elucidating the phenomenology of the nuclear fireball as it relates to the formation of debris and the fixation of device materials within debris.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.

PubMed

Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

2008-03-31

With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

PubMed Central

Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

2008-01-01

Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules. PMID:18373878

Structural, stability, and vibrational properties of BinPm clusters

NASA Astrophysics Data System (ADS)

Shen, Wanting; Han, Lihong; Liang, Dan; Zhang, Chunfang; Ruge, Quhe; Wang, Shumin; Lu, Pengfei

2018-04-01

An in-depth investigation is performed on stability mechanisms, electronic and optical properties of III-V semiconductor vapor phases clusters. First principles electronic structure calculations of CAM-B3LYP are performed on neutral BinPm (n + m ≤ 14) clusters. The geometrical evolution of all stable structures remains amorphous as the clusters size increases. Binding energies (BEs), energy gains and highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO) gaps confirm that all four-atom structures of BinPm clusters have more stable optical properties. Orbitals composition and vibrational spectra of stable clusters are analyzed. Our calculations will contribute to the study of diluted bismuth alloys and compounds.

Experimental investigation of broadband energy harvesting of a bi-stable composite piezoelectric plate

NASA Astrophysics Data System (ADS)

Pan, Diankun; Ma, Benbiao; Dai, Fuhong

2017-03-01

In this work, a bi-stable vibration energy harvester is presented to scavenge energy from ambient vibrations over a wide frequency range. This bi-stable harvester consists of a bi-stable hybrid composite plate as host structure and several pieces of piezoelectric ceramics. Three linear harvesters with the same geometry were employed as the control samples to illustrate the advantages of this bi-stable harvester. The voltage-frequency responses were measured with different g-level excitations, and the output powers across various resistances were measured at different frequencies and accelerations. Unlike the linear harvesters which are effective only near their natural frequencies, the obvious nonlinearities of this bi-stable harvester broaden its working bandwidth. Additionally, the characteristics of this bi-stable host structure contribute to the output power. Under the same condition, when this bi-stable harvester is under cross-well oscillation pattern the maximum output powers are several times higher than those of the linear harvesters. The measured highest output power of this bi-stable harvester is 36.2 mW with 38 Hz frequency and 5g acceleration (g = 9.8 m s-2).

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

PubMed

Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

2007-02-15

Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures. We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs. The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/. Supplementary data are available at Bioinformatics online.

Secondary flow vortical structures in a 180∘ elastic curved vessel with torsion under steady and pulsatile inflow conditions

NASA Astrophysics Data System (ADS)

Najjari, Mohammad Reza; Plesniak, Michael W.

2018-01-01

Secondary flow structures in a 180∘ curved pipe model of an artery are studied using particle image velocimetry. Both steady and pulsatile inflow conditions are investigated. In planar curved pipes with steady flow, multiple (two, four, six) vortices are detected. For pulsatile flow, various pairs of vortices, i.e., Dean, deformed-Dean, Lyne-type, and split-Dean, are present in the cross section of the pipe at 90∘ into the bend. The effects of nonplanar curvature (torsion) and vessel dilatation on these vortical structures are studied. Torsion distorts the symmetric secondary flows (which exist in planar curvatures) and can result in formation of more complex vortical structures. For example, the split-Dean and Lyne-type vortices with same rotation direction originating from opposite sides of the cross section tend to merge together in pulsatile flow. The vortical structures in elastic vessels with dilatation (0.61%-3.23%) are also investigated and the results are compared with rigid model results. It was found that the secondary flow structures in rigid and elastic models are similar, and hence the local compliance of the vessel does not affect the morphology of secondary flow structures.

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures

PubMed Central

Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

2009-01-01

The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

Organizing Schools into Small Units: Alternatives to Homogeneous Grouping.

ERIC Educational Resources Information Center

Oxley, Diana

1994-01-01

Large school size adversely affects attendance, school climate, student involvement. Dividing large schools into small units creates a learning and teaching context that is more stable, intimate, supportive, interdisciplinary. Kohn-Holweide, a comprehensive German secondary school, groups all students at a given grade level with the same teachers…

Students' Perceptions of Agriscience When Taught through Inquiry-Based Instruction

ERIC Educational Resources Information Center

Thoron, Andrew C.; Burleson, Sarah E.

2014-01-01

United States science scores have remained stable over the past 12 years, and as a result secondary school students have been deemed less proficient than international peers. Additionally, there has been increased pressure for accountability from both teachers and students. This highly competitive performance-based classroom environment has…

Perceived Parental Behavioral Control and Psychological Control in Chinese Adolescents in Hong Kong: A Replication

ERIC Educational Resources Information Center

Shek, Daniel T. L.

2007-01-01

Perceived paternal and maternal behavioral control (including dimensions of parental knowledge, expectation, monitoring, discipline and demandingness) and psychological control in 2,748 Chinese Secondary 2 students were examined. Results showed that two stable dimensions (paternal and maternal behavioral control) were extracted from the parental…

Oxalates as Activating Groups for Alcohols in Visible Light Photoredox Catalysis: Formation of Quaternary Centers by Redox-Neutral Fragment Coupling.

PubMed

Nawrat, Christopher C; Jamison, Christopher R; Slutskyy, Yuriy; MacMillan, David W C; Overman, Larry E

2015-09-09

Alkyl oxalates are new bench-stable alcohol-activating groups for radical generation under visible light photoredox conditions. Using these precursors, the first net redox-neutral coupling of tertiary and secondary alcohols with electron-deficient alkenes is achieved.

Ensemble-based prediction of RNA secondary structures.

PubMed

Aghaeepour, Nima; Hoos, Holger H

2013-04-24

Accurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile approaches, and improved methods for this task have received much attention over the past five years. Despite the impressive progress that as been achieved in this area, existing evaluations of the prediction accuracy achieved by various algorithms do not provide a comprehensive, statistically sound assessment. Furthermore, while there is increasing evidence that no prediction algorithm consistently outperforms all others, no work has been done to exploit the complementary strengths of multiple approaches. In this work, we present two contributions to the area of RNA secondary structure prediction. Firstly, we use state-of-the-art, resampling-based statistical methods together with a previously published and increasingly widely used dataset of high-quality RNA structures to conduct a comprehensive evaluation of existing RNA secondary structure prediction procedures. The results from this evaluation clarify the performance relationship between ten well-known existing energy-based pseudoknot-free RNA secondary structure prediction methods and clearly demonstrate the progress that has been achieved in recent years. Secondly, we introduce AveRNA, a generic and powerful method for combining a set of existing secondary structure prediction procedures into an ensemble-based method that achieves significantly higher prediction accuracies than obtained from any of its component procedures. Our new, ensemble-based method, AveRNA, improves the state of the art for energy-based, pseudoknot-free RNA secondary structure prediction by exploiting the complementary strengths of multiple existing prediction procedures, as demonstrated using a state-of-the-art statistical resampling approach. In addition, AveRNA allows an intuitive and effective control of the trade-off between false negative and false positive base pair predictions. Finally, AveRNA can make use of arbitrary sets of secondary structure prediction procedures and can therefore be used to leverage improvements in prediction accuracy offered by algorithms and energy models developed in the future. Our data, MATLAB software and a web-based version of AveRNA are publicly available at http://www.cs.ubc.ca/labs/beta/Software/AveRNA.

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.

PubMed

Li, Ying; Shi, Xiaohu; Liang, Yanchun; Xie, Juan; Zhang, Yu; Ma, Qin

2017-01-21

RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms. An alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package. RNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA comparison tools, RNApdist and RNAdistance, showcased that RNA-TVcurve can efficiently capture subtle relationships among RNAs for mutation detection and non-coding RNA classification. All the relevant results were shown in an intuitive graphical manner, and can be freely downloaded from this server. RNA-TVcurve, along with test examples and detailed documents, are available at: http://ml.jlu.edu.cn/tvcurve/ .

Dynamics of leaf litter humidity, depth and quantity: two restoration strategies failed to mimic ground microhabitat conditions of a low montane and premontane forest in Costa Rica.

PubMed

Barrientos, Zaidett

2012-09-01

Little is known about how restoration strategies affect aspects like leaf litter's quantity, depth and humidity. I analyzed leaf litter's quantity, depth and humidity yearly patterns in a primary tropical lower montane wet forest and two restored areas: a 15 year old secondary forest (unassisted restoration) and a 40 year old Cupressus lusitanica plantation (natural understory). The three habitats are located in the Rio Macho Forest Reserve, Costa Rica. Twenty litter samples were taken every three months (April 2009-April 2010) in each habitat; humidity was measured in 439g samples (average), depth and quantity were measured in five points inside 50x50cm plots. None of the restoration strategies reproduced the primary forest leaf litter humidity, depth and quantity yearly patterns. Primary forest leaf litter humidity was higher and more stable (mean=73.2), followed by secondary forest (mean=63.3) and cypress plantation (mean=52.9) (Kruskall-Wallis=77.93, n=232, p=0.00). In the primary (Kruskal-Wallis=31.63, n=78, p<0.001) and secondary (Kruskal-Wallis=11.79, n=75, p=0.008) forest litter accumulation was higher during April due to strong winds. In the primary forest (Kruskal-wallis=21.83, n=78, p<0.001) and the cypress plantation (Kruskal-wallis=39.99, n=80, p<0.001) leaf litter depth was shallow in October because heavy rains compacted it. Depth patterns were different from quantity patterns and described the leaf litter's structure in different ecosystems though the year. September 01.

Childhood Family Structure and Intergenerational Income Mobility in the United States.

PubMed

Bloome, Deirdre

2017-04-01

The declining prevalence of two-parent families helped increase income inequality over recent decades. Does family structure also condition how economic (dis)advantages pass from parents to children? If so, shifts in the organization of family life may contribute to enduring inequality between groups defined by childhood family structure. Using National Longitudinal Survey of Youth data, I combine parametric and nonparametric methods to reveal how family structure moderates intergenerational income mobility in the United States. I find that individuals raised outside stable two-parent homes are much more mobile than individuals from stable two-parent families. Mobility increases with the number of family transitions but does not vary with children's time spent coresiding with both parents or stepparents conditional on a transition. However, this mobility indicates insecurity, not opportunity. Difficulties maintaining middle-class incomes create downward mobility among people raised outside stable two-parent homes. Regardless of parental income, these people are relatively likely to become low-income adults, reflecting a new form of perverse equality. People raised outside stable two-parent families are also less likely to become high-income adults than people from stable two-parent homes. Mobility differences account for about one-quarter of family-structure inequalities in income at the bottom of the income distribution and more than one-third of these inequalities at the top.

Native aggregation as a cause of origin of temporary cellular structures needed for all forms of cellular activity, signaling and transformations.

PubMed

Matveev, Vladimir V

2010-06-09

According to the hypothesis explored in this paper, native aggregation is genetically controlled (programmed) reversible aggregation that occurs when interacting proteins form new temporary structures through highly specific interactions. It is assumed that Anfinsen's dogma may be extended to protein aggregation: composition and amino acid sequence determine not only the secondary and tertiary structure of single protein, but also the structure of protein aggregates (associates). Cell function is considered as a transition between two states (two states model), the resting state and state of activity (this applies to the cell as a whole and to its individual structures). In the resting state, the key proteins are found in the following inactive forms: natively unfolded and globular. When the cell is activated, secondary structures appear in natively unfolded proteins (including unfolded regions in other proteins), and globular proteins begin to melt and their secondary structures become available for interaction with the secondary structures of other proteins. These temporary secondary structures provide a means for highly specific interactions between proteins. As a result, native aggregation creates temporary structures necessary for cell activity."One of the principal objects of theoretical research in any department of knowledge is to find the point of view from which the subject appears in its greatest simplicity."Josiah Willard Gibbs (1839-1903).

On stability of the structure of implicit personality theory over situations.

PubMed

Hochwälder, J

1995-12-01

In the present study, the following (hitherto unaddressed) question was posed: "Is the structure of implicit personality theory stable over situations?". In order to answer this question, correlation coefficients were computed between different aspects of two trait-structures obtained under different situational conditions. The results seem to indicate that the structure of IPT is stable over situations. The results are discussed in the light of some methodological considerations.

Effect of Secondary Cooling Conditions on Solidification Structure and Central Macrosegregation in Continuously Cast High-Carbon Rectangular Billet

NASA Astrophysics Data System (ADS)

Zeng, Jie; Chen, Weiqing

2015-10-01

Solidification structures of high carbon rectangular billet with a size of 180 mm × 240 mm in different secondary cooling conditions were simulated using cellular automaton-finite element (CAFE) coupling model. The adequacy of the model was compared with the simulated and the actual macrostructures of 82B steel. Effects of the secondary cooling water intensity on solidification structures including the equiaxed grain ratio and the equiaxed grain compactness were discussed. It was shown that the equiaxed grain ratio and the equiaxed grain compactness changed in the opposite direction at different secondary cooling water intensities. Increasing the secondary cooling water intensity from 0.9 or 1.1 to 1.3 L/kg could improve the equiaxed grain compactness and decrease the equiaxed grain ratio. Besides, the industrial test was conducted to investigate the effect of different secondary cooling water intensities on the center carbon macrosegregation of 82B steel. The optimum secondary cooling water intensity was 0.9 L/kg, while the center carbon segregation degree was 1.10. The relationship between solidification structure and center carbon segregation was discussed based on the simulation results and the industrial test.

Perceptual Learning Immediately Yields New Stable Motor Coordination

ERIC Educational Resources Information Center

Wilson, Andrew D.; Snapp-Childs, Winona; Bingham, Geoffrey P.

2010-01-01

Coordinated rhythmic movement is specifically structured in humans. Movement at 0[degrees] mean relative phase is maximally stable, 180[degrees] is less stable, and other coordinations can, but must, be learned. Variations in perceptual ability play a key role in determining the observed stabilities so we investigated whether stable movements can…

Stable Orbits in the Didymos Binary Asteroid System - Useful Platforms for Exploration

NASA Astrophysics Data System (ADS)

Damme, Friedrich; Hussmann, Hauke; Wickhusen, Kai; Enrico, Mai; Oberst, Jürgen

2016-04-01

We have analyzed particle motion in binary asteroid systems to search for stable orbits. In particular, we studied the motion of particles near the asteroid 1996 GT (Didymos), proposed as a target for the AIDA mission. The combined gravity fields of the odd-shaped rotating objects moving about each other are complex. In addition, orbiting spacecraft or dust particles are affected by radiation pressure, possibly exceeding the faint gravitational forces. For the numerical integrations, we adopt parameters for size, shape, and rotation from telescopic observations. To simulate the effect of radiation pressure during a spacecraft mission, we apply a spacecraft wing-box shape model. Integrations were carried out beginning in near-circular orbits over 11 days, during which the motion of the particles were examined. Most orbits are unstable with particles escaping quickly or colliding with the asteroid bodies. However, with carefully chosen initial positions, we found stable motion (in the orbiting plane of the secondary) associated with the Lagrangian points (L4 and L5), in addition to horseshoe orbits, where particles move from one of the Lagrangian point to the other. Finally, we examined orbits in 1:2 resonances with the motion of the orbital period of the secondary. Stable conditions depend strongly on season caused by the inclination of the mutual orbit plane with respect to Didymos solar orbit. At larger distance from the asteroid pair, we find the well-known terminator orbits where gravitational attraction is balanced against radiation pressure. Stable orbits and long motion arcs are useful for long tracking runs by radio or Laser instruments and are well-suited for modelling of the ephemerides of the asteroid pair and gravity field mapping. Furthermore, these orbits may be useful as observing posts or as platforms for approach. These orbits may also represent traps for dust particles, an opportunity for dust collection - or possibly a hazard to spacecraft operation.

A new concept for active bistable twisting structures

NASA Astrophysics Data System (ADS)

Schultz, Marc R.

2005-05-01

A novel type of morphing structure capable of a large change in shape with a small energy input is discussed in this paper. The considered structures consist of two curved shells that are joined in a specific manner to form a bistable airfoil-like structure. The two stable shapes have a difference in axial twist, and the structure may be transformed between the stable shapes by a simple snap-through action. The benefit of a bistable structure of this type is that, if the stable shapes are operational shapes, power is needed only to transform the structure from one shape to another. The discussed structures could be used in aerodynamic applications such as morphing wings, or as aerodynamic control surfaces. The investigation discussed in this paper considers both experiment and finite-element analysis. Several graphite-epoxy composite and one steel device were created as proof-of-concept models. To demonstrate active control of these structures, piezocomposite actuators were applied to one of the composite structures and used to transform the structure between stable shapes. The analysis was used to compare the predicted shapes with the experimental shapes, and to study how changes to the geometric input values affected the shape and operational characteristics of the structures. The predicted shapes showed excellent agreement with the experimental shapes, and the results of the parametric study suggest that the shapes and the snap-through characteristics can be easily tailored to meet specific needs.

Variation analysis of the severe acute respiratory syndrome coronavirus putative non-structural protein 2 gene and construction of three-dimensional model.

PubMed

Lu, Jia-hai; Zhang, Ding-mei; Wang, Guo-ling; Guo, Zhong-min; Zhang, Chuan-hai; Tan, Bing-yan; Ouyang, Li-ping; Lin, Li; Liu, Yi-min; Chen, Wei-qing; Ling, Wen-hua; Yu, Xin-bing; Zhong, Nan-shan

2005-05-05

The rapid transmission and high mortality rate made severe acute respiratory syndrome (SARS) a global threat for which no efficacious therapy is available now. Without sufficient knowledge about the SARS coronavirus (SARS-CoV), it is impossible to define the candidate for the anti-SARS targets. The putative non-structural protein 2 (nsp2) (3CL(pro), following the nomenclature by Gao et al, also known as nsp5 in Snidjer et al) of SARS-CoV plays an important role in viral transcription and replication, and is an attractive target for anti-SARS drug development, so we carried on this study to have an insight into putative polymerase nsp2 of SARS-CoV Guangdong (GD) strain. The SARS-CoV strain was isolated from a SARS patient in Guangdong, China, and cultured in Vero E6 cells. The nsp2 gene was amplified by reverse transcription-polymerase chain reaction (RT-PCR) and cloned into eukaryotic expression vector pCI-neo (pCI-neo/nsp2). Then the recombinant eukaryotic expression vector pCI-neo/nsp2 was transfected into COS-7 cells using lipofectin reagent to express the nsp2 protein. The expressive protein of SARS-CoV nsp2 was analyzed by 7% sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE). The nucleotide sequence and protein sequence of GD nsp2 were compared with that of other SARS-CoV strains by nucleotide-nucleotide basic local alignment search tool (BLASTN) and protein-protein basic local alignment search tool (BLASTP) to investigate its variance trend during the transmission. The secondary structure of GD strain and that of other strains were predicted by Garnier-Osguthorpe-Robson (GOR) Secondary Structure Prediction. Three-dimensional-PSSM Protein Fold Recognition (Threading) Server was employed to construct the three-dimensional model of the nsp2 protein. The putative polymerase nsp2 gene of GD strain was amplified by RT-PCR. The eukaryotic expression vector (pCI-neo/nsp2) was constructed and expressed the protein in COS-7 cells successfully. The result of sequencing and sequence comparison with other SARS-CoV strains showed that nsp2 gene was relatively conservative during the transmission and total five base sites mutated in about 100 strains investigated, three of which in the early and middle phases caused synonymous mutation, and another two base sites variation in the late phase resulted in the amino acid substitutions and secondary structure changes. The three-dimensional structure of the nsp2 protein was successfully constructed. The results suggest that polymerase nsp2 is relatively stable during the phase of epidemic. The amino acid and secondary structure change may be important for viral infection. The fact that majority of single nucleotide variations (SNVs) are predicted to cause synonymous, as well as the result of low mutation rate of nsp2 gene in the epidemic variations, indicates that the nsp2 is conservative and could be a target for anti-SARS drugs. The three-dimensional structure result indicates that the nsp2 protein of GD strain is high homologous with 3CL(pro) of SARS-CoV urbani strain, 3CL(pro) of transmissible gastroenteritis virus and 3CL(pro) of human coronavirus 229E strain, which further suggests that nsp2 protein of GD strain possesses the activity of 3CL(pro).

Efficacy and Safety of MIN-101: A 12-Week Randomized, Double-Blind, Placebo-Controlled Trial of a New Drug in Development for the Treatment of Negative Symptoms in Schizophrenia.

PubMed

Davidson, Michael; Saoud, Jay; Staner, Corinne; Noel, Nadine; Luthringer, Elisabeth; Werner, Sandra; Reilly, Joseph; Schaffhauser, Jean-Yves; Rabinowitz, Jonathan; Weiser, Mark; Luthringer, Remy

2017-12-01

The authors assessed the efficacy, safety, and tolerability of MIN-101, a compound with affinities for sigma-2 and 5-HT 2A receptors and no direct dopamine affinities, in comparison with placebo in treating negative symptoms in stabilized patients with schizophrenia. The trial enrolled 244 patients who had been symptomatically stable for at least 3 months and had scores of at least 20 on the negative subscale of the Positive and Negative Syndrome Scale (PANSS). After at least 5 days' withdrawal from all antipsychotic medication, patients were randomly assigned to receive placebo or 32 mg/day or 64 mg/day of MIN-101 for 12 weeks. The primary outcome measure was the PANSS negative factor score (pentagonal structure model). Secondary outcome measures were PANSS total score and scores on the Clinical Global Impressions Scale (CGI), the Brief Negative Symptom Scale, the Brief Assessment of Cognition in Schizophrenia, and the Calgary Depression Scale for Schizophrenia. A statistically significant difference in PANSS negative factor score was observed, with lower scores for the MIN-101 32 mg/day and 64 mg/day groups compared with the placebo group (effect sizes, d=0.45 and d=0.57, respectively). Supporting these findings were similar effects on several of the secondary outcome measures, such as the PANSS negative symptom, total, and activation factor scores, the CGI severity item, and the Brief Negative Symptom Scale. There were no statistically significant differences in PANSS positive scale score between the MIN-101 and placebo groups. No clinically significant changes were observed in vital signs, routine laboratory values, weight, metabolic indices, and Abnormal Involuntary Movement Scale score. MIN-101 demonstrated statistically significant efficacy in reducing negative symptoms and good tolerability in stable schizophrenia patients.

Visualizing Microbial Biogeochemistry: NanoSIMS and Stable Isotope Probing (Invited)

NASA Astrophysics Data System (ADS)

Pett-Ridge, J.; Weber, P. K.

2009-12-01

Linking phylogenetic information to function in microbial communities is a key challenge for microbial ecology. Isotope-labeling experiments provide a useful means to investigate the ecophysiology of microbial populations and cells in the environment and allow measurement of nutrient transfers between cell types, symbionts and consortia. The combination of Nano-Secondary Ion Mass Spectrometry (NanoSIMS) analysis, in situ labeling and high resolution microscopy allows isotopic analysis to be linked to phylogeny and morphology and holds great promise for fine-scale studies of microbial systems. In NanoSIMS analysis, samples are sputtered with an energetic primary beam (Cs+, O-) liberating secondary ions that are separated by the mass spectrometer and detected in a suite of electron multipliers. Five isotopic species may be analyzed concurrently with spatial resolution as fine as 50nm. A high sensitivity isotope ratio ‘map’ can then be generated for the analyzed area. NanoSIMS images of 13C, 15N and Mo (a nitrogenase co-factor) localization in diazotrophic cyanobacteria show how cells differentially allocate resources within filaments and allow calculation of nutrient uptake rates on a cell by cell basis. Images of AM fungal hyphae-root and cyanobacteria-rhizobia associations indicate the mobilization and sharing (stealing?) of newly fixed C and N. In a related technique, “El-FISH”, stable isotope labeled biomass is probed with oligonucleotide-elemental labels and then imaged by NanoSIMS. In microbial consortia and cyanobacterial mats, this technique helps link microbial structure and function simultaneously even in systems with unknown and uncultivated microbes. Finally, the combination of re-engineered universal 16S oligonucleotide microarrays with NanoSIMS analyses may allow microbial identity to be linked to functional roles in complex systems such as mats and cellulose degrading hindgut communities. These newly developed methods provide correlated oligonucleotide, functional enzyme and metabolic image data and should help unravel the metabolic processes of complex microbial communities in soils, biofilms and aquatic systems.

The predicted secondary structures of class I fructose-bisphosphate aldolases.

PubMed Central

Sawyer, L; Fothergill-Gilmore, L A; Freemont, P S

1988-01-01

The results of several secondary-structure prediction programs were combined to produce an estimate of the regions of alpha-helix, beta-sheet and reverse turns for fructose-bisphosphate aldolases from human and rat muscle and liver, from Trypanosoma brucei and from Drosophila melanogaster. All the aldolase sequences gave essentially the same pattern of secondary-structure predictions despite having sequences up to 50% different. One exception to this pattern was an additional strongly predicted helix in the rat liver and Drosophila enzymes. Regions of relatively high sequence variation generally were predicted as reverse turns, and probably occur as surface loops. Most of the positions corresponding to exon boundaries are located between regions predicted to have secondary-structural elements consistent with a compact structure. The predominantly alternating alpha/beta structure predicted is consistent with the alpha/beta-barrel structure indicated by preliminary high-resolution X-ray diffraction studies on rabbit muscle aldolase [Sygusch, Beaudry & Allaire (1986) Biophys. J. 49, 287a]. Images Fig. 1. (cont.) Fig. 1. PMID:3128269

Disorder-function relationships for the cell cycle regulatory proteins p21 and p27.

PubMed

Mitrea, Diana M; Yoon, Mi-Kyung; Ou, Li; Kriwacki, Richard W

2012-04-01

The classic structure-function paradigm has been challenged by a recently identified class of proteins: intrinsically disordered proteins (IDPs). Despite their lack of stable secondary or tertiary structure, IDPs are prevalent in all forms of life and perform myriad cellular functions, including signaling and regulation. Importantly, disruption of IDP homeostasis is associated with numerous human diseases, including cancer and neurodegeneration. Despite wide recognition of IDPs, the molecular mechanisms underlying their functions are not fully understood. Here we review the structural features and disorder-function relationships for p21 and p27, two cyclin-dependent kinase (Cdk) regulators involved in controlling cell division and fate. Studies of p21 bound to Cdk2/cyclin A revealed that a helix stretching mechanism mediates binding promiscuity. Further, investigations of Tyr88-phosphorylated p27 identified a signaling conduit that controls cell division and is disrupted in certain cancers. These mechanisms rely upon a balance between nascent structure in the free state, induced folding upon binding, and persistent flexibility within functional complexes. Although these disorder-function relationships are likely to be recapitulated in other IDPs, it is also likely that the vocabulary of their mechanisms is much more extensive than is currently understood. Further study of the physical properties of IDPs and elucidation of their links with function are needed to fully understand the mechanistic language of IDPs.

Influence of Aqueous-Salt Conditions on the Structure and Dynamics of the Monomeric and Novel Dimeric forms of the Alzheimer s ABeta21-30 protein fragment

NASA Astrophysics Data System (ADS)

Smith, Micholas Dean

The behavior of the Alzheimer's related peptide Abeta is the subject of much study. In typical computational studies the environment local to the peptide is assumed to be pure water; however, in vivo the peptide is found in the extracellular space near the plasma membrane which is rich in ionic species. In this thesis, the hypothesis that the presence of group I/IIA salts will result in increased sampling of disordered structures as well as modify the dynamics of meta-stable structural motifs in the small folding nucleus of the Abeta peptide (Abeta21-30) is examined under a variety of ionic environments and was shown that of the tested salts, CaCl2 (and MgCl2, to a much lesser degree) did increase the propensity for disordered states; while, the group IA salts, KCl and NaCl, had little effect on the secondary structure of the peptide. Further, study of three familial mutations of this peptide region is also performed under aqueous salt-environments to elucidate further mechanistic details of how aqueous salts modify the region's behavior. Finally, as experimental results have highlighted that aggregation rates of the full-length peptide are modified by the presence of CaCl2, this work examines novel dimers states of Abeta21-30 and their stabilities when exposed to CaCl2.

MALDI-TOF MS and CD Spectral Analysis for Identification and Structure Prediction of a Purified, Novel, Organic Solvent Stable, Fibrinolytic Metalloprotease from Bacillus cereus B80

PubMed Central

Saxena, Rajshree

2015-01-01

The ability to predict protein function from structure is becoming increasingly important; hence, elucidation and determination of protein structure become the major steps in proteomics. The present study was undertaken for identification of metalloprotease produced by Bacillus cereus B80 and recognition of characteristics that can be industrially exploited. The enzyme was purified in three steps combining precipitation and chromatographic methods resulting in 33.5% recovery with 13.1-fold purification of enzyme which was detected as a single band with a molecular mass of 26 kDa approximately in SDS-PAGE and zymogram. The MALDI-TOF MS showed that the enzyme exhibited 70–93% similarity with zinc metalloproteases from various strains Bacillus sp. specifically from Bacillus cereus group. The sequence alignment revealed the presence of zinc-binding region VVVHEMCHMV in the most conserved C terminus region. Secondary structure of the enzyme was obtained by CD spectra and I-TASSER. The enzyme kinetics revealed a Michaelis constant (K m) of 0.140 μmol/ml and V max of 2.11 μmol/min. The application studies showed that the enzyme was able to hydrolyze various proteins with highest affinity towards casein followed by BSA and gelatin. The enzyme exhibited strong fibrinolytic, collagenolytic, and gelatinolytic properties and stability in various organic solvents. PMID:25802851

Revealing Anisotropic Spinel Formation on Pristine Li- and Mn-Rich Layered Oxide Surface and Its Impact on Cathode Performance

DOE PAGES

Kuppan, Saravanan; Shukla, Alpesh Khushalchand; Membreno, Daniel; ...

2017-01-06

Surface properties of cathode particles play important roles in the transport of ions and electrons and they may ultimately dominate cathode's performance and stability in lithium-ion batteries. Through the use of carefully prepared Li 1.2Ni 0.13Mn 0.54Co 0.13O 2 crystal samples with six distinct morphologies, surface transition-metal redox activities and crystal structural transformation are investigated as a function of surface area and surface crystalline orientation. Complementary depth-profiled core-level spectroscopy, namely, X-ray absorption spectroscopy, electron energy loss spectroscopy, and atomic-resolution scanning transmission electron microscopy, are applied in the study, presenting a fine example of combining advanced diagnostic techniques with a well-definedmore » model system of battery materials. Here, we report the following findings: (1) a thin layer of defective spinel with reduced transition metals, similar to what is reported on cycled conventional secondary particles in the literature, is found on pristine oxide surface even before cycling, and (2) surface crystal structure and chemical composition of both pristine and cycled particles are facet dependent. Oxide structural and cycling stabilities improve with maximum expression of surface facets stable against transition-metal reduction. Finally, the intricate relationships among morphology, surface reactivity and structural transformation, electrochemical performance, and stability of the cathode materials are revealed.« less

Structural and mechanistic analysis of engineered trichodiene synthase enzymes from Trichoderma harzianum: towards higher catalytic activities empowering sustainable agriculture.

PubMed

Kumari, Indu; Chaudhary, Nitika; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

2016-06-01

Trichoderma spp. are well-known bioagents for the plant growth promotion and pathogen suppression. The beneficial activities of the fungus Trichoderma spp. are attributed to their ability to produce and secrete certain secondary metabolites such as trichodermin that belongs to trichothecene family of molecules. The initial steps of trichodermin biosynthetic pathway in Trichoderma are similar to the trichothecenes from Fusarium sporotrichioides. Trichodiene synthase (TS) encoded by tri5 gene in Trichoderma catalyses the conversion of farnesyl pyrophosphate to trichodiene as reported earlier. In this study, we have carried out a comprehensive comparative sequence and structural analysis of the TS, which revealed the conserved residues involved in catalytic activity of the protein. In silico, modelled tertiary structure of TS protein showed stable structural behaviour during simulations. Two single-substitution mutants, i.e. D109E, D248Y and one double-substitution mutant (D109E and D248Y) of TS with potentially higher activities are screened out. The mutant proteins showed more stability than the wild type, an increased number of electrostatic interactions and better binding energies with the ligand, which further elucidates the amino acid residues involved in the reaction mechanism. These results will lead to devise strategies for higher TS activity to ultimately enhance the trichodermin production by Trichoderma spp. for its better exploitation in the sustainable agricultural practices.

Guanidine hydrochloride-induced alkali molten globule model of horse ferrocytochrome c.

PubMed

Jain, Rishu; Kaur, Sandeep; Kumar, Rajesh

2013-02-01

This article compares structural, kinetic and thermodynamic properties of previously unknown guanidine hydrochloride (GdnHCl)-induced alkali molten globule (MG) state of horse 'ferrocytochrome c' (ferrocyt c) with the known NaCl-induced alkali-MG state of ferrocyt c. It is well known that Cl(-) arising from GdnHCl refolds and stabilizes the acid-denatured protein to MG state. We demonstrate that the GdnH(+) arising from GdnHCl (≤0.2 M) also transforms the base-denatured CO-liganded ferrocyt c (carbonmonoxycyt c) to MG state by making the electrostatic interactions to the negative charges of the protein. Structural and molecular properties extracted from the basic spectroscopic (circular dichroism (CD), fluorescence, FTIR and NMR) experiments suggest that the GdnH(+)- and Na(+)-induced MG states of base-denatured carbonmonoxycyt c are molecular compact states containing native-like secondary structures and disordered tertiary structures. Kinetic experiments involving the measurement of the CO association to the alkaline ferrocyt c in the presence of different GdnHCl and NaCl concentrations indicate that the Na(+)-induced MG state is more constrained relative to that of GdnH(+)-induced MG state. Analyses of thermal (near UV-CD) denaturation curves of the base-denatured protein in the presence of different GdnHCl and NaCl concentration also indicate that the Na(+)-induced MG state is thermally more stable than the GdnH(+)-induced MG state.

Impact of primer dimers and self-amplifying hairpins on reverse transcription loop-mediated isothermal amplification detection of viral RNA

DOE PAGES

Meagher, Robert J.; Priye, Aashish; Light, Yooli K.; ...

2018-03-27

Loop-mediated isothermal amplification (LAMP), coupled with reverse transcription (RT), has become a popular technique for detection of viral RNA due to several desirable characteristics for use in point-of-care or low-resource settings. The large number of primers in LAMP (six per target) leads to an increased likelihood of primer-dimer interactions, and the inner primers in particular are prone to formation of stable hairpin structures due to their length (typically 40-45 bases). Although primer-dimers and hairpin structures are known features to avoid in nucleic acid amplification techniques, there is little quantitative information in literature regarding the impact of these structures on LAMPmore » or RT-LAMP assays. In this study, we examine the impact of primer-dimers and hairpins on previously-published primer sets for dengue virus and yellow fever virus. We demonstrate that minor changes to the primers to eliminate amplifiable primer dimers and hairpins improves the performance of the assays when monitored in real time with intercalating dyes, and when monitoring a fluorescent endpoint using the QUASR technique. We also discuss the thermodynamic implications of these minor changes on the overall stability of amplifiable secondary structures, and we present a single thermodynamic parameter to predict the probability of non-specific amplification associated with LAMP primers.« less

Impact of primer dimers and self-amplifying hairpins on reverse transcription loop-mediated isothermal amplification detection of viral RNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meagher, Robert J.; Priye, Aashish; Light, Yooli K.

Loop-mediated isothermal amplification (LAMP), coupled with reverse transcription (RT), has become a popular technique for detection of viral RNA due to several desirable characteristics for use in point-of-care or low-resource settings. The large number of primers in LAMP (six per target) leads to an increased likelihood of primer-dimer interactions, and the inner primers in particular are prone to formation of stable hairpin structures due to their length (typically 40-45 bases). Although primer-dimers and hairpin structures are known features to avoid in nucleic acid amplification techniques, there is little quantitative information in literature regarding the impact of these structures on LAMPmore » or RT-LAMP assays. In this study, we examine the impact of primer-dimers and hairpins on previously-published primer sets for dengue virus and yellow fever virus. We demonstrate that minor changes to the primers to eliminate amplifiable primer dimers and hairpins improves the performance of the assays when monitored in real time with intercalating dyes, and when monitoring a fluorescent endpoint using the QUASR technique. We also discuss the thermodynamic implications of these minor changes on the overall stability of amplifiable secondary structures, and we present a single thermodynamic parameter to predict the probability of non-specific amplification associated with LAMP primers.« less

Specific binding of a HeLa cell nuclear protein to RNA sequences in the human immunodeficiency virus transactivating region.

PubMed Central

Gaynor, R; Soultanakis, E; Kuwabara, M; Garcia, J; Sigman, D S

1989-01-01

The transactivator protein, tat, encoded by the human immunodeficiency virus is a key regulator of viral transcription. Activation by the tat protein requires sequences downstream of the transcription initiation site called the transactivating region (TAR). RNA derived from the TAR is capable of forming a stable stem-loop structure and the maintenance of both the stem structure and the loop sequences located between +19 and +44 is required for complete in vivo activation by tat. Gel retardation assays with RNA from both wild-type and mutant TAR constructs generated in vitro with SP6 polymerase indicated specific binding of HeLa nuclear proteins to the TAR. To characterize this RNA-protein interaction, a method of chemical "imprinting" has been developed using photoactivated uranyl acetate as the nucleolytic agent. This reagent nicks RNA under physiological conditions at all four nucleotides in a reaction that is independent of sequence and secondary structure. Specific interaction of cellular proteins with TAR RNA could be detected by enhanced cleavages or imprints surrounding the loop region. Mutations that either disrupted stem base-pairing or extensively changed the primary sequence resulted in alterations in the cleavage pattern of the TAR RNA. Structural features of the TAR RNA stem-loop essential for tat activation are also required for specific binding of the HeLa cell nuclear protein. Images PMID:2544877

Universality and diversity of folding mechanics for three-helix bundle proteins.

PubMed

Yang, Jae Shick; Wallin, Stefan; Shakhnovich, Eugene I

2008-01-22

In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo folding simulations using a single transferable all-atom potential. Using these trajectories, we examine the relaxation behavior, secondary structure formation, and transition-state ensembles (TSEs) of the two proteins and compare our results with experimental data and previous computational studies. To obtain a detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Moreover, rigorous p(fold) analysis is used to obtain representative samples of the TSEs and a good quantitative agreement between experimental and simulated Phi values is obtained for protein A. Phi values for Villin also are obtained and left as predictions to be tested by future experiments. Our analysis shows that the two-helix hairpin is a common partially stable structural motif that gets formed before entering the TSE in the studied proteins. These results together with our earlier study of Engrailed Homeodomain and recent experimental studies provide a comprehensive, atomic-level picture of folding mechanics of three-helix bundle proteins.

Albumin (BSA) adsorption onto graphite stepped surfaces

NASA Astrophysics Data System (ADS)

Rubio-Pereda, Pamela; Vilhena, J. G.; Takeuchi, Noboru; Serena, Pedro A.; Pérez, Rubén

2017-06-01

Nanomaterials are good candidates for the design of novel components with biomedical applications. For example, nano-patterned substrates may be used to immobilize protein molecules in order to integrate them in biosensing units. Here, we perform long MD simulations (up to 200 ns) using an explicit solvent and physiological ion concentrations to characterize the adsorption of bovine serum albumin (BSA) onto a nano-patterned graphite substrate. We have studied the effect of the orientation and step size on the protein adsorption and final conformation. Our results show that the protein is stable, with small changes in the protein secondary structure that are confined to the contact area and reveal the influence of nano-structuring on the spontaneous adsorption, protein-surface binding energies, and protein mobility. Although van der Waals (vdW) interactions play a dominant role, our simulations reveal the important role played by the hydrophobic lipid-binding sites of the BSA molecule in the adsorption process. The complex structure of these sites, that incorporate residues with different hydrophobic character, and their flexibility are crucial to understand the influence of the ion concentration and protein orientation in the different steps of the adsorption process. Our study provides useful information for the molecular engineering of components that require the immobilization of biomolecules and the preservation of their biological activity.

Characterization of an RNA aptamer against HPV-16 L1 virus-like particles.

PubMed

Leija-Montoya, Ana Gabriela; Benítez-Hess, María Luisa; Toscano-Garibay, Julia Dolores; Alvarez-Salas, Luis Marat

2014-10-01

The human papillomavirus (HPV) capsid is mainly composed of the L1 protein that can self-assemble into virus-like particles (VLPs) that are structurally and immunologically similar to the infectious virions. We report here the characterization of RNA aptamers that recognize baculovirus-produced HPV-16 L1 VLPs. Interaction and slot-blot binding assays showed that all isolated aptamers efficiently bound HPV-16 VLPs, although the Sc5-c3 aptamer showed the highest specificity and affinity (Kd=0.05 pM). Sc5-c3 secondary structure consisted of a hairpin with a symmetric bubble and an unstructured 3'end. Biochemical and genetic analyses showed that the Sc5-c3 main loop is directly involved on VLPs binding. In particular, binding specificity appeared mediated by five non-consecutive nucleotide positions. Experiments using bacterial-produced HPV-16 L1 resulted in low Sc5-c3 binding, suggesting that recognition of HPV-16 L1 VLPs relies on quaternary structure features not present in bacteria-produced L1 protein. Sc5-c3 produced specific and stable binding to HPV-16 L1 VLPs even in biofluid protein mixes and thus it may provide a potential diagnostic tool for active HPV infection.

Characterization of an RNA Aptamer Against HPV-16 L1 Virus-Like Particles

PubMed Central

Leija-Montoya, Ana Gabriela; Benítez-Hess, María Luisa; Toscano-Garibay, Julia Dolores

2014-01-01

The human papillomavirus (HPV) capsid is mainly composed of the L1 protein that can self-assemble into virus-like particles (VLPs) that are structurally and immunologically similar to the infectious virions. We report here the characterization of RNA aptamers that recognize baculovirus-produced HPV-16 L1 VLPs. Interaction and slot-blot binding assays showed that all isolated aptamers efficiently bound HPV-16 VLPs, although the Sc5-c3 aptamer showed the highest specificity and affinity (Kd=0.05 pM). Sc5-c3 secondary structure consisted of a hairpin with a symmetric bubble and an unstructured 3′end. Biochemical and genetic analyses showed that the Sc5-c3 main loop is directly involved on VLPs binding. In particular, binding specificity appeared mediated by five non-consecutive nucleotide positions. Experiments using bacterial-produced HPV-16 L1 resulted in low Sc5-c3 binding, suggesting that recognition of HPV-16 L1 VLPs relies on quaternary structure features not present in bacteria-produced L1 protein. Sc5-c3 produced specific and stable binding to HPV-16 L1 VLPs even in biofluid protein mixes and thus it may provide a potential diagnostic tool for active HPV infection. PMID:25111024

Structural studies of the protein endostatin in fusion with BAX BH3 death domain, a hybrid that presents enhanced antitumoral activity.

PubMed

Chura-Chambi, Rosa Maria; Arcuri, Helen Andrade; Lino, Felipe; Versati, Natan; Palma, Mario Sergio; Favaro, Denize C; Morganti, Ligia

2017-05-01

Endostatin (ES) is an antiangiogenic protein that exhibits antitumor activity in animal models. However, the activity observed in animals was not observed in human clinical trials. ES-BAX is a fusion protein composed of two functional domains: ES, which presents specificity and is internalized by activated endothelial cells and the proapoptotic BH3 domain of the protein BAX, a peptide inductor of cellular death when internalized. We have previously shown (Chura-Chambi et al., Cell Death Dis, 5, e1371, 2014) that ES-BAX presents improved antitumor activity in relation to wild-type ES. Secondary and tertiary structures of ES-BAX are similar to ES, as indicated by homology-modeling studies and molecular dynamics simulations. Tryptophan intrinsic fluorescence and circular dichroism spectroscopy corroborate these data. 15 N HSQC NMR indicates that ES-BAX is structured, but some ES residues have suffered chemical shift perturbations, suggesting that the BH3 peptide interacts with some parts of the ES protein. ES and ES-BAX present similar stability to thermal denaturation. The production of stable hybrid proteins can be a new approach to the development of therapeutic agents presenting specificity for tumoral endothelium and improved antitumor effect. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

Identification of Transthyretin Fibril Formation Inhibitors Using Structure-Based Virtual Screening.

PubMed

Ortore, Gabriella; Martinelli, Adriano

2017-08-22

Transthyretin (TTR) is the primary carrier for thyroxine (T 4 ) in cerebrospinal fluid and a secondary carrier in blood. TTR is a stable homotetramer, but certain factors, genetic or environmental, could promote its degradation to form amyloid fibrils. A docking study using crystal structures of wild-type TTR was planned; our aim was to design new ligands that are able to inhibit TTR fibril formation. The computational protocol was thought to overcome the multiple binding modes of the ligands induced by the peculiarity of the TTR binding site and by the pseudosymmetry of the site pockets, which generally weaken such structure-based studies. Two docking steps, one that is very fast and a subsequent step that is more accurate, were used to screen the Aldrich Market Select database. Five compounds were selected, and their activity toward inhibiting TTR fibril formation was assessed. Three compounds were observed to be actives, two of which have the same potency as the positive control, and the other was found to be a promising lead compound. These results validate a computational protocol that is able to archive information on the key interactions between database compounds and TTR, which is valuable for supporting further studies. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computational sensitivity study of spray dispersion and mixing on the fuel properties in a gas turbine combustor

NASA Astrophysics Data System (ADS)

Grosshans, Holger; Cao, Le; Fuchs, Laszlo; Szász, Robert-Zoltán

2017-04-01

A swirl stabilized gas turbine burner has been simulated in order to assess the effects of the fuel properties on spray dispersion and fuel-air mixing. The properties under consideration include fuel surface tension, viscosity and density. The turbulence of the gas phase is modeled applying the methodology of large eddy simulation whereas the dispersed liquid phase is described by Lagrangian particle tracking. The exchange of mass, momentum and energy between the two phases is accounted for by two-way coupling. Bag and stripping breakup regimes are considered for secondary droplet breakup, using the Reitz-Diwakar and the Taylor analogy breakup models. Moreover, a model for droplet evaporation is included. The results reveal a high sensitivity of the spray structure to variations of all investigated parameters. In particular, a decrease in the surface tension or the fuel viscosity, or an increase in the fuel density, lead to less stable liquid structures. As a consequence, smaller droplets are generated and the overall spray surface area increases, leading to faster evaporation and mixing. Furthermore, with the trajectories of the small droplets being strongly influenced by aerodynamic forces (and less by their own inertia), the spray is more affected by the turbulent structures of the gaseous phase and the spray dispersion is enhanced.

Building Honeycomb-Like Hollow Microsphere Architecture in a Bubble Template Reaction for High-Performance Lithium-Rich Layered Oxide Cathode Materials.

PubMed

Chen, Zhaoyong; Yan, Xiaoyan; Xu, Ming; Cao, Kaifeng; Zhu, Huali; Li, Lingjun; Duan, Junfei

2017-09-13

In the family of high-performance cathode materials for lithium-ion batteries, lithium-rich layered oxides come out in front because of a high reversible capacity exceeding 250 mAh g -1 . However, the long-term energy retention and high energy densities for lithium-rich layered oxide cathode materials require a stable structure with large surface areas. Here we propose a "bubble template" reaction to build "honeycomb-like" hollow microsphere architecture for a Li 1.2 Mn 0.52 Ni 0.2 Co 0.08 O 2 cathode material. Our material is designed with ca. 8-μm-sized secondary particles with hollow and highly exposed porous structures that promise a large flexible volume to achieve superior structure stability and high rate capability. Our preliminary electrochemical experiments show a high capacity of 287 mAh g -1 at 0.1 C and a capacity retention of 96% after 100 cycles at 1.0 C. Furthermore, the rate capability is superior without any other modifications, reaching 197 mAh g -1 at 3.0 C with a capacity retention of 94% after 100 cycles. This approach may shed light on a new material engineering for high-performance cathode materials.

Direct Numerical Simulations of Small-Scale Gravity Wave Instability Dynamics in Variable Stratification and Shear

NASA Astrophysics Data System (ADS)

Mixa, T.; Fritts, D. C.; Laughman, B.; Wang, L.; Kantha, L. H.

2015-12-01

Multiple observations provide compelling evidence that gravity wave dissipation events often occur in multi-scale environments having highly-structured wind and stability profiles extending from the stable boundary layer into the mesosphere and lower thermosphere. Such events tend to be highly localized and thus yield local energy and momentum deposition and efficient secondary gravity wave generation expected to have strong influences at higher altitudes [e.g., Fritts et al., 2013; Baumgarten and Fritts, 2014]. Lidars, radars, and airglow imagers typically cannot achieve the spatial resolution needed to fully quantify these small-scale instability dynamics. Hence, we employ high-resolution modeling to explore these dynamics in representative environments. Specifically, we describe numerical studies of gravity wave packets impinging on a sheet of high stratification and shear and the resulting instabilities and impacts on the gravity wave amplitude and momentum flux for various flow and gravity wave parameters. References: Baumgarten, Gerd, and David C. Fritts (2014). Quantifying Kelvin-Helmholtz instability dynamics observed in noctilucent clouds: 1. Methods and observations. Journal of Geophysical Research: Atmospheres, 119.15, 9324-9337. Fritts, D. C., Wang, L., & Werne, J. A. (2013). Gravity wave-fine structure interactions. Part I: Influences of fine structure form and orientation on flow evolution and instability. Journal of the Atmospheric Sciences, 70(12), 3710-3734.

[The therapeutic use of iodide-bromide-sodium chloride baths combined with hydrocortisone phonophoresis in patients with osteoarthrosis and gout].

PubMed

Kamenskaia, N S; Fedorova, N E

1990-01-01

Hydrocortisone phonophoresis (HPP) on the affected joints or balneotherapy with iodine bromine baths as well as the complex of these two modalities were used to treat 197 patients with osteoarthrosis. Thirty-one of the patients had secondary arthrosis due to recurrent gout attacks. Monotherapy with HPP proved beneficial in affection of 1-2 joints whereas the baths appeared preferable in polyosteoarthrosis, its association with spinal osteoarthrosis, arterial hypertension. Combined application of HPP and the baths produced more pronounced and stable effect with the best relief recorded in polyosteoarthrosis, its progression, secondary synovitis.

Sarcoid-resembling granulomatous lung disease secondary to occupational magnetite iron dust exposure.

PubMed

Xiao, Lewis; Kookana, Anil; McClure, Robert; Heraganahally, Subash

2018-08-01

Non-caseating granulomatous pulmonary conditions resembling sarcoidosis secondary to industrial/occupation exposure to magnetite iron ore dusts have been rarely documented in the literature. This is a case report of a 58-year-old blast crew member involved in iron ore/magnetite mining who presented with a 12-month history of chronic dry cough. High-resolution computed tomography revealed bilateral interstitial opacities. Lung biopsy demonstrated sarcoid-like granulomatous inflammation. Oral corticosteroid treatment improved the cough. Radiological features did not resolve despite treatment and yet remained stable following no subsequent exposure to iron mining dust.

Local Nash equilibrium in social networks.

PubMed

Zhang, Yichao; Aziz-Alaoui, M A; Bertelle, Cyrille; Guan, Jihong

2014-08-29

Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures.

Local Nash Equilibrium in Social Networks

PubMed Central

Zhang, Yichao; Aziz-Alaoui, M. A.; Bertelle, Cyrille; Guan, Jihong

2014-01-01

Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures. PMID:25169150

Local Nash Equilibrium in Social Networks

NASA Astrophysics Data System (ADS)

Zhang, Yichao; Aziz-Alaoui, M. A.; Bertelle, Cyrille; Guan, Jihong

2014-08-01

Nash equilibrium is widely present in various social disputes. As of now, in structured static populations, such as social networks, regular, and random graphs, the discussions on Nash equilibrium are quite limited. In a relatively stable static gaming network, a rational individual has to comprehensively consider all his/her opponents' strategies before they adopt a unified strategy. In this scenario, a new strategy equilibrium emerges in the system. We define this equilibrium as a local Nash equilibrium. In this paper, we present an explicit definition of the local Nash equilibrium for the two-strategy games in structured populations. Based on the definition, we investigate the condition that a system reaches the evolutionary stable state when the individuals play the Prisoner's dilemma and snow-drift game. The local Nash equilibrium provides a way to judge whether a gaming structured population reaches the evolutionary stable state on one hand. On the other hand, it can be used to predict whether cooperators can survive in a system long before the system reaches its evolutionary stable state for the Prisoner's dilemma game. Our work therefore provides a theoretical framework for understanding the evolutionary stable state in the gaming populations with static structures.

Testing Mediation Using Multiple Regression and Structural Equation Modeling Analyses in Secondary Data

ERIC Educational Resources Information Center

Li, Spencer D.

2011-01-01

Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the…

Academic Well-Being, Mathematics Performance, and Educational Aspirations in Lower Secondary Education: Changes Within a School Year

PubMed Central

Widlund, Anna; Tuominen, Heta; Korhonen, Johan

2018-01-01

It has been suggested that both performance and academic well-being play a role in adolescent students’ educational attainment and school dropout. In this study, we therefore examined, first, what kinds of academic well-being (i.e., school burnout, schoolwork engagement, and mathematics self-concept) and mathematics performance profiles can be identified among lower secondary school students (Ngrade 7 = 583, Ngrade 9 = 497); second, how stable these profiles are across one school year during the seventh and ninth grades; and, third, how students with different academic well-being and mathematics performance profiles differ with respect to their educational aspirations. By means of latent profile analyses, three groups of students in seventh grade: thriving (34%), average (51%), and negative academic well-being (15%) and four groups of students in ninth grade: thriving (25%), average (50%), negative academic well-being (18%), and low-performing (7%) with distinct well-being and mathematics performance profiles were identified. Configural frequency analyses revealed that the profiles were relatively stable across one school year; 60% of the students displayed identical profiles over time. The thriving students reported the highest educational aspirations compared to the other groups. In addition, the low-performing students in the ninth grade had the lowest educational aspirations just before the transition to upper secondary school. Practical implications as well as directions for future research are discussed. PMID:29593603

Academic Well-Being, Mathematics Performance, and Educational Aspirations in Lower Secondary Education: Changes Within a School Year.

PubMed

Widlund, Anna; Tuominen, Heta; Korhonen, Johan

2018-01-01

It has been suggested that both performance and academic well-being play a role in adolescent students' educational attainment and school dropout. In this study, we therefore examined, first, what kinds of academic well-being (i.e., school burnout, schoolwork engagement, and mathematics self-concept) and mathematics performance profiles can be identified among lower secondary school students ( N grade 7 = 583, N grade 9 = 497); second, how stable these profiles are across one school year during the seventh and ninth grades; and, third, how students with different academic well-being and mathematics performance profiles differ with respect to their educational aspirations. By means of latent profile analyses, three groups of students in seventh grade: thriving (34%), average (51%), and negative academic well-being (15%) and four groups of students in ninth grade: thriving (25%), average (50%), negative academic well-being (18%), and low-performing (7%) with distinct well-being and mathematics performance profiles were identified. Configural frequency analyses revealed that the profiles were relatively stable across one school year; 60% of the students displayed identical profiles over time. The thriving students reported the highest educational aspirations compared to the other groups. In addition, the low-performing students in the ninth grade had the lowest educational aspirations just before the transition to upper secondary school. Practical implications as well as directions for future research are discussed.

High pressure ices.

PubMed

Hermann, Andreas; Ashcroft, N W; Hoffmann, Roald

2012-01-17

H(2)O will be more resistant to metallization than previously thought. From computational evolutionary structure searches, we find a sequence of new stable and meta-stable structures for the ground state of ice in the 1-5 TPa (10 to 50 Mbar) regime, in the static approximation. The previously proposed Pbcm structure is superseded by a Pmc2(1) phase at p = 930 GPa, followed by a predicted transition to a P2(1) crystal structure at p = 1.3 TPa. This phase, featuring higher coordination at O and H, is stable over a wide pressure range, reaching 4.8 TPa. We analyze carefully the geometrical changes in the calculated structures, especially the buckling at the H in O-H-O motifs. All structures are insulating--chemistry burns a deep and (with pressure increase) lasting hole in the density of states near the highest occupied electronic levels of what might be component metallic lattices. Metallization of ice in our calculations occurs only near 4.8 TPa, where the metallic C2/m phase becomes most stable. In this regime, zero-point energies much larger than typical enthalpy differences suggest possible melting of the H sublattice, or even the entire crystal.

Subthreshold symptoms of depression in preadolescent girls are stable and predictive of depressive disorders.

PubMed

Keenan, Kate; Hipwell, Alison; Feng, Xin; Babinski, Dara; Hinze, Amanda; Rischall, Michal; Henneberger, Angela

2008-12-01

Given the risk for adolescent depression in girls to lead to a chronic course of mental illness, prevention of initial onset could have a large impact on reducing chronicity. If symptoms of depression that emerge during childhood were stable and predictive of later depressive disorders and impairment, then secondary prevention of initial onset of depressive disorders would be possible. Drawing from the Pittsburgh Girls Study, an existing longitudinal study, 232 nine-year-old girls were recruited for the present study, half of whom screened high on a measure of depression at age 8 years. Girls were interviewed about depressive symptoms using a diagnostic interview at ages 9, 10, and 11 years. Caregivers and interviewers rated impairment in each year. The stability coefficients for DSM-IV symptom counts for a 1- to 2-year interval were in the moderate range (i.e., intraclass coefficients of 0.40-0.59 for continuous symptom counts and Kendall tau-b coefficients of 0.34-0.39 for symptom level stability). Depressive disorders were also relatively stable at this age. Poverty moderated the stability, but race and pubertal stage did not. Among the girls who did not meet criteria for a depressive disorder at age 9 years, the odds of meeting criteria for depressive disorders and for demonstrating impairment at age 10 or 11 years increased by 1.9 and 1.7, respectively, for every increase in the number of depression symptoms. Early-emerging symptoms of depression in girls are stable and predictive of depressive disorders and impairment. The results suggest that secondary prevention of depression in girls may be accomplished by targeting subthreshold symptoms manifest during childhood.

Role of Tryptophan Side Chain Dynamics on the Trp-Cage Mini-Protein Folding Studied by Molecular Dynamics Simulations

PubMed Central

Kannan, Srinivasaraghavan; Zacharias, Martin

2014-01-01

The 20 residue Trp-cage mini-protein is one of smallest proteins that adopt a stable folded structure containing also well-defined secondary structure elements. The hydrophobic core is arranged around a single central Trp residue. Despite several experimental and simulation studies the detailed folding mechanism of the Trp-cage protein is still not completely understood. Starting from fully extended as well as from partially folded Trp-cage structures a series of molecular dynamics simulations in explicit solvent and using four different force fields was performed. All simulations resulted in rapid collapse of the protein to on average relatively compact states. The simulations indicate a significant dependence of the speed of folding to near-native states on the side chain rotamer state of the central Trp residue. Whereas the majority of intermediate start structures with the central Trp side chain in a near-native rotameric state folded successfully within less than 100 ns only a fraction of start structures reached near-native folded states with an initially non-native Trp side chain rotamer state. Weak restraining of the Trp side chain dihedral angles to the state in the folded protein resulted in significant acceleration of the folding both starting from fully extended or intermediate conformations. The results indicate that the side chain conformation of the central Trp residue can create a significant barrier for controlling transitions to a near native folded structure. Similar mechanisms might be of importance for the folding of other protein structures. PMID:24563686

A route to possible civil engineering materials: the case of high-pressure phases of lime

NASA Astrophysics Data System (ADS)

Bouibes, A.; Zaoui, A.

2015-07-01

Lime system has a chemical composition CaO, which is known as thermodynamically stable. The purpose here is to explore further possible phases under pressure, by means of variable-composition ab initio evolutionary algorithm. The present investigation shows surprisingly new stable compounds of lime. At ambient pressure we predict, in addition to CaO, CaO2 as new thermodynamically stable compound. The latter goes through two phases transition from C2/c space group structure to Pna21 at 1.5 GPa, and Pna21 space group structure to I4/mcm at 23.4 GPa. Under increasing pressure, further compounds such as CaO3 become the most stable and stabilize in P-421m space group structure above 65 GPa. For the necessary knowledge of the new predicted compounds, we have computed their mechanical and electronic properties in order to show and to explain the main reasons leading to the structural changes.

A route to possible civil engineering materials: the case of high-pressure phases of lime.

PubMed

Bouibes, A; Zaoui, A

2015-07-23

Lime system has a chemical composition CaO, which is known as thermodynamically stable. The purpose here is to explore further possible phases under pressure, by means of variable-composition ab initio evolutionary algorithm. The present investigation shows surprisingly new stable compounds of lime. At ambient pressure we predict, in addition to CaO, CaO2 as new thermodynamically stable compound. The latter goes through two phases transition from C2/c space group structure to Pna21 at 1.5 GPa, and Pna21 space group structure to I4/mcm at 23.4 GPa. Under increasing pressure, further compounds such as CaO3 become the most stable and stabilize in P-421m space group structure above 65 GPa. For the necessary knowledge of the new predicted compounds, we have computed their mechanical and electronic properties in order to show and to explain the main reasons leading to the structural changes.

Medieval Horse Stable; The Results of Multi Proxy Interdisciplinary Research

PubMed Central

Dejmal, Miroslav; Lisá, Lenka; Fišáková Nývltová, Miriam; Bajer, Aleš; Petr, Libor; Kočár, Petr; Kočárová, Romana; Nejman, Ladislav; Rybníček, Michal; Sůvová, Zdenka; Culp, Randy; Vavrčík, Hanuš

2014-01-01

A multi proxy approach was applied in the reconstruction of the architecture of Medieval horse stable architecture, the maintenance practices associated with that structure as well as horse alimentation at the beginning of 13th century in Central Europe. Finally, an interpretation of the local vegetation structure along Morava River, Czech Republic is presented. The investigated stable experienced two construction phases. The infill was well preserved and its composition reflects maintenance practices. The uppermost part of the infill was composed of fresh stabling, which accumulated within a few months at the end of summer. Horses from different backgrounds were kept in the stable and this is reflected in the results of isotope analyses. Horses were fed meadow grasses as well as woody vegetation, millet, oat, and less commonly hemp, wheat and rye. Three possible explanations of stable usage are suggested. The stable was probably used on a temporary basis for horses of workers employed at the castle, courier horses and horses used in battle. PMID:24670874

A secondary copulatory structure in a female insect: a clasp for a nuptial meal?

NASA Astrophysics Data System (ADS)

Gwynne, Darryl T.

2002-03-01

Secondary copulatory structures are well-known in male dragonflies and spiders. Here I report a secondary copulatory organ in female ground weta, Hemiandrus pallitarsis (Ensifera, Orthoptera - crickets and allies). The organ, located on the underside of the abdomen, appears to secure the male's genitalia during the transfer of a spermatophylax nuptial meal to this location, an area quite separate from the female's primary copulatory structures, where the sperm ampulla is attached.

RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

PubMed Central

Ellington, Roni; Wachira, James

2010-01-01

The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems. PMID:20810968

RNA secondary structure prediction by using discrete mathematics: an interdisciplinary research experience for undergraduate students.

PubMed

Ellington, Roni; Wachira, James; Nkwanta, Asamoah

2010-01-01

The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems.

Influence of secondary structure on in-source decay of protein in matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Takayama, Mitsuo; Osaka, Issey; Sakakura, Motoshi

2012-01-01

The susceptibility of the N-Cα bond of the peptide backbone to specific cleavage by in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was studied from the standpoint of the secondary structure of three proteins. A naphthalene derivative, 5-amino-1-naphtol (5,1-ANL), was used as the matrix. The resulting c'-ions, which originate from the cleavage at N-Cα bonds in flexible secondary structures such as turn and bend, and are free from intra-molecular hydrogen-bonded α-helix structure, gave relatively intense peaks. Furthermore, ISD spectra of the proteins showed that the N-Cα bonds of specific amino acid residues, namely Gly-Xxx, Xxx-Asp, and Xxx-Asn, were more susceptible to MALDI-ISD than other amino acid residues. This is in agreement with the observation that Gly, Asp and Asn residues usually located in turns, rather than α-helix. The results obtained indicate that protein molecules embedded into the matrix crystal in the MALDI experiments maintain their secondary structures as determined by X-ray crystallography, and that MALDI-ISD has the capability for providing information concerning the secondary structure of protein.

Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding.

PubMed

Newcomer, Rebecca L; Fraser, LaTasha C R; Teschke, Carolyn M; Alexandrescu, Andrei T

2015-12-15

The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining (3)JNC' couplings transmitted through H-bonds, the temperature and urea-concentration dependence of (1)HN and (15)N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and (3)JNC' H-bond couplings, are identified with an accuracy of 90% by (1)HN temperature coefficients. The accuracy is improved to 95% when (15)N temperature coefficients are also included. In contrast, the urea dependence of (1)HN and (15)N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.