Structural and Mechanistic Insights into C-P Bond Hydrolysis by Phosphonoacetate Hydrolase

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

Agarwal, Vinayak; Borisova, Svetlana A.; Metcalf, William W.

2011-12-22

Bacteria have evolved pathways to metabolize phosphonates as a nutrient source for phosphorus. In Sinorhizobium meliloti 1021, 2-aminoethylphosphonate is catabolized to phosphonoacetate, which is converted to acetate and inorganic phosphate by phosphonoacetate hydrolase (PhnA). Here we present detailed biochemical and structural characterization of PhnA that provides insights into the mechanism of C-P bond cleavage. The 1.35 {angstrom} resolution crystal structure reveals a catalytic core similar to those of alkaline phosphatases and nucleotide pyrophosphatases but with notable differences, such as a longer metal-metal distance. Detailed structure-guided analysis of active site residues and four additional cocrystal structures with phosphonoacetate substrate, acetate, phosphonoformatemore » inhibitor, and a covalently bound transition state mimic provide insight into active site features that may facilitate cleavage of the C-P bond. These studies expand upon the array of reactions that can be catalyzed by enzymes of the alkaline phosphatase superfamily.« less

Signal Transduction in Histidine Kinases: Insights from New Structures

PubMed Central

Bhate, Manasi P.; Molnar, Kathleen S.; Goulian, Mark; DeGrado, William F.

2015-01-01

Histidine kinases (HKs) are major players in bacterial signaling. There has been an explosion of new HK crystal structures in the last five years. We globally analyze the structures of HKs to yield insights into the mechanisms by which signals are transmitted to and across protein structures in this family. We interpret known enzymological data in the context of new structural data to show how asymmetry across the dimer interface is a key feature of signal transduction in HKs, and discuss how different HK domains undergo asymmetric-to-symmetric transitions during signal transduction and catalysis. A thermodynamic framework for signaling that encompasses these various properties is presented and the consequences of weak thermodynamic coupling are discussed. The synthesis of observations from enzymology, structural biology, protein engineering and thermodynamics paves the way for a deeper molecular understanding of histidine kinase signal transduction. PMID:25982528

Cross-cultural adaptation, validation and factor structure of the Insight Scale for Affective Disorders.

PubMed

de Assis da Silva, Rafael; Mograbi, Daniel C; Camelo, Evelyn V M; Morton, Gregory Duff; Landeira-Fernandez, J; Cheniaux, Elie

2015-06-01

In the last few decades, several tools for studying insight in bipolar disorders have been used. Olaya and colleagues developed the Insight Scale for Affective Disorders (ISAD), which consists of a scale measuring insight through hetero evaluation for patients with mood disorders. The objective of this work is to translate and adapt the original English version of the ISAD to Brazilian Portuguese (ISAD-BR) and to conduct an evaluation of its psychometric properties. Adaptation procedures included translation/back-translation and consultation with a panel of experts. 95 patients with the diagnosis of Type 1 bipolar disorder were evaluated with the final version of the ISAD-BR, which was applied, simultaneously, but independently, by two examiners. Internal consistency and inter-rater reliability were explored and the latent structure of the scale was investigated with principal axis factoring and promax rotation. A second-order factor analysis was conducted to test if the scale had a hierarchical factor structure. The ISAD-BR showed good internal consistency and good inter-rater reliability. The analysis pointed to a four-factor solution of the ISAD-BR: awareness of symptoms associated with activity/energy; awareness of having a disorder; awareness of self-esteem and feelings of pleasure; and awareness of social functioning and relationships. The second order factor analysis indicated a hierarchical factor structure for the ISAD-BR, with the four lower-order factors loading on a single higher-order factor. Insight into bipolar disorder is a multidimensional construct, covering different aspects of the condition and its symptomatology. Nevertheless, insight about activity/energy changes may be a crucial aspect of insight into bipolar disorder. Copyright © 2015 Elsevier B.V. All rights reserved.

The first mammalian aldehyde oxidase crystal structure: insights into substrate specificity.

PubMed

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T P; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-11-23

Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents. The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics. Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures. The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.

Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

DOE PAGES

Doughty, Benjamin; Goverapet Srinivasan, Sriram; Bryantsev, Vyacheslav S.; ...

2017-06-12

The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments,more » and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO 2 catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO 2 (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.« less

Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

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

Doughty, Benjamin; Goverapet Srinivasan, Sriram; Bryantsev, Vyacheslav S.

The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments,more » and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO 2 catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO 2 (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.« less

Improved understanding of protein complex offers insight into DNA

Science.gov Websites

replication - through its crystal structure offers new insight into fundamental mechanisms of DNA replication Advanced Photon Source (APS), a U.S. Department of Energy User Facility based at Argonne National Laboratory, to obtain the first atomic-level resolution picture of this complex. The structure shows that

Nanoscale insights on one- and two-dimensional material structures

NASA Astrophysics Data System (ADS)

Floresca, Herman Carlo

The race for smaller, faster and more efficient devices has led researchers to explore the possibilities of utilizing nanostructures for scaling. These one-dimensional and two-dimensional materials have properties that are attractive for this purpose but are still not well controlled. Control comes with a complete understanding of the materials' electrical, thermal, optical and structural characteristics but is difficult to obtain due to their small scale. This work is intended to help researchers overcome the difficulty in studying nanostructures by providing techniques for analysis and insights of nanostructures that have not been previously available. Two nanostructures were studied: silicon nanowires and graphene. The nanowires were prepared for cross-section transmission electron microscopy (TEM) to discover the effects that controlled oxidation has on the dimensions and shape of the nanowires. Since cross-section TEM is not able to provide information about surface structure, a method for manipulating the wires with orientation control was developed. With this ability, all three orthogonal views of the nanowire were compiled for a comprehensive study on its structure in terms of shape and surface roughness. Graphene was used for a two-dimensional analytical technique that took advantage of customized computer programs for data acquisition, measurement and display. With the information provided, distinctions between grain boundary types in polycrystalline graphene were made and supported by statistical information from the software's output. It was also applied to a growth series of graphene samples in conjunction with scanning electron microscopy (SEM) images and electron backscatter diffraction (EBSD) maps. The results help point to origins of graphene's polycrystalline nature. This dissertation concludes with a thought towards the future by highlighting a method that can help analyze nanostructures, which may become incorporated into the structures of large

Rayleigh Wave Ellipticity Modeling and Inversion for Shallow Structure at the Proposed InSight Landing Site in Elysium Planitia, Mars

NASA Astrophysics Data System (ADS)

Knapmeyer-Endrun, Brigitte; Golombek, Matthew P.; Ohrnberger, Matthias

2017-10-01

The SEIS (Seismic Experiment for Interior Structure) instrument onboard the InSight mission will be the first seismometer directly deployed on the surface of Mars. From studies on the Earth and the Moon, it is well known that site amplification in low-velocity sediments on top of more competent rocks has a strong influence on seismic signals, but can also be used to constrain the subsurface structure. Here we simulate ambient vibration wavefields in a model of the shallow sub-surface at the InSight landing site in Elysium Planitia and demonstrate how the high-frequency Rayleigh wave ellipticity can be extracted from these data and inverted for shallow structure. We find that, depending on model parameters, higher mode ellipticity information can be extracted from single-station data, which significantly reduces uncertainties in inversion. Though the data are most sensitive to properties of the upper-most layer and show a strong trade-off between layer depth and velocity, it is possible to estimate the velocity and thickness of the sub-regolith layer by using reasonable constraints on regolith properties. Model parameters are best constrained if either higher mode data can be used or additional constraints on regolith properties from seismic analysis of the hammer strokes of InSight's heat flow probe HP3 are available. In addition, the Rayleigh wave ellipticity can distinguish between models with a constant regolith velocity and models with a velocity increase in the regolith, information which is difficult to obtain otherwise.

Structure and stability insights into tumour suppressor p53 evolutionary related proteins.

PubMed

Pagano, Bruno; Jama, Abdullah; Martinez, Pierre; Akanho, Ester; Bui, Tam T T; Drake, Alex F; Fraternali, Franca; Nikolova, Penka V

2013-01-01

The p53 family of genes and their protein products, namely, p53, p63 and p73, have over one billion years of evolutionary history. Advances in computational biology and genomics are enabling studies of the complexities of the molecular evolution of p53 protein family to decipher the underpinnings of key biological conditions spanning from cancer through to various metabolic and developmental disorders and facilitate the design of personalised medicines. However, a complete understanding of the inherent nature of the thermodynamic and structural stability of the p53 protein family is still lacking. This is due, to a degree, to the lack of comprehensive structural information for a large number of homologous proteins and to an incomplete knowledge of the intrinsic factors responsible for their stability and how these might influence function. Here we investigate the thermal stability, secondary structure and folding properties of the DNA-binding domains (DBDs) of a range of proteins from the p53 family using biophysical methods. While the N- and the C-terminal domains of the p53 family show sequence diversity and are normally targets for post-translational modifications and alternative splicing, the central DBD is highly conserved. Together with data obtained from Molecular Dynamics simulations in solution and with structure based homology modelling, our results provide further insights into the molecular properties of evolutionary related p53 proteins. We identify some marked structural differences within the p53 family, which could account for the divergence in biological functions as well as the subtleties manifested in the oligomerization properties of this family.

Insights into the structural/conformational requirements of cytotoxic oxadiazoles as potential chemotherapeutic target binding agents

NASA Astrophysics Data System (ADS)

Alikhani, Radin; Razzaghi-Asl, Nima; Ramazani, Ali; Hosseinzadeh, Zahra

2018-07-01

A few novel previously synthesized 2,5-disubstituted 1,3,4-oxadiazoles with cytotoxic activity (1-17) were subjected to combined docking/quantum mechanical studies against chemotherapeutic targets. Selected macromolecular targets were those that were previously known to be inhibited by 1,3,4-oxadiazoles. Within this work, favorable binding modes/affinities of the oxadiazoles toward validated cancer targets were elucidated. Some oxadiazole structures exhibited ΔGbs comparable to or stronger than crystallographic ligands that were previously demonstrated to inhibit such targets. On the basis of obtained results, a general structure activity/binding relationship (SAR/SBR) was developed and a few 2,5-disubstituted 1,3,4-oxadiazole structures were proposed and virtually validated as potential cytotoxic candidates. To get more insight into structure binding relationship of candidate molecules within best correlated targets, docked conformation of the best in silico in vitro correlated oxadiazole structure was analyzed in terms of intermolecular binding energy components by functional B3LYP in association with split valence basis set using polarization functions (Def2-SVP). We believe that such modeling studies may be complementary to our previous results on the synthesis and cytotoxicity assessment of novel 1,3,4-oxadiazole derivatives through extending the scope of privileged structures toward designing new potential anti-tumor compounds.

Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight.

PubMed

Regad, Leslie; Chéron, Jean-Baptiste; Triki, Dhoha; Senac, Caroline; Flatters, Delphine; Camproux, Anne-Claude

2017-01-01

Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC), obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at http://www.mti.univ-paris-diderot.fr/recherche/plateformes/logiciels.

Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight

PubMed Central

Chéron, Jean-Baptiste; Triki, Dhoha; Senac, Caroline; Flatters, Delphine; Camproux, Anne-Claude

2017-01-01

Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC), obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at http

RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution.

PubMed

Venkataraman, Sangita; Prasad, Burra V L S; Selvarajan, Ramasamy

2018-02-10

RNA dependent RNA polymerase (RdRp) is one of the most versatile enzymes of RNA viruses that is indispensable for replicating the genome as well as for carrying out transcription. The core structural features of RdRps are conserved, despite the divergence in their sequences. The structure of RdRp resembles that of a cupped right hand and consists of fingers, palm and thumb subdomains. The catalysis involves the participation of conserved aspartates and divalent metal ions. Complexes of RdRps with substrates, inhibitors and metal ions provide a comprehensive view of their functional mechanism and offer valuable insights regarding the development of antivirals. In this article, we provide an overview of the structural aspects of RdRps and their complexes from the Group III, IV and V viruses and their structure-based phylogeny.

Atom by atom: HRTEM insights into inorganic nanotubes and fullerene-like structures

PubMed Central

Sadan, Maya Bar; Houben, Lothar; Enyashin, Andrey N.; Seifert, Gotthard; Tenne, Reshef

2008-01-01

The characterization of nanostructures down to the atomic scale is essential to understand some physical properties. Such a characterization is possible today using direct imaging methods such as aberration-corrected high-resolution transmission electron microscopy (HRTEM), when iteratively backed by advanced modeling produced by theoretical structure calculations and image calculations. Aberration-corrected HRTEM is therefore extremely useful for investigating low-dimensional structures, such as inorganic fullerene-like particles and inorganic nanotubes. The atomic arrangement in these nanostructures can lead to new insights into the growth mechanism or physical properties, where imminent commercial applications are unfolding. This article will focus on two structures that are symmetric and reproducible. The first structure that will be dealt with is the smallest stable symmetric closed-cage structure in the inorganic system, a MoS2 nanooctahedron. It is investigated by means of aberration-corrected microscopy which allowed validating the suggested DFTB-MD model. It will be shown that structures diverging from the energetically most stable structures are present in the laser ablated soot and that the alignment of the different shells is parallel, unlike the bulk material where the alignment is antiparallel. These findings correspond well with the high-energy synthetic route and they provide more insight into the growth mechanism. The second structure studied is WS2 nanotubes, which have already been shown to have a unique structure with very desirable mechanical properties. The joint HRTEM study combined with modeling reveals new information regarding the chirality of the different shells and provides a better understanding of their growth mechanism. PMID:18838681

Atom by atom: HRTEM insights into inorganic nanotubes and fullerene-like structures.

PubMed

Bar Sadan, Maya; Houben, Lothar; Enyashin, Andrey N; Seifert, Gotthard; Tenne, Reshef

2008-10-14

The characterization of nanostructures down to the atomic scale is essential to understand some physical properties. Such a characterization is possible today using direct imaging methods such as aberration-corrected high-resolution transmission electron microscopy (HRTEM), when iteratively backed by advanced modeling produced by theoretical structure calculations and image calculations. Aberration-corrected HRTEM is therefore extremely useful for investigating low-dimensional structures, such as inorganic fullerene-like particles and inorganic nanotubes. The atomic arrangement in these nanostructures can lead to new insights into the growth mechanism or physical properties, where imminent commercial applications are unfolding. This article will focus on two structures that are symmetric and reproducible. The first structure that will be dealt with is the smallest stable symmetric closed-cage structure in the inorganic system, a MoS(2) nanooctahedron. It is investigated by means of aberration-corrected microscopy which allowed validating the suggested DFTB-MD model. It will be shown that structures diverging from the energetically most stable structures are present in the laser ablated soot and that the alignment of the different shells is parallel, unlike the bulk material where the alignment is antiparallel. These findings correspond well with the high-energy synthetic route and they provide more insight into the growth mechanism. The second structure studied is WS(2) nanotubes, which have already been shown to have a unique structure with very desirable mechanical properties. The joint HRTEM study combined with modeling reveals new information regarding the chirality of the different shells and provides a better understanding of their growth mechanism.

Structural Insights into Bacillus thuringiensis Cry, Cyt and Parasporin Toxins

PubMed Central

Xu, Chengchen; Wang, Bi-Cheng; Yu, Ziniu; Sun, Ming

2014-01-01

Since the first X-ray structure of Cry3Aa was revealed in 1991, numerous structures of B. thuringiensis toxins have been determined and published. In recent years, functional studies on the mode of action and resistance mechanism have been proposed, which notably promoted the developments of biological insecticides and insect-resistant transgenic crops. With the exploration of known pore-forming toxins (PFTs) structures, similarities between PFTs and B. thuringiensis toxins have provided great insights into receptor binding interactions and conformational changes from water-soluble to membrane pore-forming state of B. thuringiensis toxins. This review mainly focuses on the latest discoveries of the toxin working mechanism, with the emphasis on structural related progress. Based on the structural features, B. thuringiensis Cry, Cyt and parasporin toxins could be divided into three categories: three-domain type α-PFTs, Cyt toxin type β-PFTs and aerolysin type β-PFTs. Structures from each group are elucidated and discussed in relation to the latest data, respectively. PMID:25229189

RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution

PubMed Central

Venkataraman, Sangita; Prasad, Burra V L S; Selvarajan, Ramasamy

2018-01-01

RNA dependent RNA polymerase (RdRp) is one of the most versatile enzymes of RNA viruses that is indispensable for replicating the genome as well as for carrying out transcription. The core structural features of RdRps are conserved, despite the divergence in their sequences. The structure of RdRp resembles that of a cupped right hand and consists of fingers, palm and thumb subdomains. The catalysis involves the participation of conserved aspartates and divalent metal ions. Complexes of RdRps with substrates, inhibitors and metal ions provide a comprehensive view of their functional mechanism and offer valuable insights regarding the development of antivirals. In this article, we provide an overview of the structural aspects of RdRps and their complexes from the Group III, IV and V viruses and their structure-based phylogeny. PMID:29439438

Structural insights into binding of small molecule inhibitors to Enhancer of Zeste Homolog 2

NASA Astrophysics Data System (ADS)

Kalinić, Marko; Zloh, Mire; Erić, Slavica

2014-11-01

Enhancer of Zeste Homolog 2 (EZH2) is a SET domain protein lysine methyltransferase (PKMT) which has recently emerged as a chemically tractable and therapeutically promising epigenetic target, evidenced by the discovery and characterization of potent and highly selective EZH2 inhibitors. However, no experimental structures of the inhibitors co-crystallized to EZH2 have been resolved, and the structural basis for their activity and selectivity remains unknown. Considering the need to minimize cross-reactivity between prospective PKMT inhibitors, much can be learned from understanding the molecular basis for selective inhibition of EZH2. Thus, to elucidate the binding of small-molecule inhibitors to EZH2, we have developed a model of its fully-formed cofactor binding site and used it to carry out molecular dynamics simulations of protein-ligand complexes, followed by molecular mechanics/generalized born surface area calculations. The obtained results are in good agreement with biochemical inhibition data and reflect the structure-activity relationships of known ligands. Our findings suggest that the variable and flexible post-SET domain plays an important role in inhibitor binding, allowing possibly distinct binding modes of inhibitors with only small variations in their structure. Insights from this study present a good basis for design of novel and optimization of existing compounds targeting the cofactor binding site of EZH2.

Structural insights into the mechanisms of drug resistance in HIV-1 protease NL4-3.

PubMed

Heaslet, Holly; Kutilek, Victoria; Morris, Garrett M; Lin, Ying-Chuan; Elder, John H; Torbett, Bruce E; Stout, C David

2006-03-03

The development of resistance to anti-retroviral drugs targeted against HIV is an increasing clinical problem in the treatment of HIV-1-infected individuals. Many patients develop drug-resistant strains of the virus after treatment with inhibitor cocktails (HAART therapy), which include multiple protease inhibitors. Therefore, it is imperative that we understand the mechanisms by which the viral proteins, in particular HIV-1 protease, develop resistance. We have determined the three-dimensional structure of HIV-1 protease NL4-3 in complex with the potent protease inhibitor TL-3 at 2.0 A resolution. We have also obtained the crystal structures of three mutant forms of NL4-3 protease containing one (V82A), three (V82A, M46I, F53L) and six (V82A, M46I, F53L, V77I, L24I, L63P) point mutations in complex with TL-3. The three protease mutants arose sequentially under ex vivo selective pressure in the presence of TL-3, and exhibit fourfold, 11-fold, and 30-fold resistance to TL-3, respectively. This series of protease crystal structures offers insights into the biochemical and structural mechanisms by which the enzyme can overcome inhibition by TL-3 while recovering some of its native catalytic activity.

Structural Insights into Functional Overlapping and Differentiation among Myosin V Motors*

PubMed Central

Nascimento, Andrey F. Z.; Trindade, Daniel M.; Tonoli, Celisa C. C.; de Giuseppe, Priscila O.; Assis, Leandro H. P.; Honorato, Rodrigo V.; de Oliveira, Paulo S. L.; Mahajan, Pravin; Burgess-Brown, Nicola A.; von Delft, Frank; Larson, Roy E.; Murakami, Mario T.

2013-01-01

Myosin V (MyoV) motors have been implicated in the intracellular transport of diverse cargoes including vesicles, organelles, RNA-protein complexes, and regulatory proteins. Here, we have solved the cargo-binding domain (CBD) structures of the three human MyoV paralogs (Va, Vb, and Vc), revealing subtle structural changes that drive functional differentiation and a novel redox mechanism controlling the CBD dimerization process, which is unique for the MyoVc subclass. Moreover, the cargo- and motor-binding sites were structurally assigned, indicating the conservation of residues involved in the recognition of adaptors for peroxisome transport and providing high resolution insights into motor domain inhibition by CBD. These results contribute to understanding the structural requirements for cargo transport, autoinhibition, and regulatory mechanisms in myosin V motors. PMID:24097982

Structure of welded joints obtained by contact weld in nanostructured titanium

NASA Astrophysics Data System (ADS)

Klimenov, V. A.; Klopotov, A. A.; Gnysov, S. F.; Vlasov, V. A.; Lychagin, D. V.; Chumaevskii, A. V.

2015-10-01

The paper presents the research of the weld structure of two Ti specimens of the type VT6 that have nano- and submicrocrystalline structures. Electrical contact welding is used to obtain welds. The acicular structure is formed in the weld area. Two types of defects are detected, namely micropores and microcracks.

New insight in magnetic saturation behavior of nickel hierarchical structures

NASA Astrophysics Data System (ADS)

Ma, Ji; Zhang, Jianxing; Liu, Chunting; Chen, Kezheng

2017-09-01

It is unanimously accepted that non-ferromagnetic inclusions in a ferromagnetic system will lower down total saturation magnetization in unit of emu/g. In this study, ;lattice strain; was found to be another key factor to have critical impact on magnetic saturation behavior of the system. The lattice strain determined assembling patterns of primary nanoparticles in hierarchical structures and was intimately related with the formation process of these architectures. Therefore, flower-necklace-like and cauliflower-like nickel hierarchical structures were used as prototype systems to evidence the relationship between assembling patterns of primary nanoparticles and magnetic saturation behaviors of these architectures. It was found that the influence of lattice strain on saturation magnetization outperformed that of non-ferromagnetic inclusions in these hierarchical structures. This will enable new insights into fundamental understanding of related magnetic effects.

Structural insights into binding of inhibitors to soluble epoxide hydrolase gained by fragment screening and X-ray crystallography.

PubMed

Amano, Yasushi; Yamaguchi, Tomohiko; Tanabe, Eiki

2014-04-15

Soluble epoxide hydrolase (sEH) is a component of the arachidonic acid cascade and is a candidate target for therapies for hypertension or inflammation. Although many sEH inhibitors are available, their scaffolds are not structurally diverse, and knowledge of their specific interactions with sEH is limited. To obtain detailed structural information about protein-ligand interactions, we conducted fragment screening of sEH, analyzed the fragments using high-throughput X-ray crystallography, and determined 126 fragment-bound structures at high resolution. Aminothiazole and benzimidazole derivatives were identified as novel scaffolds that bind to the catalytic triad of sEH with good ligand efficiency. We further identified fragment hits that bound to subpockets of sEH called the short and long branches. The water molecule conserved in the structure plays an important role in binding to the long branch, whereas Asp496 and the main chain of Phe497 form hydrogen bonds with fragment hits in the short branch. Fragment hits and their crystal structures provide structural insights into ligand binding to sEH that will facilitate the discovery of novel and potent inhibitors of sEH. Copyright © 2014 Elsevier Ltd. All rights reserved.

Insights into Fanconi Anaemia from the structure of human FANCE

PubMed Central

Nookala, Ravi K.; Hussain, Shobbir; Pellegrini, Luca

2007-01-01

Fanconi Anaemia (FA) is a cancer predisposition disorder characterized by spontaneous chromosome breakage and high cellular sensitivity to genotoxic agents. In response to DNA damage, a multi-subunit assembly of FA proteins, the FA core complex, monoubiquitinates the downstream FANCD2 protein. The FANCE protein plays an essential role in the FA process of DNA repair as the FANCD2-binding component of the FA core complex. Here we report a crystallographic and biological study of human FANCE. The first structure of a FA protein reveals the presence of a repeated helical motif that provides a template for the structural rationalization of other proteins defective in Fanconi Anaemia. The portion of FANCE defined by our crystallographic analysis is sufficient for interaction with FANCD2, yielding structural information into the mode of FANCD2 recruitment to the FA core complex. Disease-associated mutations disrupt the FANCE–FANCD2 interaction, providing structural insight into the molecular mechanisms of FA pathogenesis. PMID:17308347

Structural insights into the intertwined dimer of fyn SH2.

PubMed

Huculeci, Radu; Garcia-Pino, Abel; Buts, Lieven; Lenaerts, Tom; van Nuland, Nico

2015-12-01

Src homology 2 domains are interaction modules dedicated to the recognition of phosphotyrosine sites incorporated in numerous proteins found in intracellular signaling pathways. Here we provide for the first time structural insight into the dimerization of Fyn SH2 both in solution and in crystalline conditions, providing novel crystal structures of both the dimer and peptide-bound structures of Fyn SH2. Using nuclear magnetic resonance chemical shift analysis, we show how the peptide is able to eradicate the dimerization, leading to monomeric SH2 in its bound state. Furthermore, we show that Fyn SH2's dimer form differs from other SH2 dimers reported earlier. Interestingly, the Fyn dimer can be used to construct a completed dimer model of Fyn without any steric clashes. Together these results extend our understanding of SH2 dimerization, giving structural details, on one hand, and suggesting a possible physiological relevance of such behavior, on the other hand. © 2015 The Protein Society.

Emerging structural insights into the function of ionotropic glutamate receptors

PubMed Central

Karakas, Erkan; Regan, Michael C.; Furukawa, Hiro

2015-01-01

Summary Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that mediate excitatory neurotransmission crucial for brain development and function including learning and memory formation. Recently a wealth of structural studies on iGluRs, including AMPA receptors (AMPARs), kainate receptors, and NMDA receptors (NMDARs) became available.. These studies showed structures of non-NMDARs including AMPAR and kainate receptor in various functional states, thereby providing the first visual sense of how non-NMDAR iGluRs may function in the context of homotetramers. Furthermore, they provided the first view of heterotetrameric NMDAR ion channels, which illuminated the similarities with and differences from non-NMDARs, thus raising a mechanistic distinction between the two groups of iGluRs. Here we review mechanistic insights into iGluR functions gained through structural studies of multiple groups. PMID:25941168

Emerging structural insights into the function of ionotropic glutamate receptors.

PubMed

Karakas, Erkan; Regan, Michael C; Furukawa, Hiro

2015-06-01

Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that mediate excitatory neurotransmission crucial for brain development and function, including learning and memory formation. Recently a wealth of structural studies on iGluRs including AMPA receptors (AMPARs), kainate receptors, and NMDA receptors (NMDARs) became available. These studies showed structures of non-NMDARs including AMPAR and kainate receptor in various functional states, thereby providing the first visual sense of how non-NMDAR iGluRs may function in the context of homotetramers. Furthermore, they provided the first view of heterotetrameric NMDAR ion channels, and this illuminated the similarities with and differences from non-NMDARs, thus raising a mechanistic distinction between the two groups of iGluRs. We review mechanistic insights into iGluR functions gained through structural studies of multiple groups. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structure of Cu/Ni Nanowires Obtained by Matrix Synthesis

NASA Astrophysics Data System (ADS)

Zhigalina, O. M.; Doludenko, I. M.; Khmelenin, D. N.; Zagorskiy, D. L.; Bedin, S. A.; Ivanov, I. M.

2018-05-01

The structure of layered Cu/Ni nanowires obtained by template synthesis in 100-nm channels of track membranes has been investigated by transmission and scanning electron microscopy. The phase composition and main structural features of individual nanowires are determined. It is shown that nanowires consist of alternating Ni ( Fm3m) and Cu ( Fm3m) layers with grains up to 100 nm in size. It is found that nanowires contain also copper oxide crystallites up to 20 nm in size. The elemental composition of individual layers and their mutual arrangement are determined.

Insight, self-stigma and psychosocial outcomes in Schizophrenia: a structural equation modelling approach.

PubMed

Lien, Y-J; Chang, H-A; Kao, Y-C; Tzeng, N-S; Lu, C-W; Loh, C-H

2018-04-01

Poor insight is prevalent in patients with schizophrenia and has been associated with acute illness severity, medication non-adherence and poor treatment outcomes. Paradoxically, high insight has been associated with various undesirable outcomes, including low self-esteem, depression and low subjective quality of life (QoL) in patients with schizophrenia. Despite the growing body of studies conducted in Western countries supporting the pernicious effects of improved insight in psychosis, which bases on the level of self-stigma, the effects are unclear in non-Western societies. The current study examined the role of self-stigma in the relationship between insight and psychosocial outcomes in a Chinese population. A total of 170 outpatients with schizophrenia spectrum disorders were recruited from two general university hospitals. Sociodemographic data and clinical variables were recorded and self-report scales were employed to measure self-stigma, depression, insight, self-esteem and subjective QoL. Structural equation modelling (SEM) was used to analyse the cross-sectional data. High levels of self-stigma were reported by 39% of the participants (n = 67). The influences of insight, self-stigma, self-esteem and depression on subjective QoL were confirmed by the SEM results. Our model with the closest fit to the data (χ 2 = 33.28; df = 20; p = 0.03; χ 2/df = 1.66; CFI = 0.98; TLI = 0.97; RMSEA = 0.06) demonstrated that self-stigma might fully mediate the association of insight with low self-esteem, depression and poor subjective QoL. High insight into illness contributed to self-stigma, which caused low self-esteem and depression and, consequently, low QoL. Notably, insight did not directly affect self-esteem, depression or QoL. Furthermore, the association of insight with poor psychosocial outcomes was not moderated by self-stigma. Our findings support the mediating model of insight relevant to the poor psychosocial outcomes of individuals diagnosed with

Biophysical studies suggest a new structural arrangement of crotoxin and provide insights into its toxic mechanism

PubMed Central

Fernandes, Carlos A. H.; Pazin, Wallance M.; Dreyer, Thiago R.; Bicev, Renata N.; Cavalcante, Walter L. G.; Fortes-Dias, Consuelo L.; Ito, Amando S.; Oliveira, Cristiano L. P.; Fernandez, Roberto Morato; Fontes, Marcos R. M.

2017-01-01

Crotoxin (CTX) is the main neurotoxin found in Crotalus durissus rattlesnake venoms being composed by a nontoxic and non-enzymatic component (CA) and a toxic phospholipase A2 (CB). Previous crystallographic structures of CTX and CB provided relevant insights: (i) CTX structure showed a 1:1 molecular ratio between CA and CB, presenting three tryptophan residues in the CA/CB interface and one exposed to solvent; (ii) CB structure displayed a tetrameric conformation. This study aims to provide further information on the CTX mechanism of action by several biophysical methods. Our data show that isolated CB can in fact form tetramers in solution; however, these tetramers can be dissociated by CA titration. Furthermore, CTX exhibits a strong reduction in fluorescence intensity and lifetime compared with isolated CA and CB, suggesting that all tryptophan residues in CTX may be hidden by the CA/CB interface. By companying spectroscopy fluorescence and SAXS data, we obtained a new structural model for the CTX heterodimer in which all tryptophans are located in the interface, and the N-terminal region of CB is largely exposed to the solvent. Based on this model, we propose a toxic mechanism of action for CTX, involving the interaction of N-terminal region of CB with the target before CA dissociation. PMID:28256632

Biophysical studies suggest a new structural arrangement of crotoxin and provide insights into its toxic mechanism.

PubMed

Fernandes, Carlos A H; Pazin, Wallance M; Dreyer, Thiago R; Bicev, Renata N; Cavalcante, Walter L G; Fortes-Dias, Consuelo L; Ito, Amando S; Oliveira, Cristiano L P; Fernandez, Roberto Morato; Fontes, Marcos R M

2017-03-03

Crotoxin (CTX) is the main neurotoxin found in Crotalus durissus rattlesnake venoms being composed by a nontoxic and non-enzymatic component (CA) and a toxic phospholipase A 2 (CB). Previous crystallographic structures of CTX and CB provided relevant insights: (i) CTX structure showed a 1:1 molecular ratio between CA and CB, presenting three tryptophan residues in the CA/CB interface and one exposed to solvent; (ii) CB structure displayed a tetrameric conformation. This study aims to provide further information on the CTX mechanism of action by several biophysical methods. Our data show that isolated CB can in fact form tetramers in solution; however, these tetramers can be dissociated by CA titration. Furthermore, CTX exhibits a strong reduction in fluorescence intensity and lifetime compared with isolated CA and CB, suggesting that all tryptophan residues in CTX may be hidden by the CA/CB interface. By companying spectroscopy fluorescence and SAXS data, we obtained a new structural model for the CTX heterodimer in which all tryptophans are located in the interface, and the N-terminal region of CB is largely exposed to the solvent. Based on this model, we propose a toxic mechanism of action for CTX, involving the interaction of N-terminal region of CB with the target before CA dissociation.

Structural Insights on the Mycobacterium tuberculosis Proteasomal ATPase Mpa

PubMed Central

Wang, Tao; Li, Hua; Lin, Gang; Tang, Chunyan; Li, Dongyang; Nathan, Carl; Darwin, K. Heran; Li, Huilin

2009-01-01

Summary Proteasome-mediated protein turnover in all domains of life is an energy-dependent process that requires ATPase activity. Mycobacterium tuberculosis (Mtb) was recently shown to possess a ubiquitin-like proteasome pathway that plays an essential role in Mtb resistance to killing by products of host macrophages. Here we report our structural and biochemical investigation of Mpa, the presumptive Mtb proteasomal ATPase. We demonstrate that Mpa binds to the Mtb proteasome in the presence of ATPγS, providing the physical evidence that Mpa is the proteasomal ATPase. X-ray crystallographic determination of the conserved inter-domain showed a five-stranded double β-barrel structure containing a Greek key motif. The structure and mutagenesis indicate a major role of the inter-domain for Mpa hexamerization. Our mutational and functional studies further suggest that the central channel in the Mpa hexamer is involved in protein substrate translocation and degradation. These studies provide insights into how a bacterial proteasomal ATPase interacts with and facilitates protein degradation by the proteasome. PMID:19836337

The Manifest Association Structure of the Single-Factor Model: Insights from Partial Correlations

ERIC Educational Resources Information Center

Salgueiro, Maria de Fatima; Smith, Peter W. F.; McDonald, John W.

2008-01-01

The association structure between manifest variables arising from the single-factor model is investigated using partial correlations. The additional insights to the practitioner provided by partial correlations for detecting a single-factor model are discussed. The parameter space for the partial correlations is presented, as are the patterns of…

Proofs that Develop Insight

ERIC Educational Resources Information Center

Weber, Keith

2010-01-01

Many mathematics educators have noted that mathematicians do not only read proofs to gain conviction but also to obtain insight. The goal of this article is to discuss what this insight is from mathematicians' perspective. Based on interviews with nine research-active mathematicians, two sources of insight are discussed. The first is reading a…

Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

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

Sidhu, Navdeep S.; University of Göttingen, Tammannstrasse 4, 37077 Göttingen; Schreiber, Kathrin

2014-05-01

Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However,more » the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.« less

Effects of sub-clinical psychosis and cognitive insight on psychological well-being: a structural equation model.

PubMed

Weintraub, Marc J; Weisman de Mamani, Amy

2015-03-30

Psychological well-being has been widely researched along the psychosis spectrum, and increased psychotic symptoms are generally associated with worse well-being. Additionally, the construct of insight has been extensively studied in schizophrenia. While having greater insight has many benefits for those with schizophrenia, a paradox exists in which greater insight is also associated with poorer psychological well-being. However, it is unclear whether the link between insight and poor well-being occurs only once serious psychopathology has been established, or whether this is a more universal process seen even at lower levels on the psychosis spectrum. We used a structural modeling approach in an ethnically diverse, non-clinical sample of 420 undergraduates to evaluate the association between sub-clinical psychosis, cognitive insight and psychological well-being. As hypothesized, results indicated that sub-clinical psychotic symptoms were negatively associated with psychological well-being. The insight paradox was also substantiated, as greater cognitive insight was associated with worse psychological well-being. However, cognitive insight did not moderate the association between symptoms and well-being. The link between sub-clinical psychotic symptoms and psychological well-being as well as the insight paradox appears to emerge even before reaching threshold for a psychotic disorder. Research and clinical implications are discussed. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Structural insights into xenobiotic and inhibitor binding to human aldehyde oxidase.

PubMed

Coelho, Catarina; Foti, Alessandro; Hartmann, Tobias; Santos-Silva, Teresa; Leimkühler, Silke; Romão, Maria João

2015-10-01

Aldehyde oxidase (AOX) is a xanthine oxidase (XO)-related enzyme with emerging importance due to its role in the metabolism of drugs and xenobiotics. We report the first crystal structures of human AOX1, substrate free (2.6-Å resolution) and in complex with the substrate phthalazine and the inhibitor thioridazine (2.7-Å resolution). Analysis of the protein active site combined with steady-state kinetic studies highlight the unique features, including binding and substrate orientation at the active site, that characterize human AOX1 as an important drug-metabolizing enzyme. Structural analysis of the complex with the noncompetitive inhibitor thioridazine revealed a new, unexpected and fully occupied inhibitor-binding site that is structurally conserved among mammalian AOXs and XO. The new structural insights into the catalytic and inhibition mechanisms of human AOX that we now report will be of great value for the rational analysis of clinical drug interactions involving inhibition of AOX1 and for the prediction and design of AOX-stable putative drugs.

Structure/function relationships in serotonin transporter: new insights from the structure of a bacterial transporter.

PubMed

Rudnick, G

2006-01-01

Serotonin transporter (SERT) serves the important function of taking up serotonin (5-HT) released during serotonergic neurotransmission. It is the target for important therapeutic drugs and psychostimulants. SERT catalyzes the influx of 5-HT together with Na+ and Cl- in a 1:1:1 stoichiometry. In the same catalytic cycle, there is coupled efflux of one K+ ion. SERT is one member of a large family of amino acid and amine transporters that is believed to utilize similar mechanisms of transport. A bacterial member of this family was recently crystallized, revealing the structural basis of these transporters. In light of the new structure, previous results with SERT have been re-interpreted, providing new insight into the substrate binding site, the permeation pathway, and the conformational changes that occur during the transport cycle.

Structure of Human GIVD Cytosolic Phospholipase A2 Reveals Insights into Substrate Recognition

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

Wang, Hui; Klein, Michael G.; Snell, Gyorgy

Cytosolic phospholipases A2 (cPLA2s) consist of a family of calcium-sensitive enzymes that function to generate lipid second messengers through hydrolysis of membrane-associated glycerophospholipids. The GIVD cPLA2 (cPLA2δ) is a potential drug target for developing a selective therapeutic agent for the treatment of psoriasis. Here, we present two X-ray structures of human cPLA2δ, capturing an apo state, and in complex with a substrate-like inhibitor. Comparison of the apo and inhibitor-bound structures reveals conformational changes in a flexible cap that allows the substrate to access the relatively buried active site, providing new insight into the mechanism for substrate recognition. The cPLA2δ structuremore » reveals an unexpected second C2 domain that was previously unrecognized from sequence alignments, placing cPLA2δ into the class of membrane-associated proteins that contain a tandem pair of C2 domains. Furthermore, our structures elucidate novel inter-domain interactions and define three potential calcium-binding sites that are likely important for regulation and activation of enzymatic activity. These findings provide novel insights into the molecular mechanisms governing cPLA2's function in signal transduction.« less

Assessing cognitive insight in nonpsychiatric individuals and outpatients with schizophrenia in Taiwan: an investigation using the Beck Cognitive Insight Scale

PubMed Central

2011-01-01

Background The Beck Cognitive Insight Scale (BCIS) was designed for the assessment of the cognitive processes involved in self-reflection and the ability to modify erroneous beliefs and misinterpretations. Studies investigating the factor structure of the BCIS have indicated a two-factor model in the psychotic population. The factor structure of the BCIS, however, has not received much consideration in the nonpsychiatric population. The present study examined the factor structure and validity of the BCIS and compared its scores between nonpsychiatric individuals and outpatients with psychosis. Method The Taiwanese version of the BCIS was administered to 507 nonpsychiatric individuals and 118 outpatients with schizophrenia. The psychometric properties of the BCIS were examined through the following analyses: exploratory and confirmatory factor analyses, reliability, correlation analyses, and discriminative validity. Results The BCIS showed adequate internal consistency and stability over time. Exploratory and confirmatory factor analyses on the 15-item measure indicated a two-factor solution that supported the two dimensions of the Taiwanese BCIS, which was also observed with the original BCIS. Following the construct validation, we obtained a composite index (self-reflectiveness minus self-certainty) of the Taiwanese BCIS that reflected cognitive insight. Consistent with previous studies, our results indicated that psychosis is associated with low self-reflectiveness and high self-certainty, which possibly reflect lower cognitive insight. Our results also showed that better cognitive insight is related to worse depression in patients with schizophrenia spectrum disorders, but not in nonpsychiatric individuals. The receiver operating characteristic (ROC) analyses revealed that the area under the curve (AUC) was 0.731. A composite index of 3 was a good limit, with a sensitivity of 87% and a specificity of 51%. Conclusion The BCIS proved to be useful for measuring

Insights into the dynamics of planetary interiors obtained through the study of global distribution of volcanoes I: Empirical calibration on Earth

NASA Astrophysics Data System (ADS)

Cañon-Tapia, Edgardo; Mendoza-Borunda, Ramón

2014-06-01

The distribution of volcanic features is ultimately controlled by processes taking place beneath the surface of a planet. For this reason, characterization of volcano distribution at a global scale can be used to obtain insights concerning dynamic aspects of planetary interiors. Until present, studies of this type have focused on volcanic features of a specific type, or have concentrated on relatively small regions. In this paper, (the first of a series of three papers) we describe the distribution of volcanic features observed over the entire surface of the Earth, combining an extensive database of submarine and subaerial volcanoes. The analysis is based on spatial density contours obtained with the Fisher kernel. Based on an empirical approach that makes no a priori assumptions concerning the number of modes that should characterize the density distribution of volcanism we identified the most significant modes. Using those modes as a base, the relevant distance for the formation of clusters of volcanoes is constrained to be on the order of 100 to 200 km. In addition, it is noted that the most significant modes lead to the identification of clusters that outline the most important tectonic margins on Earth without the need of making any ad hoc assumptions. Consequently, we suggest that this method has the potential of yielding insights about the probable occurrence of tectonic features within other planets.

Magnetic apatite for structural insights on the plasma membrane

NASA Astrophysics Data System (ADS)

Stanca, Sarmiza E.; Müller, Robert; Dellith, Jan; Nietzsche, Sandor; Stöckel, Stephan; Biskup, Christoph; Deckert, Volker; Krafft, Christoph; Popp, Jürgen; Fritzsche, Wolfgang

2015-01-01

The iron oxide-hydroxyapatite (FeOxHA) nanoparticles reported here differ from those reported before by their advantage of homogeneity and simple preparation; moreover, the presence of carboxymethyldextran (CMD), together with hydroxyapatite (HA), allows access to the cellular membrane, which makes our magnetic apatite unique. These nanoparticles combine magnetic behavior, Raman label ability and the property of interaction with the cellular membrane; they therefore represent an interesting material for structural differentiation of the cell membrane. It was observed by Raman spectroscopy, scanning electron microscopy (SEM) and fluorescence microscopy that FeOxHA adheres to the plasma membrane and does not penetrate the membrane. These insights make the nanoparticles a promising material for magnetic cell sorting, e.g. in microfluidic device applications.

Magnetic apatite for structural insights on the plasma membrane.

PubMed

Stanca, Sarmiza E; Müller, Robert; Dellith, Jan; Nietzsche, Sandor; Stöckel, Stephan; Biskup, Christoph; Deckert, Volker; Krafft, Christoph; Popp, Jürgen; Fritzsche, Wolfgang

2015-01-21

The iron oxide-hydroxyapatite (FeOxHA) nanoparticles reported here differ from those reported before by their advantage of homogeneity and simple preparation; moreover, the presence of carboxymethyldextran (CMD), together with hydroxyapatite (HA), allows access to the cellular membrane, which makes our magnetic apatite unique. These nanoparticles combine magnetic behavior, Raman label ability and the property of interaction with the cellular membrane; they therefore represent an interesting material for structural differentiation of the cell membrane. It was observed by Raman spectroscopy, scanning electron microscopy (SEM) and fluorescence microscopy that FeOxHA adheres to the plasma membrane and does not penetrate the membrane. These insights make the nanoparticles a promising material for magnetic cell sorting, e.g. in microfluidic device applications.

Structure and photochromic properties of molybdenum-containing silica gels obtained by molecular-lamination method

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

Belotserkovskaya, N.G.; Dobychin, D.P.; Pak, V.N.

1992-05-10

The structure and physicochemical properties of molybdenum-containing silica gels obtained by molecular lamination have been studied quite extensively. Up to the present, however, no studies have been made of the influence of the pore structure of the original silica gel on the structure and properties of molybdenum-containing silica gels (MSG). The problem is quite important, since molybdenum silicas obtained by molecular lamination may find applications in catalysis and as sensors of UV radiation. In either case, the structure of the support is not a factor to be ignored. Here, the authors are reporting on an investigation of the structure ofmore » MSG materials with different pore structures and their susceptibility to reduction of the Mo(VI) oxide groupings when exposed to UV radiation. 16 refs., 2 figs., 2 tabs.« less

Yes, one can obtain better quality structures from routine X-ray data collection.

PubMed

Sanjuan-Szklarz, W Fabiola; Hoser, Anna A; Gutmann, Matthias; Madsen, Anders Østergaard; Woźniak, Krzysztof

2016-01-01

Single-crystal X-ray diffraction structural results for benzidine dihydrochloride, hydrated and protonated N,N,N,N-peri(dimethylamino)naphthalene chloride, triptycene, dichlorodimethyltriptycene and decamethylferrocene have been analysed. A critical discussion of the dependence of structural and thermal parameters on resolution for these compounds is presented. Results of refinements against X-ray data, cut off to different resolutions from the high-resolution data files, are compared to structural models derived from neutron diffraction experiments. The Independent Atom Model (IAM) and the Transferable Aspherical Atom Model (TAAM) are tested. The average differences between the X-ray and neutron structural parameters (with the exception of valence angles defined by H atoms) decrease with the increasing 2θmax angle. The scale of differences between X-ray and neutron geometrical parameters can be significantly reduced when data are collected to the higher, than commonly used, 2θmax diffraction angles (for Mo Kα 2θmax > 65°). The final structural and thermal parameters obtained for the studied compounds using TAAM refinement are in better agreement with the neutron values than the IAM results for all resolutions and all compounds. By using TAAM, it is still possible to obtain accurate results even from low-resolution X-ray data. This is particularly important as TAAM is easy to apply and can routinely be used to improve the quality of structural investigations [Dominiak (2015 ▸). LSDB from UBDB. University of Buffalo, USA]. We can recommend that, in order to obtain more adequate (more accurate and precise) structural and displacement parameters during the IAM model refinement, data should be collected up to the larger diffraction angles, at least, for Mo Kα radiation to 2θmax = 65° (sin θmax/λ < 0.75 Å(-1)). The TAAM approach is a very good option to obtain more adequate results even using data collected to the lower 2θmax angles. Also

Correlation of MFOLD-predicted DNA secondary structures with separation patterns obtained by capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis.

PubMed

Glavac, Damjan; Potocnik, Uros; Podpecnik, Darja; Zizek, Teofil; Smerkolj, Sava; Ravnik-Glavac, Metka

2002-04-01

We have studied 57 different mutations within three beta-globin gene promoter fragments with sizes 52 bp, 77 bp, and 193 bp by fluorescent capillary electrophoresis CE-SSCP analysis. For each mutation and wild type, energetically most-favorable predicted secondary structures were calculated for sense and antisense strands using the MFOLD DNA-folding algorithm in order to investigate if any correlation exists between predicted DNA structures and actual CE migration time shifts. The overall CE-SSCP detection rate was 100% for all mutations in three studied DNA fragments. For shorter 52 bp and 77 bp DNA fragments we obtained a positive correlation between the migration time shifts and difference in free energy values of predicted secondary structures at all temperatures. For longer 193 bp beta-globin gene fragments with 46 mutations MFOLD predicted different secondary structures for 89% of mutated strands at 25 degrees C and 40 degrees C. However, the magnitude of the mobility shifts did not necessarily correlate with their secondary structures and free energy values except for the sense strand at 40 degrees C where this correlation was statistically significant (r = 0.312, p = 0.033). Results of this study provided more direct insight into the mechanism of CE-SSCP and showed that MFOLD prediction could be helpful in making decisions about the running temperatures and in prediction of CE-SSCP data patterns, especially for shorter (50-100 bp) DNA fragments. Copyright 2002 Wiley-Liss, Inc.

Vertebrate Membrane Proteins: Structure, Function, and Insights from Biophysical Approaches

PubMed Central

MÜLLER, DANIEL J.; WU, NAN; PALCZEWSKI, KRZYSZTOF

2008-01-01

Membrane proteins are key targets for pharmacological intervention because they are vital for cellular function. Here, we analyze recent progress made in the understanding of the structure and function of membrane proteins with a focus on rhodopsin and development of atomic force microscopy techniques to study biological membranes. Membrane proteins are compartmentalized to carry out extra- and intracellular processes. Biological membranes are densely populated with membrane proteins that occupy approximately 50% of their volume. In most cases membranes contain lipid rafts, protein patches, or paracrystalline formations that lack the higher-order symmetry that would allow them to be characterized by diffraction methods. Despite many technical difficulties, several crystal structures of membrane proteins that illustrate their internal structural organization have been determined. Moreover, high-resolution atomic force microscopy, near-field scanning optical microscopy, and other lower resolution techniques have been used to investigate these structures. Single-molecule force spectroscopy tracks interactions that stabilize membrane proteins and those that switch their functional state; this spectroscopy can be applied to locate a ligand-binding site. Recent development of this technique also reveals the energy landscape of a membrane protein, defining its folding, reaction pathways, and kinetics. Future development and application of novel approaches during the coming years should provide even greater insights to the understanding of biological membrane organization and function. PMID:18321962

Structural Insights into the Coupling of Virion Assembly and Rotavirus Replication

PubMed Central

Trask, Shane D.; McDonald, Sarah M.; Patton, John T.

2013-01-01

Preface Viral replication is rapid and robust, but it is far from a chaotic process. Instead, successful production of infectious progeny requires that events occur in the correct place and at the correct time. Rotavirus, a segmented double-stranded RNA virus of the Reoviridae family, seems to govern its replication through ordered disassembly and assembly of a triple-layered icosahedral capsid. In recent years, high-resolution structural data have provided unprecedented insight into these events. In this Review, we explore the current understanding of rotavirus replication and how it compares to other Reoviridae family members. PMID:22266782

Structural insights into μ-opioid receptor activation

PubMed Central

Huang, Weijiao; Manglik, Aashish; Venkatakrishnan, A. J.; Laeremans, Toon; Feinberg, Evan N.; Sanborn, Adrian L.; Kato, Hideaki E.; Livingston, Kathryn E.; Thorsen, Thor S.; Kling, Ralf; Granier, Sébastien; Gmeiner, Peter; Husbands, Stephen M.; Traynor, John R.; Weis, William I.; Steyaert, Jan; Dror, Ron O.; Kobilka, Brian K.

2015-01-01

Summary Activation of the μ-opioid receptor (μOR) is responsible for the efficacy of the most effective analgesics. To understand the structural basis for μOR activation, we obtained a 2.1 Å X-ray crystal structure of the μOR bound to the morphinan agonist BU72 and stabilized by a G protein-mimetic camelid-antibody fragment. The BU72-stabilized changes in the μOR binding pocket are subtle and differ from those observed for agonist-bound structures of the β2 adrenergic receptor (β2AR) and the M2 muscarinic receptor (M2R). Comparison with active β2AR reveals a common rearrangement in the packing of three conserved amino acids in the core of the μOR, and molecular dynamics simulations illustrate how the ligand-binding pocket is conformationally linked to this conserved triad. Additionally, an extensive polar network between the ligand-binding pocket and the cytoplasmic domains appears to play a similar role in signal propagation for all three GPCRs. PMID:26245379

Strategies for fixing the CKM-angle γ and obtaining experimental insights into the world of electroweak penguins

NASA Astrophysics Data System (ADS)

Fleischer, Robert

1996-02-01

Using the SU(3) flavour symmetry of strong interactions, we propose strategies for extracting both the CKM-angle γ and the overlineb → overlineuu overlines tree-level amplitude T‧. We present also an approximate approach using the branching ratios for the modes B+ → π+K0, Bd0 → π-K+, overlineBd0 → π +K - and B+ → π+π0 which should be rather promising from the experimental point of view. The quantities γ and T‧ determined this way may well be used as an input to control electroweak penguins in nonleptonic B-decays as has been discussed in previous work. Following these lines, we propose strategies for obtaining quantitative insights into the physics of the electroweak penguin operators and performing some consistency checks. As a by-product, we derive an upper bound of 6° for the uncertainty originating from electroweak penguins in the α-determination by means of B → ππ decays.

New insights into structural determinants of prion protein folding and stability.

PubMed

Benetti, Federico; Legname, Giuseppe

2015-01-01

Prions are the etiological agent of fatal neurodegenerative diseases called prion diseases or transmissible spongiform encephalopathies. These maladies can be sporadic, genetic or infectious disorders. Prions are due to post-translational modifications of the cellular prion protein leading to the formation of a β-sheet enriched conformer with altered biochemical properties. The molecular events causing prion formation in sporadic prion diseases are still elusive. Recently, we published a research elucidating the contribution of major structural determinants and environmental factors in prion protein folding and stability. Our study highlighted the crucial role of octarepeats in stabilizing prion protein; the presence of a highly enthalpically stable intermediate state in prion-susceptible species; and the role of disulfide bridge in preserving native fold thus avoiding the misfolding to a β-sheet enriched isoform. Taking advantage from these findings, in this work we present new insights into structural determinants of prion protein folding and stability.

A structural insight into the P1S1 binding mode of diaminoethylphosphonic and phosphinic acids, selective inhibitors of alanine aminopeptidases

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

Węglarz-Tomczak, Ewelina; Berlicki, Łukasz; Pawełczak, Małgorzata

N0 -substituted 1,2-diaminoethylphosphonic acids and 1,2-diaminoethylphosphinic dipeptides were explored to unveil the structural context of the unexpected selectivity of these inhibitors of M1 alanine aminopeptidases (APNs) versus M17 leucine aminopeptidase (LAP). The diaminophosphonic acids were obtained via aziridines in an improved synthetic procedure that was further expanded for the phosphinic pseudodipeptide system. The inhibitory activity, measured for three M1 and one M17 metalloaminopeptidases of different sources (bacterial, human and porcine), revealed several potent compounds (e.g., Ki ¼ 65 nM of 1u for HsAPN). Two structures of an M1 representative (APN from Neisseria meningitidis) in complex with N-benzyl-1,2-diaminoethylphosphonic acid and N-cyclohexyl-1,2-more » diaminoethylphosphonic acid were determined by the X-ray crystallography. The analysis of these structures and the models of the phosphonic acid complexes of the human ortholog provided an insight into the role of the additional amino group and the hydrophobic substituents of the ligands within the S1 active site region.« less

Experimental Insights into the Origin of Defect-Structured Hibonites Found in Meteorites

NASA Technical Reports Server (NTRS)

Han. J.; Keller, L. P.; Danielson, L. R.

2016-01-01

Hibonite (CaAl12O19) is a primary, highly refractory phase occurring in many Ca-Al-rich inclusions (CAIs). Previous microstructural studies of hibonite in CAIs and their Wark-Lovering (WL) rims showed the presence of numerous stacking defects in hibonites. These defects are interpreted as the modification of the stacking sequences of spinel and Ca-containing blocks within the ideal hexagonal hibonite structure due to the presence of wider spinel blocks [3], as shown by experimental studies of reaction-sintered compounds in the CaO-Al2O3 system. We performed a series of experiments in the CaO-Al2O3-MgO system in order to provide additional in-sights into the formation processes and conditions of defect-structured hibonites found in meteorites.

The crystal structure of P450-TT heme-domain provides the first structural insights into the versatile class VII P450s.

PubMed

Tavanti, Michele; Porter, Joanne L; Levy, Colin W; Gómez Castellanos, J Rubén; Flitsch, Sabine L; Turner, Nicholas J

2018-07-02

The first crystal structure of a class VII P450, CYP116B46 from Tepidiphilus thermophilus, has been solved at 1.9 Å resolution. The structure reveals overall conservation of the P450-fold and a water conduit around the I-helix. Active site residues have been identified and sequence comparisons have been made with other class VII enzymes. A structure similarity search demonstrated that the P450-TT structure is similar to enzymes capable of oxy-functionalization of fatty acids, terpenes, macrolides, steroids and statins. The insight gained from solving this structure will provide a guideline for future engineering and modelling studies on this catalytically promiscuous class of enzymes. Copyright © 2018 Elsevier Inc. All rights reserved.

The X-Ray Crystal Structure of Escherichia coli Succinic Semialdehyde Dehydrogenase; Structural Insights into NADP+/Enzyme Interactions

PubMed Central

Langendorf, Christopher G.; Key, Trevor L. G.; Fenalti, Gustavo; Kan, Wan-Ting; Buckle, Ashley M.; Caradoc-Davies, Tom; Tuck, Kellie L.; Law, Ruby H. P.; Whisstock, James C.

2010-01-01

Background In mammals succinic semialdehyde dehydrogenase (SSADH) plays an essential role in the metabolism of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) to succinic acid (SA). Deficiency of SSADH in humans results in elevated levels of GABA and γ-Hydroxybutyric acid (GHB), which leads to psychomotor retardation, muscular hypotonia, non-progressive ataxia and seizures. In Escherichia coli, two genetically distinct forms of SSADHs had been described that are essential for preventing accumulation of toxic levels of succinic semialdehyde (SSA) in cells. Methodology/Principal Findings Here we structurally characterise SSADH encoded by the E coli gabD gene by X-ray crystallographic studies and compare these data with the structure of human SSADH. In the E. coli SSADH structure, electron density for the complete NADP+ cofactor in the binding sites is clearly evident; these data in particular revealing how the nicotinamide ring of the cofactor is positioned in each active site. Conclusions/Significance Our structural data suggest that a deletion of three amino acids in E. coli SSADH permits this enzyme to use NADP+, whereas in contrast the human enzyme utilises NAD+. Furthermore, the structure of E. coli SSADH gives additional insight into human mutations that result in disease. PMID:20174634

Structural insights into the molecular mechanisms of myasthenia gravis and their therapeutic implications

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

Noridomi, Kaori; Watanabe, Go; Hansen, Melissa N.

The nicotinic acetylcholine receptor (nAChR) is a major target of autoantibodies in myasthenia gravis (MG), an autoimmune disease that causes neuromuscular transmission dysfunction. Despite decades of research, the molecular mechanisms underlying MG have not been fully elucidated. Here, we present the crystal structure of the nAChR α1 subunit bound by the Fab fragment of mAb35, a reference monoclonal antibody that causes experimental MG and competes with ~65% of antibodies from MG patients. Our structures reveal for the first time the detailed molecular interactions between MG antibodies and a core region on nAChR α1. These structures suggest a major nAChR-binding mechanismmore » shared by a large number of MG antibodies and the possibility to treat MG by blocking this binding mechanism. Structure-based modeling also provides insights into antibody-mediated nAChR cross-linking known to cause receptor degradation. Our studies establish a structural basis for further mechanistic studies and therapeutic development of MG.« less

Insight in first-episode psychosis.

PubMed

McEvoy, Joseph P; Johnson, Jackie; Perkins, Diana; Lieberman, Jeffrey A; Hamer, Robert M; Keefe, Richard S E; Tohen, Mauricio; Glick, Ira D; Sharma, Tonmoy

2006-10-01

We report here a study examining the relationships between insight and psychopathology, cognitive performance, brain volume and co-morbid depression in 251 patients experiencing a first episode of psychosis, who were then randomly assigned to 2 years of double-blind treatment with either olanzapine or haloperidol. Repeated measures of insight were obtained at baseline and 12, 24, 52 and 104 weeks by the Insight and Treatment Attitudes Questionnaire (ITAQ). Older age, female gender and white ethnicity were associated with more insight. Higher total, positive, negative and general psychopathology scores on the Positive and Negative Syndromes Scale (PANSS) were associated with less insight. Higher depression scores were associated with more insight. Better neurocognitive function and large brain volumes were associated with more insight. More insight throughout the study was associated with longer time to medication non-adherence. However, baseline insight was not significantly related to the probability of discontinuing the study before 2 years. Insight improved significantly over the course of the study, but the improvement in insight was not significantly different between the two antipsychotic treatment groups. Multiple factors contribute to insight. Patients experiencing a first episode of psychosis who have little insight are at increased risk of discontinuing their medication.

New Insights Toward Quantitative Relationships between Lignin Reactivity to Monomers and Their Structural Characteristics.

PubMed

Ma, Ruoshui; Zhang, Xiumei; Wang, Yi; Zhang, Xiao

2018-04-27

The heterogeneous and complex structural characteristics of lignin present a significant challenge to predict its processability (e.g. depolymerization, modifications etc) to valuable products. This study provides a detailed characterization and comparison of structural properties of seven representative biorefinery lignin samples derived from forest and agricultural residues, which were subjected to representative pretreatment methods. A range of wet chemistry and spectroscopy methods were applied to determine specific lignin structural characteristics such as functional groups, inter-unit linkages and peak molecular weight. In parallel, oxidative depolymerization of these lignin samples to either monomeric phenolic compounds or dicarboxylic acids were conducted, and the product yields were quantified. Based on these results (lignin structural characteristics and monomer yields), we demonstrated for the first time to apply multiple-variable linear estimations (MVLE) approach using R statistics to gain insight toward a quantitative correlation between lignin structural properties and their conversion reactivity toward oxidative depolymerization to monomers. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure-based Insights into the Catalytic Power and Conformational Dexterity of Peroxiredoxins

PubMed Central

Hall, Andrea; Nelson, Kimberly; Poole, Leslie B.

2011-01-01

Abstract Peroxiredoxins (Prxs), some of nature's dominant peroxidases, use a conserved Cys residue to reduce peroxides. They are highly expressed in organisms from all kingdoms, and in eukaryotes they participate in hydrogen peroxide signaling. Seventy-two Prx structures have been determined that cover much of the diversity of the family. We review here the current knowledge and show that Prxs can be effectively classified by a structural/evolutionary organization into six subfamilies followed by specification of a 1-Cys or 2-Cys mechanism, and for 2-Cys Prxs, the structural location of the resolving Cys. We visualize the varied catalytic structural transitions and highlight how they differ depending on the location of the resolving Cys. We also review new insights into the question of how Prxs are such effective catalysts: the enzyme activates not only the conserved Cys thiolate but also the peroxide substrate. Moreover, the hydrogen-bonding network created by the four residues conserved in all Prx active sites stabilizes the transition state of the peroxidatic SN2 displacement reaction. Strict conservation of the peroxidatic active site along with the variation in structural transitions provides a fascinating picture of how the diverse Prxs function to break down peroxide substrates rapidly. Antioxid. Redox Signal. 15, 795–815. PMID:20969484

Process for using surface strain measurements to obtain operational loads for complex structures

NASA Technical Reports Server (NTRS)

Ko, William L. (Inventor); Richards, William Lance (Inventor)

2010-01-01

The invention is an improved process for using surface strain data to obtain real-time, operational loads data for complex structures that significantly reduces the time and cost versus current methods.

Insights into the Functions of M-T Hook Structure in HIV Fusion Inhibitor Using Molecular Modeling.

PubMed

Tan, Jianjun; Yuan, Hongling; Li, Chunhua; Zhang, Xiaoyi; Wang, Cunxin

2016-04-01

HIV-1 membrane fusion plays an important role in the process that HIV-1 entries host cells. As a treatment strategy targeting HIV-1 entry process, fusion inhibitors have been proposed. Nevertheless, development of a short peptide possessing high anti-HIV potency is considered a daunting challenge. He et al. found that two residues, Met626 and Thr627, located the upstream of the C-terminal heptad repeat of the gp41, formed a unique hook-like structure (M-T hook) that can dramatically improve the binding stability and anti-HIV activity of the inhibitors. In this work, we explored the molecular mechanism why M-T hook structure could improve the anti-HIV activity of inhibitors. Firstly, molecular dynamic simulation was used to obtain information on the time evolution between gp41 and ligands. Secondly, based on the simulations, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics Generalized Born surface area (MM-GBSA) methods were used to calculate the binding free energies. The binding free energy of the ligand with M-T hook was considerably higher than the other without M-T. Further studies showed that the hydrophobic interactions made the dominant contribution to the binding free energy. The numbers of Hydrogen bonds between gp41 and the ligand with M-T hook structure were more than the other. These findings should provide insights into the inhibition mechanism of the short peptide fusion inhibitors and be useful for the rational design of novel fusion inhibitors in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structural Studies of Silver Nanoparticles Obtained Through Single-Step Green Synthesis

NASA Astrophysics Data System (ADS)

Prasad Peddi, Siva; Abdallah Sadeh, Bilal

2015-10-01

Green synthesis of silver Nanoparticles (AGNP's) has been the most prominent among the metallic nanoparticles for research for over a decade and half now due to both the simplicity of preparation and the applicability of biological species with extensive applications in medicine and biotechnology to reduce and trap the particles. The current article uses Eclipta Prostrata leaf extract as the biological species to cap the AGNP's through a single step process. The characterization data obtained was used for the analysis of the sample structure. The article emphasizes the disquisition of their shape and size of the lattice parameters and proposes a general scheme and a mathematical model for the analysis of their dependence. The data of the synthesized AGNP's has been used to advantage through the introduction of a structural shape factor for the crystalline nanoparticles. The properties of the structure of the AGNP's proposed and evaluated through a theoretical model was undeviating with the experimental consequences. This modus operandi gives scope for the structural studies of ultrafine particles prepared using biological methods.

Application of information theory to a three-body coarse-grained representation of proteins in the PDB: insights into the structural and evolutionary roles of residues in protein structure.

PubMed

Thompson, Jared J; Tabatabaei Ghomi, Hamed; Lill, Markus A

2014-12-01

Knowledge-based methods for analyzing protein structures, such as statistical potentials, primarily consider the distances between pairs of bodies (atoms or groups of atoms). Considerations of several bodies simultaneously are generally used to characterize bonded structural elements or those in close contact with each other, but historically do not consider atoms that are not in direct contact with each other. In this report, we introduce an information-theoretic method for detecting and quantifying distance-dependent through-space multibody relationships between the sidechains of three residues. The technique introduced is capable of producing convergent and consistent results when applied to a sufficiently large database of randomly chosen, experimentally solved protein structures. The results of our study can be shown to reproduce established physico-chemical properties of residues as well as more recently discovered properties and interactions. These results offer insight into the numerous roles that residues play in protein structure, as well as relationships between residue function, protein structure, and evolution. The techniques and insights presented in this work should be useful in the future development of novel knowledge-based tools for the evaluation of protein structure. © 2014 Wiley Periodicals, Inc.

Conservation and Divergence of Mediator Structure and Function: Insights from Plants.

PubMed

Dolan, Whitney L; Chapple, Clint

2017-01-01

The Mediator complex is a large, multisubunit, transcription co-regulator that is conserved across eukaryotes. Studies of the Arabidopsis Mediator complex and its subunits have shown that it functions in nearly every aspect of plant development and fitness. In addition to revealing mechanisms of regulation of plant-specific pathways, studies of plant Mediator complexes have the potential to shed light on the conservation and divergence of Mediator structure and function across Kingdoms and plant lineages. The majority of insights into plant Mediator function have come from Arabidopsis because it is the only plant from which Mediator has been purified and from which an array of Mediator mutants have been isolated by forward and reverse genetics. So far, these studies indicate that, despite low sequence similarity between many orthologous subunits, the overall structure and function of Mediator is well conserved between Kingdoms. Several studies have also expanded our knowledge of Mediator to other plant species, opening avenues of investigation into the role of Mediator in plant adaptation and fitness.

Statistical mechanics of protein structural transitions: Insights from the island model

PubMed Central

Kobayashi, Yukio

2016-01-01

The so-called island model of protein structural transition holds that hydrophobic interactions are the key to both the folding and function of proteins. Herein, the genesis and statistical mechanical basis of the island model of transitions are reviewed, by presenting the results of simulations of such transitions. Elucidating the physicochemical mechanism of protein structural formation is the foundation for understanding the hierarchical structure of life at the microscopic level. Based on the results obtained to date using the island model, remaining problems and future work in the field of protein structures are discussed, referencing Professor Saitô’s views on the hierarchic structure of science. PMID:28409078

Structural insights into the interaction of IL-33 with its receptors.

PubMed

Liu, Xi; Hammel, Michal; He, Yanfeng; Tainer, John A; Jeng, U-Ser; Zhang, Linqi; Wang, Shuying; Wang, Xinquan

2013-09-10

Interleukin (IL)-33 is an important member of the IL-1 family that has pleiotropic activities in innate and adaptive immune responses in host defense and disease. It signals through its ligand-binding primary receptor ST2 and IL-1 receptor accessory protein (IL-1RAcP), both of which are members of the IL-1 receptor family. To clarify the interaction of IL-33 with its receptors, we determined the crystal structure of IL-33 in complex with the ectodomain of ST2 at a resolution of 3.27 Å. Coupled with structure-based mutagenesis and binding assay, the structural results define the molecular mechanism by which ST2 specifically recognizes IL-33. Structural comparison with other ligand-receptor complexes in the IL-1 family indicates that surface-charge complementarity is critical in determining ligand-binding specificity of IL-1 primary receptors. Combined crystallography and small-angle X-ray-scattering studies reveal that ST2 possesses hinge flexibility between the D3 domain and D1D2 module, whereas IL-1RAcP exhibits a rigid conformation in the unbound state in solution. The molecular flexibility of ST2 provides structural insights into domain-level conformational change of IL-1 primary receptors upon ligand binding, and the rigidity of IL-1RAcP explains its inability to bind ligands directly. The solution architecture of IL-33-ST2-IL-1RAcP complex from small-angle X-ray-scattering analysis resembles IL-1β-IL-1RII-IL-1RAcP and IL-1β-IL-1RI-IL-1RAcP crystal structures. The collective results confer IL-33 structure-function relationships, supporting and extending a general model for ligand-receptor assembly and activation in the IL-1 family.

Structural Insights into the Calcium-Mediated Allosteric Transition in the C-Terminal Domain of Calmodulin from Nuclear Magnetic Resonance Measurements.

PubMed

Kukic, Predrag; Lundström, Patrik; Camilloni, Carlo; Evenäs, Johan; Akke, Mikael; Vendruscolo, Michele

2016-01-12

Calmodulin is a two-domain signaling protein that becomes activated upon binding cooperatively two pairs of calcium ions, leading to large-scale conformational changes that expose its binding site. Despite significant advances in understanding the structural biology of calmodulin functions, the mechanistic details of the conformational transition between closed and open states have remained unclear. To investigate this transition, we used a combination of molecular dynamics simulations and nuclear magnetic resonance (NMR) experiments on the Ca(2+)-saturated E140Q C-terminal domain variant. Using chemical shift restraints in replica-averaged metadynamics simulations, we obtained a high-resolution structural ensemble consisting of two conformational states and validated such an ensemble against three independent experimental data sets, namely, interproton nuclear Overhauser enhancements, (15)N order parameters, and chemical shift differences between the exchanging states. Through a detailed analysis of this structural ensemble and of the corresponding statistical weights, we characterized a calcium-mediated conformational transition whereby the coordination of Ca(2+) by just one oxygen of the bidentate ligand E140 triggers a concerted movement of the two EF-hands that exposes the target binding site. This analysis provides atomistic insights into a possible Ca(2+)-mediated activation mechanism of calmodulin that cannot be achieved from static structures alone or from ensemble NMR measurements of the transition between conformations.

Structural insights into FRS2α PTB domain recognition by neurotrophin receptor TrkB.

PubMed

Zeng, Lei; Kuti, Miklos; Mujtaba, Shiraz; Zhou, Ming-Ming

2014-07-01

The fibroblast growth factor receptor (FGFR) substrate 2 (FRS2) family proteins function as scaffolding adapters for receptor tyrosine kinases (RTKs). The FRS2α proteins interact with RTKs through the phosphotyrosine-binding (PTB) domain and transfer signals from the activated receptors to downstream effector proteins. Here, we report the nuclear magnetic resonance structure of the FRS2α PTB domain bound to phosphorylated TrkB. The structure reveals that the FRS2α-PTB domain is comprised of two distinct but adjacent pockets for its mutually exclusive interaction with either nonphosphorylated juxtamembrane region of the FGFR, or tyrosine phosphorylated peptides TrkA and TrkB. The new structural insights suggest rational design of selective small molecules through targeting of the two conjunct pockets in the FRS2α PTB domain. © 2014 Wiley Periodicals, Inc.

Insight in schizophrenia: involvement of self-reflection networks?

PubMed

van der Meer, Lisette; de Vos, Annerieke E; Stiekema, Annemarie P M; Pijnenborg, Gerdina H M; van Tol, Marie-José; Nolen, Willem A; David, Anthony S; Aleman, André

2013-11-01

Impaired insight is a common feature in psychosis and an important predictor of variables such as functional outcome, prognosis, and treatment adherence. A cognitive process that may underlie insight in psychosis is self-reflection, or the conscious evaluation of one's traits and characteristics. The current study aims to investigate the neural correlates of self-reflective processing and its relationship with insight in schizophrenia. Forty-seven schizophrenia patients and 21 healthy controls performed a self-reflection task in a functional magnetic resonance imaging (fMRI) scanner. The tasks comprised a self-reflection, close other-reflection, and a semantic (baseline) condition. Insight scores were obtained with the Schedule of Assessment of Insight Expanded. In addition, cognitive insight scores were obtained (Beck Cognitive Insight Scale [BCIS]). Schizophrenia patients demonstrated less activation in the posterior cingulate cortex in the self- and other-reflection conditions and less activation in the precuneus in the other-reflection condition compared with healthy controls. Better insight was associated with greater response in the inferior frontal gyrus, anterior insula, and inferior parietal lobule during self-reflection. In addition, better cognitive insight was associated with higher activation in ventromedial prefrontal cortex during self-reflection. In the current study, evidence for a relationship between self-reflection and insight in patients with schizophrenia was found in brain areas related to self-reflection, self/other distinction and source attribution. The findings support the rationale for a treatment that is currently under evaluation, which attempts to increase insight by enhancing self-reflection.

Insights on the structural perturbations in human MTHFR Ala222Val mutant by protein modeling and molecular dynamics.

PubMed

Abhinand, P A; Shaikh, Faraz; Bhakat, Soumendranath; Radadiya, Ashish; Bhaskar, L V K S; Shah, Anamik; Ragunath, P K

2016-01-01

Methylenetetrahydrofolate reductase (MTHFR) protein catalyzes the only biochemical reaction which produces methyltetrahydrofolate, the active form of folic acid essential for several molecular functions. The Ala222Val polymorphism of human MTHFR encodes a thermolabile protein associated with increased risk of neural tube defects and cardiovascular disease. Experimental studies have shown that the mutation does not affect the kinetic properties of MTHFR, but inactivates the protein by increasing flavin adenine dinucleotide (FAD) loss. The lack of completely solved crystal structure of MTHFR is an impediment in understanding the structural perturbations caused by the Ala222Val mutation; computational modeling provides a suitable alternative. The three-dimensional structure of human MTHFR protein was obtained through homology modeling, by taking the MTHFR structures from Escherichia coli and Thermus thermophilus as templates. Subsequently, the modeled structure was docked with FAD using Glide, which revealed a very good binding affinity, authenticated by a Glide XP score of -10.3983 (kcal mol(-1)). The MTHFR was mutated by changing Alanine 222 to Valine. The wild-type MTHFR-FAD complex and the Ala222Val mutant MTHFR-FAD complex were subjected to molecular dynamics simulation over 50 ns period. The average difference in backbone root mean square deviation (RMSD) between wild and mutant variant was found to be ~.11 Å. The greater degree of fluctuations in the mutant protein translates to increased conformational stability as a result of mutation. The FAD-binding ability of the mutant MTHFR was also found to be significantly lowered as a result of decreased protein grip caused by increased conformational flexibility. The study provides insights into the Ala222Val mutation of human MTHFR that induces major conformational changes in the tertiary structure, causing a significant reduction in the FAD-binding affinity.

Insight in schizophrenia: a review.

PubMed

Dam, Jesper

2006-01-01

The issue of insight in schizophrenia must be assumed to be one of the most important aspects of the clinical examination. Comprehensive studies have shown that between 50% and 80% of all patients suffering from schizophrenia do not believe that they have a disorder. In recent years, poor insight in schizophrenia has been the subject of increasing interest, as manifested in a number of studies discussed in the present review. Some of these studies focus on insight correlated to various parameters such as psychopathology, neuropsychology, clinical relevance and compliance. Other studies refer to more theoretical implications, among these the issue of defining the concept of insight: whether insight can be seen as a "primary" phenomenon in schizophrenia, and whether insight may be graduated, dimensioned or increased. Several authors have developed rating scales in an attempt to obtain a measure for the degree or dimension of insight. Here, the range of parameters employed gives an excellent impression of the complexity of the concept of insight. In the concluding discussion, a phenomenological aspect is brought in, in an attempt to place the concept of insight in relation to disturbances of the self in schizophrenia and to primary symptoms in schizophrenia, amongst these autism.

Viewing Golgi structure and function from a different perspective--insights from electron tomography.

PubMed

Marsh, Brad J; Pavelka, Margit

2013-01-01

Historically, ultrastructural investigations, which have focused on elucidating the biological idiosyncrasies of the Golgi apparatus, have tended towards oversimplified or fallacious hypotheses when postulating how the Golgi apparatus reorganizes itself both structurally and functionally to fulfill the plethora of cellular processes underpinned by this complex organelle. Key questions are still unanswered with regard to how changes in Golgi architecture correlate so reproducibly to changes in its functional priorities under different physiological conditions or experimental perturbations. This fact alone serves to highlight how the technical limitations associated with conventional two-dimensional imaging approaches employed in the past failed to adequately capture the extraordinary complexity of the Golgi's three-dimensional (3D) structure-now a hallmark of this challenging organelle. Consequently, this has hampered progress towards developing a clear understanding of how changes in its structure and function typically occur in parallel. In this chapter, we highlight but a few of the significant new insights regarding variations in the Golgi's structure-function relationships that have been afforded over recent years through advanced electron microscopic techniques for 3D image reconstruction, commonly referred to as electron tomography. Copyright © 2013 Elsevier Inc. All rights reserved.

Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation

PubMed Central

Lawrence, Sara L.; Feil, Susanne C.; Morton, Craig J.; Farrand, Allison J.; Mulhern, Terrence D.; Gorman, Michael A.; Wade, Kristin R.; Tweten, Rodney K.; Parker, Michael W.

2015-01-01

Pore-forming proteins are weapons often used by bacterial pathogens to breach the membrane barrier of target cells. Despite their critical role in infection important structural aspects of the mechanism of how these proteins assemble into pores remain unknown. Streptococcus pneumoniae is the world’s leading cause of pneumonia, meningitis, bacteremia and otitis media. Pneumolysin (PLY) is a major virulence factor of S. pneumoniae and a target for both small molecule drug development and vaccines. PLY is a member of the cholesterol-dependent cytolysins (CDCs), a family of pore-forming toxins that form gigantic pores in cell membranes. Here we present the structure of PLY determined by X-ray crystallography and, in solution, by small-angle X-ray scattering. The crystal structure reveals PLY assembles as a linear oligomer that provides key structural insights into the poorly understood early monomer-monomer interactions of CDCs at the membrane surface. PMID:26403197

Structural insight of dopamine β-hydroxylase, a drug target for complex traits, and functional significance of exonic single nucleotide polymorphisms.

PubMed

Kapoor, Abhijeet; Shandilya, Manish; Kundu, Suman

2011-01-01

Human dopamine β-hydroxylase (DBH) is an important therapeutic target for complex traits. Several single nucleotide polymorphisms (SNPs) have also been identified in DBH with potential adverse physiological effect. However, difficulty in obtaining diffractable crystals and lack of a suitable template for modeling the protein has ensured that neither crystallographic three-dimensional structure nor computational model for the enzyme is available to aid rational drug design, prediction of functional significance of SNPs or analytical protein engineering. Adequate biochemical information regarding human DBH, structural coordinates for peptidylglycine alpha-hydroxylating monooxygenase and computational data from a partial model of rat DBH were used along with logical manual intervention in a novel way to build an in silico model of human DBH. The model provides structural insight into the active site, metal coordination, subunit interface, substrate recognition and inhibitor binding. It reveals that DOMON domain potentially promotes tetramerization, while substrate dopamine and a potential therapeutic inhibitor nepicastat are stabilized in the active site through multiple hydrogen bonding. Functional significance of several exonic SNPs could be described from a structural analysis of the model. The model confirms that SNP resulting in Ala318Ser or Leu317Pro mutation may not influence enzyme activity, while Gly482Arg might actually do so being in the proximity of the active site. Arg549Cys may cause abnormal oligomerization through non-native disulfide bond formation. Other SNPs like Glu181, Glu250, Lys239 and Asp290 could potentially inhibit tetramerization thus affecting function. The first three-dimensional model of full-length human DBH protein was obtained in a novel manner with a set of experimental data as guideline for consistency of in silico prediction. Preliminary physicochemical tests validated the model. The model confirms, rationalizes and provides

Insights into material and structural basis of bone fragility from diseases associated with fractures: how determinants of the biomechanical properties of bone are compromised by disease.

PubMed

Chavassieux, P; Seeman, E; Delmas, P D

2007-04-01

Minimal trauma fractures in bone diseases are the result of bone fragility. Rather than considering bone fragility as being the result of a reduced amount of bone, we recognize that bone fragility is the result of changes in the material and structural properties of bone. A better understanding of the contribution of each component of the material composition and structure and how these interact to maintain whole bone strength is obtained by the study of metabolic bone diseases. Disorders of collagen (osteogenesis imperfecta and Paget's disease of bone), mineral content, composition and distribution (fluorosis and osteomalacia); diseases of high remodeling (postmenopausal osteoporosis, hyperparathyroidism, and hyperthyroidism) and low remodeling (osteopetrosis, pycnodysostosis); and other diseases (idiopathic male osteoporosis, corticosteroid-induced osteoporosis) produce abnormalities in the material composition and structure that lead to bone fragility. Observations in patients and in animal models provide insights on the biomechanical consequences of these illnesses and the nature of the qualities of bone that determine its strength.

Insight in Schizophrenia: Involvement of Self-Reflection Networks?

PubMed Central

de Vos, Annerieke E.

2013-01-01

Background: Impaired insight is a common feature in psychosis and an important predictor of variables such as functional outcome, prognosis, and treatment adherence. A cognitive process that may underlie insight in psychosis is self-reflection, or the conscious evaluation of one’s traits and characteristics. The current study aims to investigate the neural correlates of self-reflective processing and its relationship with insight in schizophrenia. Methods: Forty-seven schizophrenia patients and 21 healthy controls performed a self-reflection task in a functional magnetic resonance imaging (fMRI) scanner. The tasks comprised a self-reflection, close other-reflection, and a semantic (baseline) condition. Insight scores were obtained with the Schedule of Assessment of Insight Expanded. In addition, cognitive insight scores were obtained (Beck Cognitive Insight Scale [BCIS]). Results: Schizophrenia patients demonstrated less activation in the posterior cingulate cortex in the self- and other-reflection conditions and less activation in the precuneus in the other-reflection condition compared with healthy controls. Better insight was associated with greater response in the inferior frontal gyrus, anterior insula, and inferior parietal lobule during self-reflection. In addition, better cognitive insight was associated with higher activation in ventromedial prefrontal cortex during self-reflection. Conclusion: In the current study, evidence for a relationship between self-reflection and insight in patients with schizophrenia was found in brain areas related to self-reflection, self/other distinction and source attribution. The findings support the rationale for a treatment that is currently under evaluation, which attempts to increase insight by enhancing self-reflection. PMID:23104865

Chemokines and their receptors: insights from molecular modeling and crystallography.

PubMed

Kufareva, Irina

2016-10-01

Chemokines are small secreted proteins that direct cell migration in development, immunity, inflammation, and cancer. They do so by binding and activating specific G protein coupled receptors on the surface of migrating cells. Despite the importance of receptor:chemokine interactions, their structural basis remained unclear for a long time. In 2015, the first atomic resolution insights were obtained with the publication of X-ray structures for two distantly related receptors bound to chemokines. In conjunction with experiment-guided molecular modeling, the structures suggest a conserved receptor:chemokine complex architecture, while highlighting the diverse details and functional roles of individual interaction epitopes. Novel findings promote the development and detailed structural interpretation of the canonical two-site hypothesis of receptor:chemokine recognition, and suggest new avenues for pharmacological modulation of chemokine receptors. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Beck Cognitive Insight Scale (BCIS): translation and validation of the Taiwanese version.

PubMed

Kao, Yu-Chen; Liu, Yia-Ping

2010-04-09

Over the last few decades, research concerning the insight of patients with schizophrenia and its relationships with other clinical variables has been given much attention in the clinical setting. Since that time, a series of instruments assessing insight have been developed. The purpose of this study was to examine the reliability and validity of the Taiwanese version of the Beck Cognitive Insight Scale (BCIS). The BCIS is a self-administered instrument designed to evaluate cognitive processes that involves reevaluating patients' anomalous experiences and specific misinterpretations. The English language version of the BCIS was translated into Taiwanese for use in this study. A total of 180 subjects with and without psychosis completed the Taiwanese version of the BCIS and additional evaluations to assess researcher-rated insight scales and psychopathology. Psychometric properties (factor structures and various types of reliability and validity) were assessed for this translated questionnaire. Overall, the Taiwanese version of the BCIS showed good reliability and stability over time. This translated scale comprised a two-factor solution corresponding to reflective attitude and certain attitude subscales. Following the validation of the internal structure of the scale, we obtained an R-C (reflective attitude minus certain attitude) index of the translated BCIS, representing the measurement of cognitive insight by subtracting the score of the certain attitude subscale from that of the reflective attitude subscale. As predicted, the differences in mean reflective attitude, certain attitude and R-C index between subjects with and without psychosis were significant. Our data also demonstrated that psychotic patients were significantly less reflective, more confident in their beliefs, and had less cognitive insight compared with nonpsychotic control groups. In light of these findings, we believe that the Taiwanese version of BCIS is a valid and reliable instrument for

Optimal atomic structure of amorphous silicon obtained from density functional theory calculations

NASA Astrophysics Data System (ADS)

Pedersen, Andreas; Pizzagalli, Laurent; Jónsson, Hannes

2017-06-01

Atomic structure of amorphous silicon consistent with several reported experimental measurements has been obtained from annealing simulations using electron density functional theory calculations and a systematic removal of weakly bound atoms. The excess energy and density with respect to the crystal are well reproduced in addition to radial distribution function, angular distribution functions, and vibrational density of states. No atom in the optimal configuration is locally in a crystalline environment as deduced by ring analysis and common neighbor analysis, but coordination defects are present at a level of 1%-2%. The simulated samples provide structural models of this archetypal disordered covalent material without preconceived notion of the atomic ordering or fitting to experimental data.

Salts employed in hydrophobic interaction chromatography can change protein structure - insights from protein-ligand interaction thermodynamics, circular dichroism spectroscopy and small angle X-ray scattering.

PubMed

Komaromy, Andras Z; Kulsing, Chadin; Boysen, Reinhard I; Hearn, Milton T W

2015-03-01

Key requirements of protein purification by hydrophobic interaction chromatography (HIC) are preservation of the tertiary/quaternary structure, maintenance of biological function, and separation of the correctly folded protein from its unfolded forms or aggregates. This study examines the relationship between the HIC retention behavior of hen egg white lysozyme (HEWL) in high concentrations of several kosmotropic salts and its conformation, assessed by circular dichroism (CD) spectroscopy. Further, the physicochemical properties of HEWL in the presence of high concentrations of ammonium sulfate, sodium chloride and magnesium chloride were investigated by small angle X-ray scattering (SAXS) at different temperatures. Radii of gyration were extrapolated from Guinier approximations and the indirect transform program GNOM with protein-protein interaction and contrast variation taken into account. A bead model simulation provided information on protein structural changes using ab initio reconstruction with GASBOR. These results correlated to the secondary structure content obtained from CD spectroscopy of HEWL. These changes in SAXS and CD data were consistent with heat capacity ΔCp -values obtained from van't Hoff plot analyses of the retention data. Collectively, these insights enable informed decisions to be made on the choice of chromatographic conditions, leading to improved separation selectivity and opportunities for innovative column-assisted protein refolding methods. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural conversion of the transformer protein RfaH: new insights derived from protein structure prediction and molecular dynamics simulations.

PubMed

Balasco, Nicole; Barone, Daniela; Vitagliano, Luigi

2015-01-01

Recent structural investigations have shown that the C-terminal domain (CTD) of the transcription factor RfaH undergoes unique structural modifications that have a profound impact into its functional properties. These modifications cause a complete change in RfaH(CTD) topology that converts from an α-hairpin to a β-barrel fold. To gain insights into the determinants of this major structural conversion, we here performed computational studies (protein structure prediction and molecular dynamics simulations) on RfaH(CTD). Although these analyses, in line with literature data, suggest that the isolated RfaH(CTD) has a strong preference for the β-barrel fold, they also highlight that a specific region of the protein is endowed with a chameleon conformational behavior. In particular, the Leu-rich region (residues 141-145) has a good propensity to adopt both α-helical and β-structured states. Intriguingly, in the RfaH homolog NusG, whose CTD uniquely adopts the β-barrel fold, the corresponding region is rich in residues as Val or Ile that present a strong preference for the β-structure. On this basis, we suggest that the presence of this Leu-rich element in RfaH(CTD) may be responsible for the peculiar structural behavior of the domain. The analysis of the sequences of RfaH family (PfamA code PF02357) unraveled that other members potentially share the structural properties of RfaH(CTD). These observations suggest that the unusual conformational behavior of RfaH(CTD) may be rare but not unique.

ZnO nanoparticles obtained by ball milling technique: Structural, micro-structure, optical and photo-catalytic properties

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

Balamurugan, S., E-mail: scandium.chemistry@gmail.com; Joy, Josny; Godwin, M. Anto

The ZnO nanoparticles were obtained by ball milling of commercial grade ZnO powder at 250 rpm for 20 h and studied their structural, micro-structure, optical and photo-catalytic properties. Due to ball milling significant decrease in lattice parameters and average crystalline size is noticed for the as-milled ZnO nano powder. The HRSEM images of the as-milled powder consist of agglomerated fine spherical nanoparticles in the range of ~10-20 nm. The room temperature PL spectrum of as-milled ZnO nano powder excited under 320 nm reveals two emission bands at ~406 nm (violet emission) and ~639 nm (green emission). Interestingly about 98 % of photo degradation of methylene (MB)more » by the ZnO catalyst is achieved at 100 minutes of solar light irradiation.« less

Structural insights into 5‧ flap DNA unwinding and incision by the human FAN1 dimer

NASA Astrophysics Data System (ADS)

Zhao, Qi; Xue, Xiaoyu; Longerich, Simonne; Sung, Patrick; Xiong, Yong

2014-12-01

Human FANCD2-associated nuclease 1 (FAN1) is a DNA structure-specific nuclease involved in the processing of DNA interstrand crosslinks (ICLs). FAN1 maintains genomic stability and prevents tissue decline in multiple organs, yet it confers ICL-induced anti-cancer drug resistance in several cancer subtypes. Here we report three crystal structures of human FAN1 in complex with a 5‧ flap DNA substrate, showing that two FAN1 molecules form a head-to-tail dimer to locate the lesion, orient the DNA and unwind a 5‧ flap for subsequent incision. Biochemical experiments further validate our model for FAN1 action, as structure-informed mutations that disrupt protein dimerization, substrate orientation or flap unwinding impair the structure-specific nuclease activity. Our work elucidates essential aspects of FAN1-DNA lesion recognition and a unique mechanism of incision. These structural insights shed light on the cellular mechanisms underlying organ degeneration protection and cancer drug resistance mediated by FAN1.

Secretins revealed: structural insights into the giant gated outer membrane portals of bacteria.

PubMed

Majewski, Dorothy D; Worrall, Liam J; Strynadka, Natalie Cj

2018-03-23

The acquisition and evolution of customized and often highly complex secretion systems allows Gram-negative bacteria to efficiently passage large macromolecules across both inner and outer membranes and, in some cases, that of the infected host. Essential to the virulence and ultimate survival of the many pathogenic species that encode them, secretion systems export a wide variety of effector proteins and DNA as well as the downstream extracellular filaments of the secretion apparatus themselves. Although these customized secretion systems differ in their cytosolic and inner membrane components, several commonly rely on the secretin family of giant pores to allow these large substrates to traverse the outer membrane. Recently, several near-atomic resolution cryo-EM secretin structures have unveiled the first insights into the unique structural motifs required for outer membrane localization, assembly, hallmark ultrastable nature, spontaneous membrane insertion, and mechanism of action-including the requisite central gating needed to prevent deleterious passage of periplasmic contents to the extracellular space. Copyright © 2018. Published by Elsevier Ltd.

Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction.

PubMed

Casino, Patricia; Rubio, Vicente; Marina, Alberto

2009-10-16

The chief mechanism used by bacteria for sensing their environment is based on two conserved proteins: a sensor histidine kinase (HK) and an effector response regulator (RR). The signal transduction process involves highly conserved domains of both proteins that mediate autokinase, phosphotransfer, and phosphatase activities whose output is a finely tuned RR phosphorylation level. Here, we report the structure of the complex between the entire cytoplasmic portion of Thermotoga maritima class I HK853 and its cognate, RR468, as well as the structure of the isolated RR468, both free and BeF(3)(-) bound. Our results provide insight into partner specificity in two-component systems, recognition of the phosphorylation state of each partner, and the catalytic mechanism of the phosphatase reaction. Biochemical analysis shows that the HK853-catalyzed autokinase reaction proceeds by a cis autophosphorylation mechanism within the HK subunit. The results suggest a model for the signal transduction mechanism in two-component systems.

Structure and Absolute Configuration of Jurassic Polyketide-Derived Spiroborate Pigments Obtained from Microgram Quantities.

PubMed

Wolkenstein, Klaus; Sun, Han; Falk, Heinz; Griesinger, Christian

2015-10-28

Complete structural elucidation of natural products is often challenging due to structural complexity and limited availability. This is true for present-day secondary metabolites, but even more for exceptionally preserved secondary metabolites of ancient organisms that potentially provide insights into the evolutionary history of natural products. Here, we report the full structure and absolute configuration of the borolithochromes, enigmatic boron-containing pigments from a Jurassic putative red alga, from samples of less than 50 μg using microcryoprobe NMR, circular dichroism spectroscopy, and density functional theory calculations and reveal their polyketide origin. The pigments are identified as spiroborates with two pentacyclic sec-butyl-trihydroxy-methyl-benzo[gh]tetraphen-one ligands and less-substituted derivatives. The configuration of the sec-butyl group is found to be (S). Because the exceptional benzo[gh]tetraphene scaffold is otherwise only observed in the recently discovered polyketide clostrubin from a present-day Clostridium bacterium, the Jurassic borolithochromes now can be unambiguously linked to the modern polyketide, providing evidence that the fossil pigments are almost originally preserved secondary metabolites and suggesting that the pigments in fact may have been produced by an ancient bacterium. The borolithochromes differ fundamentally from previously described boronated polyketides and represent the first boronated aromatic polyketides found so far. Our results demonstrate the potential of microcryoprobe NMR in the analysis of previously little-explored secondary metabolites from ancient organisms and reveal the evolutionary significance of clostrubin-type polyketides.

Structural insights into biased G protein-coupled receptor signaling revealed by fluorescence spectroscopy.

PubMed

Rahmeh, Rita; Damian, Marjorie; Cottet, Martin; Orcel, Hélène; Mendre, Christiane; Durroux, Thierry; Sharma, K Shivaji; Durand, Grégory; Pucci, Bernard; Trinquet, Eric; Zwier, Jurriaan M; Deupi, Xavier; Bron, Patrick; Banères, Jean-Louis; Mouillac, Bernard; Granier, Sébastien

2012-04-24

G protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters, representing the largest group of therapeutic targets. Recent studies show that some GPCRs signal through both G protein and arrestin pathways in a ligand-specific manner. Ligands that direct signaling through a specific pathway are known as biased ligands. The arginine-vasopressin type 2 receptor (V2R), a prototypical peptide-activated GPCR, is an ideal model system to investigate the structural basis of biased signaling. Although the native hormone arginine-vasopressin leads to activation of both the stimulatory G protein (Gs) for the adenylyl cyclase and arrestin pathways, synthetic ligands exhibit highly biased signaling through either Gs alone or arrestin alone. We used purified V2R stabilized in neutral amphipols and developed fluorescence-based assays to investigate the structural basis of biased signaling for the V2R. Our studies demonstrate that the Gs-biased agonist stabilizes a conformation that is distinct from that stabilized by the arrestin-biased agonists. This study provides unique insights into the structural mechanisms of GPCR activation by biased ligands that may be relevant to the design of pathway-biased drugs.

Structural Insights into Amyloid Oligomers of the Parkinson Disease-related Protein α-Synuclein*

PubMed Central

Gallea, J. Ignacio; Celej, M. Soledad

2014-01-01

The presence of intraneuronal deposits mainly formed by amyloid fibrils of the presynaptic protein α-synuclein (AS) is a hallmark of Parkinson disease. Currently, neurotoxicity is attributed to prefibrillar oligomeric species rather than the insoluble aggregates, although their mechanisms of toxicity remain elusive. Structural details of the supramolecular organization of AS oligomers are critically needed to decipher the structure-toxicity relationship underlying their pathogenicity. In this study, we employed site-specific fluorescence to get a deeper insight into the internal architecture of AS oligomeric intermediates. We demonstrate that AS oligomers are ordered assemblies possessing a well defined pattern of intermolecular contacts. Some of these contacts involve regions that form the β-sheet core in the fibrillar state, although their spatial arrangement may differ in the two aggregated forms. However, even though the two termini are excluded from the fibrillar core, they are engaged in a number of intermolecular interactions within the oligomer. Therefore, substantial structural remodeling of early oligomeric interactions is essential for fibril growth. The intermolecular contacts identified in AS oligomers can serve as targets for the rational design of anti-amyloid compounds directed at preventing oligomeric interactions/reorganizations. PMID:25143382

Structure and properties of composite iron-based coatings obtained by the electromechanical technique

NASA Astrophysics Data System (ADS)

Dubinskii, N. A.

2007-09-01

The influence of the electrolyte temperature and current density on the content of inclusions of powder particles in composite coatings obtained by the electrochemical technique has been investigated. It has been found that the wear resistance of iron coatings with inclusions of powder particles of aluminum, kaolin, and calcium silicate increases from 5 to 10 times compared to coating without inclusions of disperse particles, and the friction coefficient therewith decreases from 0.097 to 0.026. It has been shown that the mechanical properties of iron obtained by the method of electrochemical deposition depend on their fine structure. The regimes of deposition of iron-based coatings have been optimized.

Structure of a nanobody-stabilized active state of the β(2) adrenoceptor.

PubMed

Rasmussen, Søren G F; Choi, Hee-Jung; Fung, Juan Jose; Pardon, Els; Casarosa, Paola; Chae, Pil Seok; Devree, Brian T; Rosenbaum, Daniel M; Thian, Foon Sun; Kobilka, Tong Sun; Schnapp, Andreas; Konetzki, Ingo; Sunahara, Roger K; Gellman, Samuel H; Pautsch, Alexander; Steyaert, Jan; Weis, William I; Kobilka, Brian K

2011-01-13

G protein coupled receptors (GPCRs) exhibit a spectrum of functional behaviours in response to natural and synthetic ligands. Recent crystal structures provide insights into inactive states of several GPCRs. Efforts to obtain an agonist-bound active-state GPCR structure have proven difficult due to the inherent instability of this state in the absence of a G protein. We generated a camelid antibody fragment (nanobody) to the human β(2) adrenergic receptor (β(2)AR) that exhibits G protein-like behaviour, and obtained an agonist-bound, active-state crystal structure of the receptor-nanobody complex. Comparison with the inactive β(2)AR structure reveals subtle changes in the binding pocket; however, these small changes are associated with an 11 Å outward movement of the cytoplasmic end of transmembrane segment 6, and rearrangements of transmembrane segments 5 and 7 that are remarkably similar to those observed in opsin, an active form of rhodopsin. This structure provides insights into the process of agonist binding and activation.

Structural Insights Into DNA Repair by RNase T—An Exonuclease Processing 3′ End of Structured DNA in Repair Pathways

PubMed Central

Hsiao, Yu-Yuan; Fang, Woei-Horng; Lee, Chia-Chia; Chen, Yi-Ping; Yuan, Hanna S.

2014-01-01

DNA repair mechanisms are essential for preservation of genome integrity. However, it is not clear how DNA are selected and processed at broken ends by exonucleases during repair pathways. Here we show that the DnaQ-like exonuclease RNase T is critical for Escherichia coli resistance to various DNA-damaging agents and UV radiation. RNase T specifically trims the 3′ end of structured DNA, including bulge, bubble, and Y-structured DNA, and it can work with Endonuclease V to restore the deaminated base in an inosine-containing heteroduplex DNA. Crystal structure analyses further reveal how RNase T recognizes the bulge DNA by inserting a phenylalanine into the bulge, and as a result the 3′ end of blunt-end bulge DNA can be digested by RNase T. In contrast, the homodimeric RNase T interacts with the Y-structured DNA by a different binding mode via a single protomer so that the 3′ overhang of the Y-structured DNA can be trimmed closely to the duplex region. Our data suggest that RNase T likely processes bulge and bubble DNA in the Endonuclease V–dependent DNA repair, whereas it processes Y-structured DNA in UV-induced and various other DNA repair pathways. This study thus provides mechanistic insights for RNase T and thousands of DnaQ-like exonucleases in DNA 3′-end processing. PMID:24594808

Microscopic insight into the structure of gallium isotopes

NASA Astrophysics Data System (ADS)

Verma, Preeti; Sharma, Chetan; Singh, Suram; Bharti, Arun; Khosa, S. K.

2012-07-01

Projected Shell Model technique has been applied to odd-A71-81Ga nuclei with the deformed single-particle states generated by the standard Nilsson potential. Various nuclear structure quantities have been calculated with this technique and compared with the available experimental data in the present work. The known experimental data of the yrast bands in these nuclei are persuasively described and the band diagrams obtained for these nuclei show that the yrast bands in these odd-A Ga isotopes don't belong to the single intrinsic state only but also have multi-particle states. The back-bending in moment of inertia and the electric quadrupole transitions are also calculated.

Composition of the mitochondrial electron transport chain in acanthamoeba castellanii: structural and evolutionary insights.

PubMed

Gawryluk, Ryan M R; Chisholm, Kenneth A; Pinto, Devanand M; Gray, Michael W

2012-11-01

The mitochondrion, derived in evolution from an α-proteobacterial progenitor, plays a key metabolic role in eukaryotes. Mitochondria house the electron transport chain (ETC) that couples oxidation of organic substrates and electron transfer to proton pumping and synthesis of ATP. The ETC comprises several multiprotein enzyme complexes, all of which have counterparts in bacteria. However, mitochondrial ETC assemblies from animals, plants and fungi are generally more complex than their bacterial counterparts, with a number of 'supernumerary' subunits appearing early in eukaryotic evolution. Little is known, however, about the ETC of unicellular eukaryotes (protists), which are key to understanding the evolution of mitochondria and the ETC. We present an analysis of the ETC proteome from Acanthamoeba castellanii, an ecologically, medically and evolutionarily important member of Amoebozoa (sister to Opisthokonta). Data obtained from tandem mass spectrometric (MS/MS) analyses of purified mitochondria as well as ETC complexes isolated via blue native polyacrylamide gel electrophoresis are combined with the results of bioinformatic queries of sequence databases. Our bioinformatic analyses have identified most of the ETC subunits found in other eukaryotes, confirming and extending previous observations. The assignment of proteins as ETC subunits by MS/MS provides important insights into the primary structures of ETC proteins and makes possible, through the use of sensitive profile-based similarity searches, the identification of novel constituents of the ETC along with the annotation of highly divergent but phylogenetically conserved ETC subunits. © 2012 Elsevier B.V. All rights reserved.

Structural and Mechanistic Insights into Unusual Thiol Disulfide Oxidoreductase

PubMed Central

Garcin, Edwige B.; Bornet, Olivier; Elantak, Latifa; Vita, Nicolas; Pieulle, Laetitia; Guerlesquin, Françoise; Sebban-Kreuzer, Corinne

2012-01-01

Cytoplasmic desulfothioredoxin (Dtrx) from the anaerobe Desulfovibrio vulgaris Hildenborough has been identified as a new member of the thiol disulfide oxidoreductase family. The active site of Dtrx contains a particular consensus sequence, CPHC, never seen in the cytoplasmic thioredoxins and generally found in periplasmic oxidases. Unlike canonical thioredoxins (Trx), Dtrx does not present any disulfide reductase activity, but it presents instead an unusual disulfide isomerase activity. We have used NMR spectroscopy to gain insights into the structure and the catalytic mechanism of this unusual Dtrx. The redox potential of Dtrx (−181 mV) is significantly less reducing than that of canonical Trx. A pH dependence study allowed the determination of the pKa of all protonable residues, including the cysteine and histidine residues. Thus, the pKa values for the thiol group of Cys31 and Cys34 are 4.8 and 11.3, respectively. The His33 pKa value, experimentally determined for the first time, differs notably as a function of the redox states, 7.2 for the reduced state and 4.6 for the oxidized state. These data suggest an important role for His33 in the molecular mechanism of Dtrx catalysis that is confirmed by the properties of mutant DtrxH33G protein. The NMR structure of Dtrx shows a different charge repartition compared with canonical Trx. The results presented are likely indicative of the involvement of this protein in the catalysis of substrates specific of the anaerobe cytoplasm of DvH. The study of Dtrx is an important step toward revealing the molecular details of the thiol-disulfide oxidoreductase catalytic mechanism. PMID:22128175

Clostridium perfringens: insight into virulence evolution and population structure.

PubMed

Sawires, Youhanna S; Songer, J Glenn

2006-02-01

Clostridium perfringens is an important pathogen in veterinary and medical fields. Diseases caused by this organism are in many cases life threatening or fatal. At the same time, it is part of the ecological community of the intestinal tract of man and animals. Virulence in this species is not fully understood and it does seem that there is erratic distribution of the toxin/enzyme genes within C. perfringens population. We used the recently developed multiple-locus variable-number tandem repeat analysis (MLVA) scheme to investigate the evolution of virulence and population structure of this species. Analysis of the phylogenetic signal indicates that acquisition of the major toxin genes as well as other plasmid-borne toxin genes is a recent evolutionary event and their maintenance is essentially a function of the selective advantage they confer in certain niches under different conditions. In addition, it indicates the ability of virulent strains to cause disease in different host species. More interestingly, there is evidence that certain normal flora strains are virulent when they gain access to a different host species. Analysis of the population structure indicates that recombination events are the major tool that shapes the population and this panmixia is interrupted by frequent clonal expansion that mostly corresponds to disease processes. The signature of positive selection was detected in alpha toxin gene, suggesting the possibility of adaptive alleles on the other chromosomally encoded determinants. Finally, C. perfringens proved to have a dynamic population and availability of more genome sequences and use of comparative proteomics and animal modeling would provide more insight into the virulence of this organism.

Single-crystal structure determination of hydrous minerals and insights into a wet deep lower mantle

NASA Astrophysics Data System (ADS)

Zhang, L.; Yuan, H.; Meng, Y.; Popov, D.

2017-12-01

Water enters the Earth's interior through hydrated subducting slabs. How deep within the lower mantle (670-2900 km depth) can water be transported down and stored depends upon the availability of hydrous phases that is thermodynamically stable under the high P-T conditions and have a sufficiently high density to sink through the lower mantle. Phase H [MgSiH2O4] (1) and the δ-AlOOH (2) form solid solutions that are stable in the deep lower mantle (3), but the solid solution phase is 10% lighter than the corresponding lower mantle. Recent experimental discoveries of the pyrite (Py) structured FeO2 and FeOOH (4-6) suggest that these Fe-enriched phases can be transported to the deepest lower mantle owing to their high density. We have further discovered a very dense hydrous phase in (Fe,Al)OOH with a previously unknown hexagonal symmetry and this phase is stable relative to the Py-phase under extreme high P-T conditions in the deep lower mantle. Through in situ multigrain analysis (7) and single-crystal structure determination of the hydrous minerals at P-Tconditions of the deep lower mantle, we can obtain detailed structure information of the hydrous phases and therefore provide insights into the hydration mechanism in the deep lower mantle. These highly stable hydrous minerals extend the water cycle at least to the depth of 2900 km. 1. M. Nishi et al., Nature Geoscience 7, 224-227 (2014). 2. E. Ohtani, K. Litasov, A. Suzuki, T. Kondo, Geophysical Research Letters 28, 3991-3993 (2001). 3. I. Ohira et al., Earth and Planetary Science Letters 401, 12-17 (2014). 4. Q. Hu et al., Proceedings of the National Academy of Sciences of the United States of America 114, 1498-1501 (2017). 5. M. Nishi, Y. Kuwayama, J. Tsuchiya, T. Tsuchiya, Nature 547, 205-208 (2017). 6. Q. Hu et al., Nature 534, 241-244 (2016). 7. L. Zhang et al., American Mineralogist 101, 231-234 (2016).

Electron Microscopy Structural Insights into CPAP Oligomeric Behavior: A Plausible Assembly Process of a Supramolecular Scaffold of the Centrosome

PubMed Central

Alvarez-Cabrera, Ana L.; Delgado, Sandra; Gil-Carton, David; Mortuza, Gulnahar B.; Montoya, Guillermo; Sorzano, Carlos O. S.; Tang, Tang K.; Carazo, Jose M.

2017-01-01

Centrosomal P4.1-associated protein (CPAP) is a cell cycle regulated protein fundamental for centrosome assembly and centriole elongation. In humans, the region between residues 897–1338 of CPAP mediates interactions with other proteins and includes a homodimerization domain. CPAP mutations cause primary autosomal recessive microcephaly and Seckel syndrome. Despite of the biological/clinical relevance of CPAP, its mechanistic behavior remains unclear and its C-terminus (the G-box/TCP domain) is the only part whose structure has been solved. This situation is perhaps due in part to the challenges that represent obtaining the protein in a soluble, homogeneous state for structural studies. Our work constitutes a systematic structural analysis on multiple oligomers of HsCPAP897−1338, using single-particle electron microscopy (EM) of negatively stained (NS) samples. Based on image classification into clearly different regular 3D maps (putatively corresponding to dimers and tetramers) and direct observation of individual images representing other complexes of HsCPAP897−1338 (i.e., putative flexible monomers and higher-order multimers), we report a dynamic oligomeric behavior of this protein, where different homo-oligomers coexist in variable proportions. We propose that dimerization of the putative homodimer forms a putative tetramer which could be the structural unit for the scaffold that either tethers the pericentriolar material to centrioles or promotes procentriole elongation. A coarse fitting of atomic models into the NS 3D maps at resolutions around 20 Å is performed only to complement our experimental data, allowing us to hypothesize on the oligomeric composition of the different complexes. In this way, the current EM work represents an initial step toward the structural characterization of different oligomers of CPAP, suggesting further insights to understand how this protein works, contributing to the elucidation of control mechanisms for centriole

Structural Insights into SraP-Mediated Staphylococcus aureus Adhesion to Host Cells

PubMed Central

Zhang, Juan; Wang, Lei; Bai, Xiao-Hui; Zhang, Shi-Jie; Ren, Yan-Min; Li, Na; Zhang, Yong-Hui; Zhang, Zhiyong; Gong, Qingguo; Mei, Yide; Xue, Ting; Zhang, Jing-Ren; Chen, Yuxing; Zhou, Cong-Zhao

2014-01-01

Staphylococcus aureus, a Gram-positive bacterium causes a number of devastating human diseases, such as infective endocarditis, osteomyelitis, septic arthritis and sepsis. S. aureus SraP, a surface-exposed serine-rich repeat glycoprotein (SRRP), is required for the pathogenesis of human infective endocarditis via its ligand-binding region (BR) adhering to human platelets. It remains unclear how SraP interacts with human host. Here we report the 2.05 Å crystal structure of the BR of SraP, revealing an extended rod-like architecture of four discrete modules. The N-terminal legume lectin-like module specifically binds to N-acetylneuraminic acid. The second module adopts a β-grasp fold similar to Ig-binding proteins, whereas the last two tandem repetitive modules resemble eukaryotic cadherins but differ in calcium coordination pattern. Under the conditions tested, small-angle X-ray scattering and molecular dynamic simulation indicated that the three C-terminal modules function as a relatively rigid stem to extend the N-terminal lectin module outwards. Structure-guided mutagenesis analyses, in addition to a recently identified trisaccharide ligand of SraP, enabled us to elucidate that SraP binding to sialylated receptors promotes S. aureus adhesion to and invasion into host epithelial cells. Our findings have thus provided novel structural and functional insights into the SraP-mediated host-pathogen interaction of S. aureus. PMID:24901708

Structural insights into the anti-HIV activity of the Oscillatoria agardhii agglutinin homolog lectin family.

PubMed

Koharudin, Leonardus M I; Kollipara, Sireesha; Aiken, Christopher; Gronenborn, Angela M

2012-09-28

Oscillatoria agardhii agglutinin homolog (OAAH) proteins belong to a recently discovered lectin family. All members contain a sequence repeat of ~66 amino acids, with the number of repeats varying among different family members. Apart from data for the founding member OAA, neither three-dimensional structures, information about carbohydrate binding specificities, nor antiviral activity data have been available up to now for any other members of the OAAH family. To elucidate the structural basis for the antiviral mechanism of OAAHs, we determined the crystal structures of Pseudomonas fluorescens and Myxococcus xanthus lectins. Both proteins exhibit the same fold, resembling the founding family member, OAA, with minor differences in loop conformations. Carbohydrate binding studies by NMR and x-ray structures of glycan-lectin complexes reveal that the number of sugar binding sites corresponds to the number of sequence repeats in each protein. As for OAA, tight and specific binding to α3,α6-mannopentaose was observed. All the OAAH proteins described here exhibit potent anti-HIV activity at comparable levels. Altogether, our results provide structural details of the protein-carbohydrate interaction for this novel lectin family and insights into the molecular basis of their HIV inactivation properties.

Insight and white matter fractional anisotropy in first-episode schizophrenia.

PubMed

Asmal, Laila; du Plessis, Stefan; Vink, Matthijs; Fouche, Jean-Paul; Chiliza, Bonginkosi; Emsley, Robin

2017-05-01

Impaired insight is a hallmark feature of schizophrenia. Structural studies implicate predominantly prefrontal, cingulate, cuneus/precuneus, and inferior temporal brain regions. The cortical midline structures (CMS) are also implicated in functional studies primarily through self-reflective processing tasks. However, few studies have explored the relationship between white matter tracts and insight in schizophrenia, and none in first-episode schizophrenia (FES). Here, we examined for fractional anisotropy (FA) differences in 89 minimally treated FES patients and 98 matched controls, and identified those FA differences associated with impaired clinical insight in patients. We found widespread FA reduction in FES patients compared to controls. Poorer insight in patients was predicted by lower FA values in a number of white matter tracts with a predilection for tracts associated with cortical midline structures (fronto-occipital, cingulate, cingulate hippocampus, uncinate, anterior corona radiata), and more severe depressive symptoms. The association between FA abnormalities and insight was most robust for the awareness of symptoms and illness awareness domains. Our study implicates a network of tracts involved in impaired insight in schizophrenia with a predilection for the CMS. This study is a first step in delineating the white matter tracts involved in insight impairment in schizophrenia prior to chronicity. Copyright © 2016. Published by Elsevier B.V.

The CONNECT project: Combining macro- and micro-structure.

PubMed

Assaf, Yaniv; Alexander, Daniel C; Jones, Derek K; Bizzi, Albero; Behrens, Tim E J; Clark, Chris A; Cohen, Yoram; Dyrby, Tim B; Huppi, Petra S; Knoesche, Thomas R; Lebihan, Denis; Parker, Geoff J M; Poupon, Cyril; Anaby, Debbie; Anwander, Alfred; Bar, Leah; Barazany, Daniel; Blumenfeld-Katzir, Tamar; De-Santis, Silvia; Duclap, Delphine; Figini, Matteo; Fischi, Elda; Guevara, Pamela; Hubbard, Penny; Hofstetter, Shir; Jbabdi, Saad; Kunz, Nicolas; Lazeyras, Francois; Lebois, Alice; Liptrot, Matthew G; Lundell, Henrik; Mangin, Jean-François; Dominguez, David Moreno; Morozov, Darya; Schreiber, Jan; Seunarine, Kiran; Nava, Simone; Poupon, Cyril; Riffert, Till; Sasson, Efrat; Schmitt, Benoit; Shemesh, Noam; Sotiropoulos, Stam N; Tavor, Ido; Zhang, Hui Gary; Zhou, Feng-Lei

2013-10-15

In recent years, diffusion MRI has become an extremely important tool for studying the morphology of living brain tissue, as it provides unique insights into both its macrostructure and microstructure. Recent applications of diffusion MRI aimed to characterize the structural connectome using tractography to infer connectivity between brain regions. In parallel to the development of tractography, additional diffusion MRI based frameworks (CHARMED, AxCaliber, ActiveAx) were developed enabling the extraction of a multitude of micro-structural parameters (axon diameter distribution, mean axonal diameter and axonal density). This unique insight into both tissue microstructure and connectivity has enormous potential value in understanding the structure and organization of the brain as well as providing unique insights to abnormalities that underpin disease states. The CONNECT (Consortium Of Neuroimagers for the Non-invasive Exploration of brain Connectivity and Tracts) project aimed to combine tractography and micro-structural measures of the living human brain in order to obtain a better estimate of the connectome, while also striving to extend validation of these measurements. This paper summarizes the project and describes the perspective of using micro-structural measures to study the connectome. Copyright © 2013 Elsevier Inc. All rights reserved.

Self-Assembly of Phenylalanine Oligopeptides: Insights from Experiments and Simulations

PubMed Central

Tamamis, Phanourios; Adler-Abramovich, Lihi; Reches, Meital; Marshall, Karen; Sikorski, Pawel; Serpell, Louise; Gazit, Ehud; Archontis, Georgios

2009-01-01

Abstract Studies of peptide-based nanostructures provide general insights into biomolecular self-assembly and can lead material engineering toward technological applications. The diphenylalanine peptide (FF) self-assembles into discrete, hollow, well ordered nanotubes, and its derivatives form nanoassemblies of various morphologies. Here we demonstrate for the first time, to our knowledge, the formation of planar nanostructures with β-sheet content by the triphenylalanine peptide (FFF). We characterize these structures using various microscopy and spectroscopy techniques. We also obtain insights into the interactions and structural properties of the FF and FFF nanostructures by 0.4-μs, implicit-solvent, replica-exchange, molecular-dynamics simulations of aqueous FF and FFF solutions. In the simulations the peptides form aggregates, which often contain open or ring-like peptide networks, as well as elementary and network-containing structures with β-sheet characteristics. The networks are stabilized by polar and nonpolar interactions, and by the surrounding aggregate. In particular, the charged termini of neighbor peptides are involved in hydrogen-bonding interactions and their aromatic side chains form “T-shaped” contacts, as in three-dimensional FF crystals. These interactions may assist the FF and FFF self-assembly at the early stage, and may also stabilize the mature nanostructures. The FFF peptides have higher network propensities and increased aggregate stabilities with respect to FF, which can be interpreted energetically. PMID:19527662

Structural insights into the unique inhibitory mechanism of the silkworm protease inhibitor serpin18

PubMed Central

Guo, Peng-Chao; Dong, Zhaoming; Zhao, Ping; Zhang, Yan; He, Huawei; Tan, Xiang; Zhang, Weiwei; Xia, Qingyou

2015-01-01

Serpins generally serve as inhibitors that utilize a mobile reactive center loop (RCL) as bait to trap protease targets. Here, we present the crystal structure of serpin18 from Bombyx mori at 1.65 Å resolution, which has a very short and stable RCL. Activity analysis showed that the inhibitory target of serpin18 is a cysteine protease rather than a serine protease. Notably, this inhibitiory reaction results from the formation of an intermediate complex, which then follows for the digestion of protease and inhibitor into small fragments. This activity differs from previously reported modes of inhibition for serpins. Our findings have thus provided novel structural insights into the unique inhibitory mechanism of serpin18. Furthermore, one physiological target of serpin18, fibroinase, was identified, which enables us to better define the potential role for serpin18 in regulating fibroinase activity during B. mori development. PMID:26148664

[Insight, neurocognition and psychopathology in schizophrenia].

PubMed

Gil, D; Bengochea, R; Arrieta, M; Alvarez, A; Sánchez, R; Diego, M

2006-01-01

In recent years, research has been aimed at finding variables mediating between neurocognition and psychosocial functioning in schizophrenia, proposing insight as one of these variables. Some authors have found associations between insight and functional outcome, and between insight and symptomatology, although these associations remain unclear. These different findings could be explained by the insight definition used. The current study evaluates insight unidimensionally and multidimensionally and studies its relationship with cognitive and psychopathological variables. The sample consisted of 94 subjects admitted to an outpatient Psychosocial Rehabilitation Program, all diagnosed of schizophrenia according to ICD-10 diagnostic criteria. A brief version of the Neuropsychology Battery Test Barcelona and the Wisconsin Card Sorting Test were used to evaluate cognitive variables. The Positive and Negative Syndrome Scale (PANSS) was used to evaluate psychopathology. Insight was assessed with the PANSS item ((lack of judgment and insight)), and with a semi-structured interview. Two insight factors were found, one including more specific knowledge about the disease and its consequences (cognitive factor), that is related to executive functions, and another referring to unspecific knowledge about suffering from an illness and the need for treatment (psychotic factor). Each factor was statistically related to positive symptoms and superior cognitive functions. These findings support a relationship between insight and low cognitive performance.

Insight into Evolution, Processing and Performance of Multi-length-scale Structures in Planar Heterojunction Perovskite Solar Cells.

PubMed

Huang, Yu-Ching; Tsao, Cheng-Si; Cho, Yi-Ju; Chen, Kuan-Chen; Chiang, Kai-Ming; Hsiao, Sheng-Yi; Chen, Chang-Wen; Su, Chun-Jen; Jeng, U-Ser; Lin, Hao-Wu

2015-09-04

The structural characterization correlated to the processing control of hierarchical structure of planar heterojunction perovskite layer is still incomplete due to the limitations of conventional microscopy and X-ray diffraction. This present study performed the simultaneously grazing-incidence small-angle scattering and wide-angle scattering (GISAXS/GIWAXS) techniques to quantitatively probe the hierarchical structure of the planar heterojunction perovskite solar cells. The result is complementary to the currently microscopic study. Correlation between the crystallization behavior, crystal orientation, nano- and meso-scale internal structure and surface morphology of perovskite film as functions of various processing control parameters is reported for the first time. The structural transition from the fractal pore network to the surface fractal can be tuned by the chloride percentage. The GISAXS/GIWAXS measurement provides the comprehensive understanding of concurrent evolution of the film morphology and crystallization correlated to the high performance. The result can provide the insight into formation mechanism and rational synthesis design.

Insight into Evolution, Processing and Performance of Multi-length-scale Structures in Planar Heterojunction Perovskite Solar Cells

NASA Astrophysics Data System (ADS)

Huang, Yu-Ching; Tsao, Cheng-Si; Cho, Yi-Ju; Chen, Kuan-Chen; Chiang, Kai-Ming; Hsiao, Sheng-Yi; Chen, Chang-Wen; Su, Chun-Jen; Jeng, U.-Ser; Lin, Hao-Wu

2015-09-01

The structural characterization correlated to the processing control of hierarchical structure of planar heterojunction perovskite layer is still incomplete due to the limitations of conventional microscopy and X-ray diffraction. This present study performed the simultaneously grazing-incidence small-angle scattering and wide-angle scattering (GISAXS/GIWAXS) techniques to quantitatively probe the hierarchical structure of the planar heterojunction perovskite solar cells. The result is complementary to the currently microscopic study. Correlation between the crystallization behavior, crystal orientation, nano- and meso-scale internal structure and surface morphology of perovskite film as functions of various processing control parameters is reported for the first time. The structural transition from the fractal pore network to the surface fractal can be tuned by the chloride percentage. The GISAXS/GIWAXS measurement provides the comprehensive understanding of concurrent evolution of the film morphology and crystallization correlated to the high performance. The result can provide the insight into formation mechanism and rational synthesis design.

Structural insights into the functional versatility of WW domain-containing oxidoreductase tumor suppressor

PubMed Central

2015-01-01

Recent work on WW domain-containing oxidoreductase (WWOX) tumor suppressor is beginning to shed new light on both the molecular mechanism of action of its WW domains as well as the contiguous catalytic domain. Herein, the structural basis underlying the ability of WW1 domain to bind to various physiological ligands and how the orphan WW2 tandem partner synergizes its ligand binding in the context of WW1–WW2 tandem module of WWOX is discussed. Notably, the WW domains within the WW1–WW2 tandem module physically associate so as to adopt a fixed spatial orientation relative to each other. In this manner, the association of WW2 domain with WW1 hinders ligand binding to the latter. Consequently, ligand binding to WW1 domain not only results in the displacement of WW2 lid but also disrupts the fixed orientation of WW domains in the liganded conformation. Equally importantly, structure-guided functional approach suggests that the catalytic domain of WWOX likely serves as a retinal oxidoreductase that catalyzes the reversible oxidation and reduction of all-trans-retinal. Collectively, this review provides structural insights into the functional versatility of a key signaling protein with important implications on its biology. PMID:25662954

Structural insights into the functional versatility of WW domain-containing oxidoreductase tumor suppressor.

PubMed

Farooq, Amjad

2015-03-01

Recent work on WW domain-containing oxidoreductase (WWOX) tumor suppressor is beginning to shed new light on both the molecular mechanism of action of its WW domains as well as the contiguous catalytic domain. Herein, the structural basis underlying the ability of WW1 domain to bind to various physiological ligands and how the orphan WW2 tandem partner synergizes its ligand binding in the context of WW1-WW2 tandem module of WWOX is discussed. Notably, the WW domains within the WW1-WW2 tandem module physically associate so as to adopt a fixed spatial orientation relative to each other. In this manner, the association of WW2 domain with WW1 hinders ligand binding to the latter. Consequently, ligand binding to WW1 domain not only results in the displacement of WW2 lid but also disrupts the fixed orientation of WW domains in the liganded conformation. Equally importantly, structure-guided functional approach suggests that the catalytic domain of WWOX likely serves as a retinal oxidoreductase that catalyzes the reversible oxidation and reduction of all-trans-retinal. Collectively, this review provides structural insights into the functional versatility of a key signaling protein with important implications on its biology. © 2015 by the Society for Experimental Biology and Medicine.

Multi Length Scale Imaging of Flocculated Estuarine Sediments; Insights into their Complex 3D Structure

NASA Astrophysics Data System (ADS)

Wheatland, Jonathan; Bushby, Andy; Droppo, Ian; Carr, Simon; Spencer, Kate

2015-04-01

Suspended estuarine sediments form flocs that are compositionally complex, fragile and irregularly shaped. The fate and transport of suspended particulate matter (SPM) is determined by the size, shape, density, porosity and stability of these flocs and prediction of SPM transport requires accurate measurements of these three-dimensional (3D) physical properties. However, the multi-scaled nature of flocs in addition to their fragility makes their characterisation in 3D problematic. Correlative microscopy is a strategy involving the spatial registration of information collected at different scales using several imaging modalities. Previously, conventional optical microscopy (COM) and transmission electron microscopy (TEM) have enabled 2-dimensional (2D) floc characterisation at the gross (> 1 µm) and sub-micron scales respectively. Whilst this has proven insightful there remains a critical spatial and dimensional gap preventing the accurate measurement of geometric properties and an understanding of how structures at different scales are related. Within life sciences volumetric imaging techniques such as 3D micro-computed tomography (3D µCT) and focused ion beam scanning electron microscopy [FIB-SEM (or FIB-tomography)] have been combined to characterise materials at the centimetre to micron scale. Combining these techniques with TEM enables an advanced correlative study, allowing material properties across multiple spatial and dimensional scales to be visualised. The aims of this study are; 1) to formulate an advanced correlative imaging strategy combining 3D µCT, FIB-tomography and TEM; 2) to acquire 3D datasets; 3) to produce a model allowing their co-visualisation; 4) to interpret 3D floc structure. To reduce the chance of structural alterations during analysis samples were first 'fixed' in 2.5% glutaraldehyde/2% formaldehyde before being embedding in Durcupan resin. Intermediate steps were implemented to improve contrast and remove pore water, achieved by the

Insights into the structure of mixed CO 2/CH 4 in gas hydrates

DOE PAGES

Everett, S. Michelle; Rawn, Claudia J.; Chakoumakos, Bryan C.; ...

2015-05-12

The exchange of carbon dioxide for methane in natural gas hydrates is an attractive approach to harvesting CH 4 for energy production while simultaneously sequestering CO 2. In addition to the energy and environmental implications, the solid solution of clathrate hydrate (CH 4) 1-x(CO 2) x·5.75H 2O provides a model system to study how the distinct bonding and shapes of CH 4 and CO 2 influence the structure and properties of the compound. In this paper, high-resolution neutron diffraction was used to examine mixed CO 2/CH 4 gas hydrates. CO 2-rich hydrates had smaller lattice parameters, which were attributed tomore » the higher affinity of the CO 2 molecule interacting with H 2O molecules that form the surrounding cages, and resulted in a reduction in the unit-cell volume. Experimental nuclear scattering densities illustrate how the cage occupants and energy landscape change with composition. Finally, these results provide important insights on the impact and mechanisms for the structure of mixed CH 4/CO 2 gas hydrate.« less

Inhibition of strigolactone receptors by N-phenylanthranilic acid derivatives: Structural and functional insights.

PubMed

Hamiaux, Cyril; Drummond, Revel S M; Luo, Zhiwei; Lee, Hui Wen; Sharma, Prachi; Janssen, Bart J; Perry, Nigel B; Denny, William A; Snowden, Kimberley C

2018-04-27

The strigolactone (SL) family of plant hormones regulates a broad range of physiological processes affecting plant growth and development and also plays essential roles in controlling interactions with parasitic weeds and symbiotic fungi. Recent progress elucidating details of SL biosynthesis, signaling, and transport offers many opportunities for discovering new plant-growth regulators via chemical interference. Here, using high-throughput screening and downstream biochemical assays, we identified N -phenylanthranilic acid derivatives as potent inhibitors of the SL receptors from petunia (DAD2), rice (OsD14), and Arabidopsis (AtD14). Crystal structures of DAD2 and OsD14 in complex with inhibitors further provided detailed insights into the inhibition mechanism, and in silico modeling of 19 other plant strigolactone receptors suggested that these compounds are active across a large range of plant species. Altogether, these results provide chemical tools for investigating SL signaling and further define a framework for structure-based approaches to design and validate optimized inhibitors of SL receptors for specific plant targets. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Human acid sphingomyelinase structures provide insight to molecular basis of Niemann–Pick disease

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

Zhou, Yan-Feng; Metcalf, Matthew C.; Garman, Scott C.

Acid sphingomyelinase (ASM) hydrolyzes sphingomyelin to ceramide and phosphocholine, essential components of myelin in neurons. Genetic alterations in ASM lead to ASM deficiency (ASMD) and have been linked to Niemann–Pick disease types A and B. Olipudase alfa, a recombinant form of human ASM, is being developed as enzyme replacement therapy to treat the non-neurological manifestations of ASMD. Here we present the human ASM holoenzyme and product bound structures encompassing all of the functional domains. The catalytic domain has a metallophosphatase fold, and two zinc ions and one reaction product phosphocholine are identified in a histidine-rich active site. The structures revealmore » the underlying catalytic mechanism, in which two zinc ions activate a water molecule for nucleophilic attack of the phosphodiester bond. Docking of sphingomyelin provides a model that allows insight into the selectivity of the enzyme and how the ASM domains collaborate to complete hydrolysis. Mapping of known mutations provides a basic understanding on correlations between enzyme dysfunction and phenotypes observed in ASMD patients.« less

Human acid sphingomyelinase structures provide insight to molecular basis of Niemann–Pick disease

PubMed Central

Zhou, Yan-Feng; Metcalf, Matthew C.; Garman, Scott C.; Edmunds, Tim; Qiu, Huawei; Wei, Ronnie R.

2016-01-01

Acid sphingomyelinase (ASM) hydrolyzes sphingomyelin to ceramide and phosphocholine, essential components of myelin in neurons. Genetic alterations in ASM lead to ASM deficiency (ASMD) and have been linked to Niemann–Pick disease types A and B. Olipudase alfa, a recombinant form of human ASM, is being developed as enzyme replacement therapy to treat the non-neurological manifestations of ASMD. Here we present the human ASM holoenzyme and product bound structures encompassing all of the functional domains. The catalytic domain has a metallophosphatase fold, and two zinc ions and one reaction product phosphocholine are identified in a histidine-rich active site. The structures reveal the underlying catalytic mechanism, in which two zinc ions activate a water molecule for nucleophilic attack of the phosphodiester bond. Docking of sphingomyelin provides a model that allows insight into the selectivity of the enzyme and how the ASM domains collaborate to complete hydrolysis. Mapping of known mutations provides a basic understanding on correlations between enzyme dysfunction and phenotypes observed in ASMD patients. PMID:27725636

Insights on synergy of materials and structures in biomimetic platelet-matrix composites

NASA Astrophysics Data System (ADS)

Sakhavand, Navid; Shahsavari, Rouzbeh

2018-01-01

Hybrid materials such as biomimetic platelet-matrix composites are in high demand to confer low weight and multifunctional mechanical properties. This letter reports interfacial-bond regulated assembly of polymers on cement-an archetype model with significant infrastructure applications. We demonstrate a series of 20+ molecular dynamics studies on decoding and optimizing the complex interfacial interactions including the role and types of various heterogeneous, competing interfacial bonds that are key to adhesion and interfacial strength. Our results show an existence of an optimum overlap length scale (˜15 nm) between polymers and cement crystals, exhibiting the best balance of strength, toughness, stiffness, and ductility for the composite. This finding, combined with the fundamental insights into the nature of interfacial bonds, provides key hypotheses for selection and processing of constituents to deliberate the best synergy in the structure and materials of platelet-matrix composites.

Insight and psychopathology in never-treated schizophrenia.

PubMed

Tirupati, Srinivasan; Padmavati, Raman; Thara, Rangaswamy; McCreadie, Robin G

2007-01-01

Insight is a feature of schizophrenia related to psychopathology, which could be modified by treatment. The real relationship will be more evident in the never-treated state. This study compared insight and its relationship to psychopathology in 143 never-treated patients with chronic schizophrenia with 183 treated patients. The treated patients had not received any structured intervention for improvement of insight. The item on insight and judgment from the Positive and Negative Syndrome Scale for schizophrenia was used as a measure of insight. Never-treated patients were more ill and poorer in insight than the TT group. Sex, age, duration of illness, negative symptoms related to insight only in the TT group. Positive symptoms score correlated with insight in both the groups, but negative symptoms correlated with insight only among the treated patients. Delusions, uncooperativeness, and poor attention predicted 27% of variation in the level of insight in the never-treated, whereas age; duration of illness; and symptoms of emotional withdrawal, difficulty in abstract thinking, and uncooperativeness predicted 30.3% of variation in insight of the TT group. The observed differences between the never-treated and treated subjects were due to influence of treatment on the association between insight and psychopathology. A subgroup of patients with a treatment-resistant trait of negative symptoms associated with poor insight was hypothesized.

Crystal structure of Anoxybacillus α-amylase provides insights into maltose binding of a new glycosyl hydrolase subclass.

PubMed

Chai, Kian Piaw; Othman, Noor Farhan Binti; Teh, Aik-Hong; Ho, Kok Lian; Chan, Kok-Gan; Shamsir, Mohd Shahir; Goh, Kian Mau; Ng, Chyan Leong

2016-03-15

A new subfamily of glycosyl hydrolase family GH13 was recently proposed for α-amylases from Anoxybacillus species (ASKA and ADTA), Geobacillus thermoleovorans (GTA, Pizzo, and GtamyII), Bacillus aquimaris (BaqA), and 95 other putative protein homologues. To understand this new GH13 subfamily, we report crystal structures of truncated ASKA (TASKA). ASKA is a thermostable enzyme capable of producing high levels of maltose. Unlike GTA, biochemical analysis showed that Ca(2+) ion supplementation enhances the catalytic activities of ASKA and TASKA. The crystal structures reveal the presence of four Ca(2+) ion binding sites, with three of these binding sites are highly conserved among Anoxybacillus α-amylases. This work provides structural insights into this new GH13 subfamily both in the apo form and in complex with maltose. Furthermore, structural comparison of TASKA and GTA provides an overview of the conformational changes accompanying maltose binding at each subsite.

Dynamic Nuclear Polarization NMR Spectroscopy of Polymeric Carbon Nitride Photocatalysts: Insights into Structural Defects and Reactivity.

PubMed

Li, Xiaobo; Sergeyev, Ivan V; Aussenac, Fabien; Masters, Anthony F; Maschmeyer, Thomas; Hook, James M

2018-06-04

Metal-free polymeric carbon nitrides (PCNs) are promising photocatalysts for solar hydrogen production, but their structure-photoactivity relationship remains elusive. Two PCNs were characterized by dynamic-nuclear-polarization-enhanced solid-state NMR spectroscopy, which circumvented the need for specific labeling with either 13 C- or 15 N-enriched precursors. Rapid 1D and 2D data acquisition was possible, providing insights into the structural contrasts between the PCNs. Compared to PCN_B with lower performance, PCN_P is a more porous and more active photocatalyst that is richer in terminal N-H bonds not associated with interpolymer chains. It is proposed that terminal N-H groups act as efficient carrier traps and reaction sites. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kinetic and Structural Insights into the Mechanism of AMPylation by VopS Fic Domain*

PubMed Central

Luong, Phi; Kinch, Lisa N.; Brautigam, Chad A.; Grishin, Nick V.; Tomchick, Diana R.; Orth, Kim

2010-01-01

The bacterial pathogen Vibrio parahemeolyticus manipulates host signaling pathways during infections by injecting type III effectors into the cytoplasm of the target cell. One of these effectors, VopS, blocks actin assembly by AMPylation of a conserved threonine residue in the switch 1 region of Rho GTPases. The modified GTPases are no longer able to interact with downstream effectors due to steric hindrance by the covalently linked AMP moiety. Herein we analyze the structure of VopS and its evolutionarily conserved catalytic residues. Steady-state analysis of VopS mutants provides kinetic understanding on the functional role of each residue for AMPylation activity by the Fic domain. Further mechanistic analysis of VopS with its two substrates, ATP and Cdc42, demonstrates that VopS utilizes a sequential mechanism to AMPylate Rho GTPases. Discovery of a ternary reaction mechanism along with structural insight provides critical groundwork for future studies for the family of AMPylators that modify hydroxyl-containing residues with AMP. PMID:20410310

Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity

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

Sayer, Christopher; Isupov, Michail N.; Westlake, Aaron

2013-04-01

The X-ray structures of two ω-aminotransferases from P. aeruginosa and C. violaceum in complex with an inhibitor offer the first detailed insight into the structural basis of the substrate specificity of these industrially important enzymes. The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes showmore » activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases.« less

Structure of human POFUT2: insights into thrombospondin type 1 repeat fold and O-fucosylation

PubMed Central

Chen, Chun-I; Keusch, Jeremy J; Klein, Dominique; Hess, Daniel; Hofsteenge, Jan; Gut, Heinz

2012-01-01

Protein O-fucosylation is a post-translational modification found on serine/threonine residues of thrombospondin type 1 repeats (TSR). The fucose transfer is catalysed by the enzyme protein O-fucosyltransferase 2 (POFUT2) and >40 human proteins contain the TSR consensus sequence for POFUT2-dependent fucosylation. To better understand O-fucosylation on TSR, we carried out a structural and functional analysis of human POFUT2 and its TSR substrate. Crystal structures of POFUT2 reveal a variation of the classical GT-B fold and identify sugar donor and TSR acceptor binding sites. Structural findings are correlated with steady-state kinetic measurements of wild-type and mutant POFUT2 and TSR and give insight into the catalytic mechanism and substrate specificity. By using an artificial mini-TSR substrate, we show that specificity is not primarily encoded in the TSR protein sequence but rather in the unusual 3D structure of a small part of the TSR. Our findings uncover that recognition of distinct conserved 3D fold motifs can be used as a mechanism to achieve substrate specificity by enzymes modifying completely folded proteins of very wide sequence diversity and biological function. PMID:22588082

Induced structural changes of humic acid by exposure of polystyrene microplastics: A spectroscopic insight.

PubMed

Chen, Wei; Ouyang, Zhen-Yu; Qian, Chen; Yu, Han-Qing

2018-02-01

The occurrence of microplastics (MPs) as emerging contaminants in the environment may cause changes in water or sediment characteristics, and further affect their biogeochemical cycles. Thus, insights into the interactions between dissolved organic matter (DOM) and MPs are essential for the assessment of environmental impacts of MPs in ecosystems. Integrating spectroscopic methods with chemometric analyses, this work explored the chemical and microstructural changes of DOM-MP complex to reveal the mechanism of DOM-MP interaction at a molecular level. MPs were found to interact with the aromatic structure of DOM via π-π conjugation, then be entrapped in the DOM polymers by the carboxyl groups and C=O bonds, constituting a highly conjugated co-polymer with increased electron density. This induced the fluorescence intensity increase in DOM. The interaction affinity of DOM-MP was highly dependent on the MP size and solution pH. This work offers a new insight into the impact of MP discharge on environment and may provide an analytical framework for evaluating MP hetero-aggregation and the roles of MPs in the transportation of other contaminants. Furthermore, the integrated methods used in this work exhibit potential applications in exploring the fragmentation processes of MPs and formation of secondary MPs under natural conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Insights into structural variations and genome rearrangements in prokaryotic genomes.

PubMed

Periwal, Vinita; Scaria, Vinod

2015-01-01

Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Mean motion resonances. [of asteroid belt structure

NASA Technical Reports Server (NTRS)

Froeschle, CL.; Greenberg, R.

1989-01-01

Recent research on the resonant structure of the asteroid belt is reviewed. The resonant mechanism is discussed, and analytical models for the study of mean motion resonances are examined. Numerical averaging methods and mapping methods are considered. It is shown how fresh insight can be obtained by means of a new semianalytical approach.

Structural and Mechanistic Insights into the Latrophilin3-FLRT3 Complex that Mediates Glutamatergic Synapse Development.

PubMed

Ranaivoson, Fanomezana M; Liu, Qun; Martini, Francesca; Bergami, Francesco; von Daake, Sventja; Li, Sheng; Lee, David; Demeler, Borries; Hendrickson, Wayne A; Comoletti, Davide

2015-09-01

Latrophilins (LPHNs) are adhesion-like G-protein-coupled receptors implicated in attention-deficit/hyperactivity disorder. Recently, LPHN3 was found to regulate excitatory synapse number through trans interactions with fibronectin leucine-rich repeat transmembrane 3 (FLRT3). By isothermal titration calorimetry, we determined that only the olfactomedin (OLF) domain of LPHN3 is necessary for FLRT3 association. By multi-crystal native single-wavelength anomalous diffraction phasing, we determined the crystal structure of the OLF domain. This structure is a five-bladed β propeller with a Ca(2+) ion bound in the central pore, which is capped by a mobile loop that allows the ion to exchange with the solvent. The crystal structure of the OLF/FLRT3 complex shows that LPHN3-OLF in the closed state binds with high affinity to the concave face of FLRT3-LRR with a combination of hydrophobic and charged residues. Our study provides structural and functional insights into the molecular mechanism underlying the contribution of LPHN3/FLRT3 to the development of glutamatergic synapses. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structure and Properties of Sio2 Nanopowder Obtained From High-Silica Raw Materials by Plasma Method

NASA Astrophysics Data System (ADS)

Kosmachev, P. V.; Vlasov, V. A.; Skripnikova, N. K.

2017-06-01

The paper presents a plasma-assisted generation of nanodisperse powder obtained from diatomite, a natural high-silica material. The structure and properties of the obtained material are investigated using the transmission electron microscopy, energy dispersive X-Ray spectroscopy, infrared and X-ray photoelectron spectroscopies, and Brunauer-Emmett-Teller method. It is clearly shown that the obtained SiO2 nanoparticles are spherical, polydisperse and represented in the form of agglomerates. The specific surface of this nanopowder is 32 m2/g. Thermodynamic modeling of the plasma-assisted process is used to obtain the equilibrium compositions of condensed and gaseous reaction products. The plasma process is performed within the 300-5000 K temperature range.

Structural Insights into DD-Fold Assembly and Caspase-9 Activation by the Apaf-1 Apoptosome.

PubMed

Su, Tsung-Wei; Yang, Chao-Yu; Kao, Wen-Pin; Kuo, Bai-Jiun; Lin, Shan-Meng; Lin, Jung-Yaw; Lo, Yu-Chih; Lin, Su-Chang

2017-03-07

Death domain (DD)-fold assemblies play a crucial role in regulating the signaling to cell survival or death. Here we report the crystal structure of the caspase recruitment domain (CARD)-CARD disk of the human apoptosome. The structure surprisingly reveals that three 1:1 Apaf-1:procaspase-9 CARD protomers form a novel helical DD-fold assembly on the heptameric wheel-like platform of the apoptosome. The small-angle X-ray scattering and multi-angle light scattering data also support that three protomers could form an oligomeric complex similar to the crystal structure. Interestingly, the quasi-equivalent environment of CARDs could generate different quaternary CARD assemblies. We also found that the type II interaction is conserved in all DD-fold complexes, whereas the type I interaction is found only in the helical DD-fold assemblies. This study provides crucial insights into the caspase activation mechanism, which is tightly controlled by a sophisticated and highly evolved CARD assembly on the apoptosome, and also enables better understanding of the intricate DD-fold assembly. Copyright © 2017 Elsevier Ltd. All rights reserved.

Method for obtaining structure and interactions from oriented lipid bilayers

PubMed Central

Lyatskaya, Yulia; Liu, Yufeng; Tristram-Nagle, Stephanie; Katsaras, John; Nagle, John F.

2009-01-01

Precise calculations are made of the scattering intensity I(q) from an oriented stack of lipid bilayers using a realistic model of fluctuations. The quantities of interest include the bilayer bending modulus Kc , the interbilayer interaction modulus B, and bilayer structure through the form factor F(qz). It is shown how Kc and B may be obtained from data at large qz where fluctuations dominate. Good estimates of F(qz) can be made over wide ranges of qz by using I(q) in q regions away from the peaks and for qr≠0 where details of the scattering domains play little role. Rough estimates of domain sizes can also be made from smaller qz data. Results are presented for data taken on fully hydrated, oriented DOPC bilayers in the Lα phase. These results illustrate the advantages of oriented samples compared to powder samples. PMID:11304287

Three-dimensional structure of the NLRP7 pyrin domain: insight into pyrin-pyrin-mediated effector domain signaling in innate immunity.

PubMed

Pinheiro, Anderson S; Proell, Martina; Eibl, Clarissa; Page, Rebecca; Schwarzenbacher, Robert; Peti, Wolfgang

2010-08-27

The innate immune system provides an initial line of defense against infection. Nucleotide-binding domain- and leucine-rich repeat-containing protein (NLR or (NOD-like)) receptors play a critical role in the innate immune response by surveying the cytoplasm for traces of intracellular invaders and endogenous stress signals. NLRs themselves are multi-domain proteins. Their N-terminal effector domains (typically a pyrin or caspase activation and recruitment domain) are responsible for driving downstream signaling and initiating the formation of inflammasomes, multi-component complexes necessary for cytokine activation. However, the currently available structures of NLR effector domains have not yet revealed the mechanism of their differential modes of interaction. Here, we report the structure and dynamics of the N-terminal pyrin domain of NLRP7 (NLRP7 PYD) obtained by NMR spectroscopy. The NLRP7 PYD adopts a six-alpha-helix bundle death domain fold. A comparison of conformational and dynamics features of the NLRP7 PYD with other PYDs showed distinct differences for helix alpha3 and loop alpha2-alpha3, which, in NLRP7, is stabilized by a strong hydrophobic cluster. Moreover, the NLRP7 and NLRP1 PYDs have different electrostatic surfaces. This is significant, because death domain signaling is driven by electrostatic contacts and stabilized by hydrophobic interactions. Thus, these results provide new insights into NLRP signaling and provide a first molecular understanding of inflammasome formation.

Structural insights into the role of diphthamide on elongation factor 2 in messenger RNA reading frame maintenance.

PubMed

Pellegrino, Simone; Demeshkina, Natalia; Mancera-Martinez, Eder; Melnikov, Sergey; Simonetti, Angelita; Myasnikov, Alexander; Yusupov, Marat; Yusupova, Gulnara; Hashem, Yaser

2018-06-07

One of the most critical steps of protein biosynthesis is the coupled movement of messenger RNA (mRNA), that encodes genetic information, with transfer RNAs (tRNAs) on the ribosome. In eukaryotes this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species. Here we present near-atomic resolution cryo-EM structures of yeast 80S ribosome complexes containing mRNA, tRNA and eEF2 trapped in different GTP-hydrolysis states which provide further structural insights on the role of diphthamide in the mechanism of translation fidelity in eukaryotes. Copyright © 2018. Published by Elsevier Ltd.

Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation

NASA Astrophysics Data System (ADS)

Di Giovanni, James P.; Barkley, Robert M.; Jones, David N. M.; Hankin, Joseph A.; Murphy, Robert C.

2018-04-01

Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H]- ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H]- and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H2O-CO2]- and [M-H-H2O]- displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H2O]- ion from LTB4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H2O]- product ions from LTB4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. [Figure not available: see fulltext.

Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation.

PubMed

Di Giovanni, James P; Barkley, Robert M; Jones, David N M; Hankin, Joseph A; Murphy, Robert C

2018-04-23

Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H] - ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H] - and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H 2 O-CO 2 ] - and [M-H-H 2 O] - displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H 2 O] - ion from LTB 4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H 2 O] - product ions from LTB 4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. Graphical Abstract ᅟ.

Crystal structure of Anoxybacillus α-amylase provides insights into maltose binding of a new glycosyl hydrolase subclass

PubMed Central

Chai, Kian Piaw; Othman, Noor Farhan Binti; Teh, Aik-Hong; Ho, Kok Lian; Chan, Kok-Gan; Shamsir, Mohd Shahir; Goh, Kian Mau; Ng, Chyan Leong

2016-01-01

A new subfamily of glycosyl hydrolase family GH13 was recently proposed for α-amylases from Anoxybacillus species (ASKA and ADTA), Geobacillus thermoleovorans (GTA, Pizzo, and GtamyII), Bacillus aquimaris (BaqA), and 95 other putative protein homologues. To understand this new GH13 subfamily, we report crystal structures of truncated ASKA (TASKA). ASKA is a thermostable enzyme capable of producing high levels of maltose. Unlike GTA, biochemical analysis showed that Ca2+ ion supplementation enhances the catalytic activities of ASKA and TASKA. The crystal structures reveal the presence of four Ca2+ ion binding sites, with three of these binding sites are highly conserved among Anoxybacillus α-amylases. This work provides structural insights into this new GH13 subfamily both in the apo form and in complex with maltose. Furthermore, structural comparison of TASKA and GTA provides an overview of the conformational changes accompanying maltose binding at each subsite. PMID:26975884

Insights into a spatially embedded social network from a large-scale snowball sample

NASA Astrophysics Data System (ADS)

Illenberger, J.; Kowald, M.; Axhausen, K. W.; Nagel, K.

2011-12-01

Much research has been conducted to obtain insights into the basic laws governing human travel behaviour. While the traditional travel survey has been for a long time the main source of travel data, recent approaches to use GPS data, mobile phone data, or the circulation of bank notes as a proxy for human travel behaviour are promising. The present study proposes a further source of such proxy-data: the social network. We collect data using an innovative snowball sampling technique to obtain details on the structure of a leisure-contacts network. We analyse the network with respect to its topology, the individuals' characteristics, and its spatial structure. We further show that a multiplication of the functions describing the spatial distribution of leisure contacts and the frequency of physical contacts results in a trip distribution that is consistent with data from the Swiss travel survey.

Structure of the manganese complex in photosystem II: insights from X-ray spectroscopy.

PubMed Central

Yachandra, Vittal K

2002-01-01

We have used Mn K-edge absorption and Kbeta emission spectroscopy to determine the oxidation states of the Mn complex in the various S states. We have started exploring the new technique of resonant inelastic X-ray scattering spectroscopy; this technique can be characterized as a Raman process that uses K-edge energies (1s to 4p, ca. 6550 eV) to obtain L-edge-like spectra (2p to 3d, ca. 650 eV). The relevance of these data to the oxidation states and structure of the Mn complex is presented. We have obtained extended X-ray absorption fine structure data from the S(0) and S(3) states and observed heterogeneity in the Mn-Mn distances leading us to conclude that there may be three rather than two di-mu-oxo-bridged units present per tetranuclear Mn cluster. In addition, we have obtained data using Ca and Sr X-ray spectroscopy that provide evidence for a heteronuclear Mn-Ca cluster. The possibility of three di-mu-oxo-bridged Mn-Mn moieties and the proximity of Ca is incorporated into developing structural models for the Mn cluster. The involvement of bridging and terminal O ligands of Mn in the mechanism of oxygen evolution is discussed in the context of our X-ray spectroscopy results. PMID:12437873

Simulations in Medicine and Biology: Insights and perspectives

NASA Astrophysics Data System (ADS)

Spyrou, George M.

2015-01-01

Modern medicine and biology have been transformed into quantitative sciences of high complexity, with challenging objectives. The aims of medicine are related to early diagnosis, effective therapy, accurate intervention, real time monitoring, procedures/systems/instruments optimization, error reduction, and knowledge extraction. Concurrently, following the explosive production of biological data concerning DNA, RNA, and protein biomolecules, a plethora of questions has been raised in relation to their structure and function, the interactions between them, their relationships and dependencies, their regulation and expression, their location, and their thermodynamic characteristics. Furthermore, the interplay between medicine and biology gives rise to fields like molecular medicine and systems biology which are further interconnected with physics, mathematics, informatics, and engineering. Modelling and simulation is a powerful tool in the fields of Medicine and Biology. Simulating the phenomena hidden inside a diagnostic or therapeutic medical procedure, we are able to obtain control on the whole system and perform multilevel optimization. Furthermore, modelling and simulation gives insights in the various scales of biological representation, facilitating the understanding of the huge amounts of derived data and the related mechanisms behind them. Several examples, as well as the insights and the perspectives of simulations in biomedicine will be presented.

The Structural Basis of IKs Ion-Channel Activation: Mechanistic Insights from Molecular Simulations.

PubMed

Ramasubramanian, Smiruthi; Rudy, Yoram

2018-06-05

Relating ion channel (iCh) structural dynamics to physiological function remains a challenge. Current experimental and computational techniques have limited ability to explore this relationship in atomistic detail over physiological timescales. A framework associating iCh structure to function is necessary for elucidating normal and disease mechanisms. We formulated a modeling schema that overcomes the limitations of current methods through applications of artificial intelligence machine learning. Using this approach, we studied molecular processes that underlie human IKs voltage-mediated gating. IKs malfunction underlies many debilitating and life-threatening diseases. Molecular components of IKs that underlie its electrophysiological function include KCNQ1 (a pore-forming tetramer) and KCNE1 (an auxiliary subunit). Simulations, using the IKs structure-function model, reproduced experimentally recorded saturation of gating-charge displacement at positive membrane voltages, two-step voltage sensor (VS) movement shown by fluorescence, iCh gating statistics, and current-voltage relationship. Mechanistic insights include the following: 1) pore energy profile determines iCh subconductance; 2) the entire protein structure, not limited to the pore, contributes to pore energy and channel subconductance; 3) interactions with KCNE1 result in two distinct VS movements, causing gating-charge saturation at positive membrane voltages and current activation delay; and 4) flexible coupling between VS and pore permits pore opening at lower VS positions, resulting in sequential gating. The new modeling approach is applicable to atomistic scale studies of other proteins on timescales of physiological function. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Maturing Glycoproteomics Technologies Provide Unique Structural Insights into the N-glycoproteome and Its Regulation in Health and Disease*

PubMed Central

Packer, Nicolle H.; Schulz, Benjamin L.

2016-01-01

The glycoproteome remains severely understudied because of significant analytical challenges associated with glycoproteomics, the system-wide analysis of intact glycopeptides. This review introduces important structural aspects of protein N-glycosylation and summarizes the latest technological developments and applications in LC-MS/MS-based qualitative and quantitative N-glycoproteomics. These maturing technologies provide unique structural insights into the N-glycoproteome and its synthesis and regulation by complementing existing methods in glycoscience. Modern glycoproteomics is now sufficiently mature to initiate efforts to capture the molecular complexity displayed by the N-glycoproteome, opening exciting opportunities to increase our understanding of the functional roles of protein N-glycosylation in human health and disease. PMID:26929216

Structure investigations of ferromagnetic Co-Ni-Al alloys obtained by powder metallurgy.

PubMed

Maziarz, W; Dutkiewicz, J; Lityńska-Dobrzyńska, L; Santamarta, R; Cesari, E

2010-03-01

Elemental powders of Co, Ni and Al in the proper amounts to obtain Co(35)Ni(40)Al(25) and Co(40)Ni(35)Al(25) nominal compositions were ball milled in a high-energy mill for 80 h. After 40 h of milling, the formation of a Co (Ni, Al) solid solution with f.c.c. structure was verified by a change of the original lattice parameter and crystallite size. Analytical transmission electron microscopy observations and X-ray diffraction measurements of the final Co (Ni, Al) solid solution showed that the crystallite size scattered from 4 to 8 nm and lattice parameter a = 0.36086 nm. The chemical EDS point analysis of the milled powder particles allowed the calculation of the e/a ratio and revealed a high degree of chemical homogeneity of the powders. Hot pressing in vacuum of the milled powders resulted in obtaining compacts with a density of about 70% of the theoretical one. An additional heat treatment increased the density and induced the martensitic transformation in a parent phase. Selected area diffraction patterns and dark field images obtained from the heat-treated sample revealed small grains around 300 nm in diameter consisting mainly of the ordered gamma phase (gamma'), often appearing as twins, and a small amount of the L1(0) ordered martensite.

Structure-activity relationships of aminocoumarin-type gyrase and topoisomerase IV inhibitors obtained by combinatorial biosynthesis.

PubMed

Flatman, Ruth H; Eustaquio, Alessandra; Li, Shu-Ming; Heide, Lutz; Maxwell, Anthony

2006-04-01

Novobiocin and clorobiocin are gyrase inhibitors produced by Streptomyces strains. Structurally, the two compounds differ only by substitution at two positions: CH3 versus Cl at position 8' of the aminocoumarin ring and carbamoyl versus 5-methyl-pyrrol-2-carbonyl (MePC) at the 3"-OH of noviose. Using genetic engineering, we generated a series of analogs carrying H, CH3, or Cl at 8' and H, carbamoyl, or MePC at 3"-OH. Comparison of the gyrase inhibitory activities of all nine structural permutations confirmed that acylation of 3"-OH is essential for activity, with MePC being more effective than carbamoyl. Substitution at 8' further enhanced activity, but the effect of CH3 or Cl depended on the nature of the acyl group at 3": in the presence of carbamoyl at 3", CH3 resulted in higher activity; in the presence of MePC at 3", Cl resulted in higher activity. This suggests that the structures of both natural compounds are highly evolved for optimal interaction with gyrase. In a second series of experiments, clorobiocin derivatives with and without the methyl group at 4"-OH of noviose, and with different positions of the MePC group of noviose, were tested. Again clorobiocin was superior to all of its analogs. The activities of all compounds were also tested against topoisomerase IV (topo IV). Clorobiocin stood out as a remarkably effective topo IV inhibitor. The relative activities of the different compounds toward topo IV showed a pattern similar to that of the relative gyrase-inhibitory activities. This is the first report of a systematic evaluation of a series of aminocoumarins against both gyrase and topo IV. The results give further insight into the structure-activity relationships of aminocoumarin antibiotics.

Structure-Activity Relationships of Aminocoumarin-Type Gyrase and Topoisomerase IV Inhibitors Obtained by Combinatorial Biosynthesis

PubMed Central

Flatman, Ruth H.; Eustaquio, Alessandra; Li, Shu-Ming; Heide, Lutz; Maxwell, Anthony

2006-01-01

Novobiocin and clorobiocin are gyrase inhibitors produced by Streptomyces strains. Structurally, the two compounds differ only by substitution at two positions: CH3 versus Cl at position 8′ of the aminocoumarin ring and carbamoyl versus 5-methyl-pyrrol-2-carbonyl (MePC) at the 3"-OH of noviose. Using genetic engineering, we generated a series of analogs carrying H, CH3, or Cl at 8′ and H, carbamoyl, or MePC at 3"-OH. Comparison of the gyrase inhibitory activities of all nine structural permutations confirmed that acylation of 3"-OH is essential for activity, with MePC being more effective than carbamoyl. Substitution at 8′ further enhanced activity, but the effect of CH3 or Cl depended on the nature of the acyl group at 3": in the presence of carbamoyl at 3", CH3 resulted in higher activity; in the presence of MePC at 3", Cl resulted in higher activity. This suggests that the structures of both natural compounds are highly evolved for optimal interaction with gyrase. In a second series of experiments, clorobiocin derivatives with and without the methyl group at 4"-OH of noviose, and with different positions of the MePC group of noviose, were tested. Again clorobiocin was superior to all of its analogs. The activities of all compounds were also tested against topoisomerase IV (topo IV). Clorobiocin stood out as a remarkably effective topo IV inhibitor. The relative activities of the different compounds toward topo IV showed a pattern similar to that of the relative gyrase-inhibitory activities. This is the first report of a systematic evaluation of a series of aminocoumarins against both gyrase and topo IV. The results give further insight into the structure-activity relationships of aminocoumarin antibiotics. PMID:16569821

New Insights in Tropospheric Ozone and its Variability

NASA Technical Reports Server (NTRS)

Oman, Luke D.; Douglass, Anne R.; Ziemke, Jerry R.; Rodriquez, Jose M.

2011-01-01

We have produced time-slice simulations using the Goddard Earth Observing System Version 5 (GEOS-5) coupled to a comprehensive stratospheric and tropospheric chemical mechanism. These simulations are forced with observed sea surface temperatures over the past 25 years and use constant specified surface emissions, thereby providing a measure of the dynamically controlled ozone response. We examine the model performance in simulating tropospheric ozone and its variability. Here we show targeted comparisons results from our simulations with a multi-decadal tropical tropospheric column ozone dataset obtained from satellite observations of total column ozone. We use SHADOZ ozonesondes to gain insight into the observed vertical response and compare with the simulated vertical structure. This work includes but is not limited to ENSO related variability.

Structural and functional insights into the HIV-1 maturation inhibitor binding pocket.

PubMed

Waki, Kayoko; Durell, Stewart R; Soheilian, Ferri; Nagashima, Kunio; Butler, Scott L; Freed, Eric O

2012-01-01

Processing of the Gag precursor protein by the viral protease during particle release triggers virion maturation, an essential step in the virus replication cycle. The first-in-class HIV-1 maturation inhibitor dimethylsuccinyl betulinic acid [PA-457 or bevirimat (BVM)] blocks HIV-1 maturation by inhibiting the cleavage of the capsid-spacer peptide 1 (CA-SP1) intermediate to mature CA. A structurally distinct molecule, PF-46396, was recently reported to have a similar mode of action to that of BVM. Because of the structural dissimilarity between BVM and PF-46396, we hypothesized that the two compounds might interact differentially with the putative maturation inhibitor-binding pocket in Gag. To test this hypothesis, PF-46396 resistance was selected for in vitro. Resistance mutations were identified in three regions of Gag: around the CA-SP1 cleavage site where BVM resistance maps, at CA amino acid 201, and in the CA major homology region (MHR). The MHR mutants are profoundly PF-46396-dependent in Gag assembly and release and virus replication. The severe defect exhibited by the inhibitor-dependent MHR mutants in the absence of the compound is also corrected by a second-site compensatory change far downstream in SP1, suggesting structural and functional cross-talk between the HIV-1 CA MHR and SP1. When PF-46396 and BVM were both present in infected cells they exhibited mutually antagonistic behavior. Together, these results identify Gag residues that line the maturation inhibitor-binding pocket and suggest that BVM and PF-46396 interact differentially with this putative pocket. These findings provide novel insights into the structure-function relationship between the CA MHR and SP1, two domains of Gag that are critical to both assembly and maturation. The highly conserved nature of the MHR across all orthoretroviridae suggests that these findings will be broadly relevant to retroviral assembly. Finally, the results presented here provide a framework for increased

Problems in obtaining perfect images by single-particle electron cryomicroscopy of biological structures in amorphous ice.

PubMed

Henderson, Richard; McMullan, Greg

2013-02-01

Theoretical considerations together with simulations of single-particle electron cryomicroscopy images of biological assemblies in ice demonstrate that atomic structures should be obtainable from images of a few thousand asymmetric units, provided the molecular weight of the whole assembly being studied is greater than the minimum needed for accurate position and orientation determination. However, with present methods of specimen preparation and current microscope and detector technologies, many more particles are needed, and the alignment of smaller assemblies is difficult or impossible. Only larger structures, with enough signal to allow good orientation determination and with enough images to allow averaging of many hundreds of thousands or even millions of asymmetric units, have successfully produced high-resolution maps. In this review, we compare the contrast of experimental electron cryomicroscopy images of two smaller molecular assemblies, namely apoferritin and beta-galactosidase, with that expected from perfect simulated images calculated from their known X-ray structures. We show that the contrast and signal-to-noise ratio of experimental images still require significant improvement before it will be possible to realize the full potential of single-particle electron cryomicroscopy. In particular, although reasonably good orientations can be obtained for beta-galactosidase, we have been unable to obtain reliable orientation determination from experimental images of apoferritin. Simulations suggest that at least 2-fold improvement of the contrast in experimental images at ~10 Å resolution is needed and should be possible.

Structural and magnetic properties of FeCoC system obtained by mechanical alloying

NASA Astrophysics Data System (ADS)

Rincón Soler, A. I.; Rodríguez Jacobo, R. R.; Medina Barreto, M. H.; Cruz-Muñoz, B.

2017-11-01

Fe96-XCoXC4 (x = 0, 10, 20, 30, 40 at. %) alloys were obtained by mechanical alloying of Fe, C and Co powders using high-energy milling. The structural and magnetic properties of the alloy system were analyzed by X-ray diffraction, Scanning Electron Microscopy (SEM), Vibrating Sample Magnetometer (VSM) and Mössbauer Spectrometry at room temperature. The X-ray diffraction patterns showed a BCC-FeCoC structure phase for all samples, as well as a lattice parameter that slightly decreases with Co content. The saturation magnetization and coercive field were analyzed as a function of Co content. The Mössbauer spectra were fitted with a hyperfine magnetic field distribution showing the ferromagnetic behavior and the disordered character of the samples. The mean hyperfine magnetic field remained nearly constant (358 T) with Co content.

Structure of the vacuolar H+-ATPase rotary motor reveals new mechanistic insights.

PubMed

Rawson, Shaun; Phillips, Clair; Huss, Markus; Tiburcy, Felix; Wieczorek, Helmut; Trinick, John; Harrison, Michael A; Muench, Stephen P

2015-03-03

Vacuolar H(+)-ATPases are multisubunit complexes that operate with rotary mechanics and are essential for membrane proton transport throughout eukaryotes. Here we report a ∼ 1 nm resolution reconstruction of a V-ATPase in a different conformational state from that previously reported for a lower-resolution yeast model. The stator network of the V-ATPase (and by implication that of other rotary ATPases) does not change conformation in different catalytic states, and hence must be relatively rigid. We also demonstrate that a conserved bearing in the catalytic domain is electrostatic, contributing to the extraordinarily high efficiency of rotary ATPases. Analysis of the rotor axle/membrane pump interface suggests how rotary ATPases accommodate different c ring stoichiometries while maintaining high efficiency. The model provides evidence for a half channel in the proton pump, supporting theoretical models of ion translocation. Our refined model therefore provides new insights into the structure and mechanics of the V-ATPases. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Large-scale brain network associated with creative insight: combined voxel-based morphometry and resting-state functional connectivity analyses.

PubMed

Ogawa, Takeshi; Aihara, Takatsugu; Shimokawa, Takeaki; Yamashita, Okito

2018-04-24

Creative insight occurs with an "Aha!" experience when solving a difficult problem. Here, we investigated large-scale networks associated with insight problem solving. We recruited 232 healthy participants aged 21-69 years old. Participants completed a magnetic resonance imaging study (MRI; structural imaging and a 10 min resting-state functional MRI) and an insight test battery (ITB) consisting of written questionnaires (matchstick arithmetic task, remote associates test, and insight problem solving task). To identify the resting-state functional connectivity (RSFC) associated with individual creative insight, we conducted an exploratory voxel-based morphometry (VBM)-constrained RSFC analysis. We identified positive correlations between ITB score and grey matter volume (GMV) in the right insula and middle cingulate cortex/precuneus, and a negative correlation between ITB score and GMV in the left cerebellum crus 1 and right supplementary motor area. We applied seed-based RSFC analysis to whole brain voxels using the seeds obtained from the VBM and identified insight-positive/negative connections, i.e. a positive/negative correlation between the ITB score and individual RSFCs between two brain regions. Insight-specific connections included motor-related regions whereas creative-common connections included a default mode network. Our results indicate that creative insight requires a coupling of multiple networks, such as the default mode, semantic and cerebral-cerebellum networks.

Structural insight of DNA topoisomerases I from camptothecin-producing plants revealed by molecular dynamics simulations.

PubMed

Sirikantaramas, Supaart; Meeprasert, Arthitaya; Rungrotmongkol, Thanyada; Fuji, Hideyoshi; Hoshino, Tyuji; Sudo, Hiroshi; Yamazaki, Mami; Saito, Kazuki

2015-05-01

DNA topoisomerase I (Top1) catalyzes changes in DNA topology by cleaving and rejoining one strand of the double stranded (ds)DNA. Eukaryotic Top1s are the cellular target of the plant-derived anticancer indole alkaloid camptothecin (CPT), which reversibly stabilizes the Top1-dsDNA complex. However, CPT-producing plants, including Camptotheca acuminata, Ophiorrhiza pumila and Ophiorrhiza liukiuensis, are highly resistant to CPT because they possess point-mutated Top1. Here, the adaptive convergent evolution is reported between CPT production ability and mutations in their Top1, as a universal resistance mechanism found in all tested CPT-producing plants. This includes Nothapodytes nimmoniana, one of the major sources of CPT. To obtain a structural insight of the resistance mechanism, molecular dynamics simulations of CPT- resistant and -sensitive plant Top1s complexed with dsDNA and topotecan (a CPT derivative) were performed, these being compared to that for the CPT-sensitive human Top1. As a result, two mutations, Val617Gly and Asp710Gly, were identified in O. pumila Top1 and C. acuminata Top1, respectively. The substitutions at these two positions, surprisingly, are the same as those found in a CPT derivative-resistant human colon adenocarcinoma cell line. The results also demonstrated an increased linker flexibility of the CPT-resistant Top1, providing an additional explanation for the resistance mechanism found in CPT-producing plants. These mutations could reflect the long evolutionary adaptation of CPT-producing plant Top1s to confer a higher degree of resistance. Copyright © 2015 Elsevier Ltd. All rights reserved.

Insight into the microscopic structure of an AdS black hole from a thermodynamical phase transition.

PubMed

Wei, Shao-Wen; Liu, Yu-Xiao

2015-09-11

Comparing with an ordinary thermodynamic system, we investigate the possible microscopic structure of a charged anti-de Sitter black hole completely from the thermodynamic viewpoint. The number density of the black hole molecules is introduced to measure the microscopic degrees of freedom of the black hole. We found that the number density suffers a sudden change accompanied by a latent heat when the black hole system crosses the small-large black hole coexistence curve, while when the system passes the critical point, it encounters a second-order phase transition with a vanishing latent heat due to the continuous change of the number density. Moreover, the thermodynamic scalar curvature suggests that there is a weak attractive interaction between two black hole molecules. These phenomena might cast new insight into the underlying microscopic structure of a charged anti-de Sitter black hole.

Base pairing and structural insights into the 5-formylcytosine in RNA duplex

PubMed Central

Wang, Rui; Luo, Zhipu; He, Kaizhang; Delaney, Michael O.; Chen, Doris; Sheng, Jia

2016-01-01

Abstract 5-Formylcytidine (f5C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m5C) through 5-hydroxymethylcytidine (hm5C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f5C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5′-GUA(f5C)GUAC-3′]2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f5C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex. PMID:27079978

Atomic Structure and Properties of Extended Defects in Silicon

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

Buczko, R.; Chisholm, M.F.; Kaplan, T.

1998-10-15

The Z-contrast technique represents a new approach to high-resolution electron microscopy allowing for the first time incoherent imaging of materials on the atomic scale. The key advantages of the technique, an intrinsically higher resolution limit and directly interpretable, compositionally sensitive imaging, allow a new level of insight into the atomic configurations of extended defects in silicon. This experimental technique has been combined with theoretical calculations (a combination of first principles, tight binding, and classical methods) to extend this level of insight by obtaining the energetic and electronic structure of the defects.

Insights into Platypus Population Structure and History from Whole-Genome Sequencing.

PubMed

Martin, Hilary C; Batty, Elizabeth M; Hussin, Julie; Westall, Portia; Daish, Tasman; Kolomyjec, Stephen; Piazza, Paolo; Bowden, Rory; Hawkins, Margaret; Grant, Tom; Moritz, Craig; Grutzner, Frank; Gongora, Jaime; Donnelly, Peter

2018-05-01

The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10-9/bp/generation (95% CI 4.1 × 10-9-1.2 × 10-8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.

Insights into Platypus Population Structure and History from Whole-Genome Sequencing

PubMed Central

Martin, Hilary C; Hussin, Julie; Westall, Portia; Daish, Tasman; Kolomyjec, Stephen; Piazza, Paolo; Bowden, Rory; Hawkins, Margaret; Grant, Tom; Moritz, Craig; Grutzner, Frank; Gongora, Jaime; Donnelly, Peter

2018-01-01

Abstract The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10−9/bp/generation (95% CI 4.1 × 10−9–1.2 × 10−8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species. PMID:29688544

Insight into structural phase transitions from the decoupled anharmonic mode approximation.

PubMed

Adams, Donat J; Passerone, Daniele

2016-08-03

We develop a formalism (decoupled anharmonic mode approximation, DAMA) that allows calculation of the vibrational free energy using density functional theory even for materials which exhibit negative curvature of the potential energy surface with respect to atomic displacements. We investigate vibrational modes beyond the harmonic approximation and approximate the potential energy surface with the superposition of the accurate potential along each normal mode. We show that the free energy can stabilize crystal structures at finite temperatures which appear dynamically unstable at T  =  0. The DAMA formalism is computationally fast because it avoids statistical sampling through molecular dynamics calculations, and is in principle completely ab initio. It is free of statistical uncertainties and independent of model parameters, but can give insight into the mechanism of a structural phase transition. We apply the formalism to the perovskite cryolite, and investigate the temperature-driven phase transition from the P21/n to the Immm space group. We calculate a phase transition temperature between 710 and 950 K, in fair agreement with the experimental value of 885 K. This can be related to the underestimation of the interaction of the vibrational states. We also calculate the main axes of the thermal ellipsoid and can explain the experimentally observed increase of its volume for the fluorine by 200-300% throughout the phase transition. Our calculations suggest the appearance of tunneling states in the high temperature phase. The convergence of the vibrational DOS and of the critical temperature with respect of reciprocal space sampling is investigated using the polarizable-ion model.

Insight into structural phase transitions from the decoupled anharmonic mode approximation

NASA Astrophysics Data System (ADS)

Adams, Donat J.; Passerone, Daniele

2016-08-01

We develop a formalism (decoupled anharmonic mode approximation, DAMA) that allows calculation of the vibrational free energy using density functional theory even for materials which exhibit negative curvature of the potential energy surface with respect to atomic displacements. We investigate vibrational modes beyond the harmonic approximation and approximate the potential energy surface with the superposition of the accurate potential along each normal mode. We show that the free energy can stabilize crystal structures at finite temperatures which appear dynamically unstable at T  =  0. The DAMA formalism is computationally fast because it avoids statistical sampling through molecular dynamics calculations, and is in principle completely ab initio. It is free of statistical uncertainties and independent of model parameters, but can give insight into the mechanism of a structural phase transition. We apply the formalism to the perovskite cryolite, and investigate the temperature-driven phase transition from the P21/n to the Immm space group. We calculate a phase transition temperature between 710 and 950 K, in fair agreement with the experimental value of 885 K. This can be related to the underestimation of the interaction of the vibrational states. We also calculate the main axes of the thermal ellipsoid and can explain the experimentally observed increase of its volume for the fluorine by 200-300% throughout the phase transition. Our calculations suggest the appearance of tunneling states in the high temperature phase. The convergence of the vibrational DOS and of the critical temperature with respect of reciprocal space sampling is investigated using the polarizable-ion model.

Structural Insights into the Mechanisms of Antibody-Mediated Neutralization of Flavivirus Infection: Implications for Vaccine Development

PubMed Central

Pierson, Theodore C.; Fremont, Daved H.; Kuhn, Richard J.; Diamond, Michael S.

2009-01-01

Flaviviruses are a group of small RNA viruses that cause severe disease in humans worldwide and are the target of several vaccine development programs. A primary goal of these efforts is to elicit a protective humoral response directed against the envelope proteins arrayed on the surface of the flavivirus virion. Advances in the structural biology of these viruses has catalyzed rapid progress toward understanding the complexity of the flavivirus immunogen and the molecular basis of antibody-mediated neutralization. These insights have identified factors that govern the potency of neutralizing antibodies and will inform the design and evaluation of novel vaccines. PMID:18779049

INSIGHT AGONISTES: A READING OF SOPHOCLES'S OEDIPUS THE KING.

PubMed

Mahon, Eugene J

2015-07-01

In this reading of Sophocles's Oedipus the King, the author suggests that insight can be thought of as the main protagonist of the tragedy. He personifies this depiction of insight, calling it Insight Agonistes, as if it were the sole conflicted character on the stage, albeit masquerading at times as several other characters, including gods, sphinxes, and oracles. This psychoanalytic reading of the text lends itself to an analogy between psychoanalytic process and Sophocles's tragic hero. The author views insight as always transgressing against, always at war with a conservative, societal, or intrapsychic chorus of structured elements. A clinical vignette is presented to illustrate this view of insight. © 2015 The Psychoanalytic Quarterly, Inc.

Predicting Welding Distortion in a Panel Structure with Longitudinal Stiffeners Using Inherent Deformations Obtained by Inverse Analysis Method

PubMed Central

Liang, Wei; Murakawa, Hidekazu

2014-01-01

Welding-induced deformation not only negatively affects dimension accuracy but also degrades the performance of product. If welding deformation can be accurately predicted beforehand, the predictions will be helpful for finding effective methods to improve manufacturing accuracy. Till now, there are two kinds of finite element method (FEM) which can be used to simulate welding deformation. One is the thermal elastic plastic FEM and the other is elastic FEM based on inherent strain theory. The former only can be used to calculate welding deformation for small or medium scale welded structures due to the limitation of computing speed. On the other hand, the latter is an effective method to estimate the total welding distortion for large and complex welded structures even though it neglects the detailed welding process. When the elastic FEM is used to calculate the welding-induced deformation for a large structure, the inherent deformations in each typical joint should be obtained beforehand. In this paper, a new method based on inverse analysis was proposed to obtain the inherent deformations for weld joints. Through introducing the inherent deformations obtained by the proposed method into the elastic FEM based on inherent strain theory, we predicted the welding deformation of a panel structure with two longitudinal stiffeners. In addition, experiments were carried out to verify the simulation results. PMID:25276856

Predicting welding distortion in a panel structure with longitudinal stiffeners using inherent deformations obtained by inverse analysis method.

PubMed

Liang, Wei; Murakawa, Hidekazu

2014-01-01

Welding-induced deformation not only negatively affects dimension accuracy but also degrades the performance of product. If welding deformation can be accurately predicted beforehand, the predictions will be helpful for finding effective methods to improve manufacturing accuracy. Till now, there are two kinds of finite element method (FEM) which can be used to simulate welding deformation. One is the thermal elastic plastic FEM and the other is elastic FEM based on inherent strain theory. The former only can be used to calculate welding deformation for small or medium scale welded structures due to the limitation of computing speed. On the other hand, the latter is an effective method to estimate the total welding distortion for large and complex welded structures even though it neglects the detailed welding process. When the elastic FEM is used to calculate the welding-induced deformation for a large structure, the inherent deformations in each typical joint should be obtained beforehand. In this paper, a new method based on inverse analysis was proposed to obtain the inherent deformations for weld joints. Through introducing the inherent deformations obtained by the proposed method into the elastic FEM based on inherent strain theory, we predicted the welding deformation of a panel structure with two longitudinal stiffeners. In addition, experiments were carried out to verify the simulation results.

Structural insights into methanol-stable variants of lipase T6 from Geobacillus stearothermophilus.

PubMed

Dror, Adi; Kanteev, Margarita; Kagan, Irit; Gihaz, Shalev; Shahar, Anat; Fishman, Ayelet

2015-11-01

Enzymatic production of biodiesel by transesterification of triglycerides and alcohol, catalyzed by lipases, offers an environmentally friendly and efficient alternative to the chemically catalyzed process while using low-grade feedstocks. Methanol is utilized frequently as the alcohol in the reaction due to its reactivity and low cost. However, one of the major drawbacks of the enzymatic system is the presence of high methanol concentrations which leads to methanol-induced unfolding and inactivation of the biocatalyst. Therefore, a methanol-stable lipase is of great interest for the biodiesel industry. In this study, protein engineering was applied to substitute charged surface residues with hydrophobic ones to enhance the stability in methanol of a lipase from Geobacillus stearothermophilus T6. We identified a methanol-stable variant, R374W, and combined it with a variant found previously, H86Y/A269T. The triple mutant, H86Y/A269T/R374W, had a half-life value at 70 % methanol of 324 min which reflects an 87-fold enhanced stability compared to the wild type together with elevated thermostability in buffer and in 50 % methanol. This variant also exhibited an improved biodiesel yield from waste chicken oil compared to commercial Lipolase 100L® and Novozyme® CALB. Crystal structures of the wild type and the methanol-stable variants provided insights regarding structure-stability correlations. The most prominent features were the extensive formation of new hydrogen bonds between surface residues directly or mediated by structural water molecules and the stabilization of Zn and Ca binding sites. Mutation sites were also characterized by lower B-factor values calculated from the X-ray structures indicating improved rigidity.

More insights into early brain development through statistical analyses of eigen-structural elements of diffusion tensor imaging using multivariate adaptive regression splines

PubMed Central

Chen, Yasheng; Zhu, Hongtu; An, Hongyu; Armao, Diane; Shen, Dinggang; Gilmore, John H.; Lin, Weili

2013-01-01

The aim of this study was to characterize the maturational changes of the three eigenvalues (λ1 ≥ λ2 ≥ λ3) of diffusion tensor imaging (DTI) during early postnatal life for more insights into early brain development. In order to overcome the limitations of using presumed growth trajectories for regression analysis, we employed Multivariate Adaptive Regression Splines (MARS) to derive data-driven growth trajectories for the three eigenvalues. We further employed Generalized Estimating Equations (GEE) to carry out statistical inferences on the growth trajectories obtained with MARS. With a total of 71 longitudinal datasets acquired from 29 healthy, full-term pediatric subjects, we found that the growth velocities of the three eigenvalues were highly correlated, but significantly different from each other. This paradox suggested the existence of mechanisms coordinating the maturations of the three eigenvalues even though different physiological origins may be responsible for their temporal evolutions. Furthermore, our results revealed the limitations of using the average of λ2 and λ3 as the radial diffusivity in interpreting DTI findings during early brain development because these two eigenvalues had significantly different growth velocities even in central white matter. In addition, based upon the three eigenvalues, we have documented the growth trajectory differences between central and peripheral white matter, between anterior and posterior limbs of internal capsule, and between inferior and superior longitudinal fasciculus. Taken together, we have demonstrated that more insights into early brain maturation can be gained through analyzing eigen-structural elements of DTI. PMID:23455648

Structure of a [NiFe] hydrogenase maturation protease HycI provides insights into its substrate selectivity.

PubMed

Kwon, Sunghark; Nishitani, Yuichi; Hirao, Yoshinori; Kanai, Tamotsu; Atomi, Haruyuki; Miki, Kunio

2018-04-15

The immature large subunit of [NiFe] hydrogenases undergoes C-terminal cleavage by a specific protease in the final step of the post-translational process before assembly with other subunits. It has been reported that the [NiFe] hydrogenase maturation protease HycI from Thermococcus kodakarensis (TkHycI) has the catalytic ability to target the membrane-bound hydrogenase large subunit MbhL from T. kodakarensis. However, the detailed mechanism of its substrate recognition remains elusive. We determined the crystal structure of TkHycI at 1.59 Å resolution to clarify how TkHycI recognizes its own substrate MbhL. Although the overall structure of TkHycI is similar to that of its homologous protease TkHybD, TkHycI adopts a larger loop than TkHybD, thereby creating a broad and deep cleft. We analyzed the structural properties of the TkHycI cleft probably involved in its substrate recognition. Our findings provide novel and profound insights into the substrate selectivity of TkHycI. Copyright © 2018 Elsevier Inc. All rights reserved.

Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.

PubMed

Pingault, Lise; Choulet, Frédéric; Alberti, Adriana; Glover, Natasha; Wincker, Patrick; Feuillet, Catherine; Paux, Etienne

2015-02-10

Because of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before. By combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level. Our analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation.

The Self-Organization of Insight: Entropy and Power Laws in Problem Solving

ERIC Educational Resources Information Center

Stephen, Damian G.; Dixon, James A.

2008-01-01

Explaining emergent structure remains a challenge for all areas of cognitive science, and problem solving is no exception. The modern study of insight has drawn attention to the issue of emergent cognitive structure in problem solving research. We propose that the explanation of insight is beyond the scope of conventional approaches to cognitive…

Toward a Model of Cognitive Insight in First-Episode Psychosis: Verbal Memory and Hippocampal Structure

PubMed Central

Buchy, L.; Czechowska, Y.; Chochol, C.; Malla, A.; Joober, R.; Pruessner, J.; Lepage, M.

2010-01-01

Our previous work has linked verbal learning and memory with cognitive insight, but not clinical insight, in individuals with a first-episode psychosis (FEP). The current study reassessed the neurocognitive basis of cognitive and clinical insight and explored their neural basis in 61 FEP patients. Cognitive insight was measured with the Beck Cognitive Insight Scale (BCIS) and clinical insight with the Scale to assess Unawareness of Mental Disorder (SUMD). Global measures for 7 domains of cognition were examined. Hippocampi were manually segmented in to 3 parts: the body, head, and tail. Verbal learning and memory significantly correlated with the BCIS composite index. Composite index scores were significantly associated with total left hippocampal (HC) volume; partial correlations, however, revealed that this relationship was attributable largely to verbal memory performance. The BCIS self-certainty subscale significantly and inversely correlated with bilateral HC volumes, and these associations were independent of verbal learning and memory performance. The BCIS self-reflectiveness subscale significantly correlated with verbal learning and memory but not with HC volume. No significant correlations emerged between the SUMD and verbal memory or HC volume. These results strengthen our previous assertion that in individuals with an FEP cognitive insight may rely on memory whereby current experiences are appraised based on previous ones. The HC may be a viable location among others for the brain system that underlies aspects of cognitive insight in individuals with an FEP. PMID:19346315

An insight into the pharmacophores of phosphodiesterase-5 inhibitors from synthetic and crystal structural studies

PubMed Central

Chen, Gong; Wang, Huanchen; Robinson, Howard; Cai, Jiwen; Wan, Yiqian; Ke, Hengming

2008-01-01

Selective inhibitors of cyclic nucleotide phosphodiesterase-5 (PDE5) have been used as drugs for treatment of male erectile dysfunction and pulmonary hypertension. An insight into the pharmacophores of PDE5 inhibitors is essential for development of second generation of PDE5 inhibitors, but has not been completely illustrated. Here we report the synthesis of a new class of the sildenafil derivatives and a crystal structure of the PDE5 catalytic domain in complex with 5-(2-ethoxy-5-(sulfamoyl)-3-thienyl)-1-methyl-3-propyl-1,6-dihydro-7H-pyrazolo[4,3-d] pyrimidin-7-one (12). Inhibitor 12 induces conformational change of the H-loop (residues 660–683), which is different from any of the known PDE5 structures. The pyrazolopyrimidinone groups of 12 and sildenafil are well superimposed, but their sulfonamide groups show a positional difference of as much as 1.5 Å. The structure-activity analysis suggests that a small hydrophobic pocket and the H-loop of PDE5 are important for the inhibitor affinity, in addition to two common elements for binding of almost all the PDE inhibitors: the stack against the phenylalanine and the hydrogen bond with the invariant glutamine. However, the PDE5-12 structure does not provide a full explanation to affinity changes of the inhibitors. Thus alternatives such as conformational change of the M-loop are open and further structural study is required. PMID:18346713

Silicon Graphics' IRIS InSight: An SGML Success Story.

ERIC Educational Resources Information Center

Glushko, Robert J.; Kershner, Ken

1993-01-01

Offers a case history of the development of the Silicon Graphics "IRIS InSight" system, a system for viewing on-line documentation using Standard Generalized Markup Language. Notes that SGML's explicit encoding of structure and separation of structure and presentation make possible structure-based search, alternative structural views of…

Working wonders? investigating insight with magic tricks.

PubMed

Danek, Amory H; Fraps, Thomas; von Müller, Albrecht; Grothe, Benedikt; Ollinger, Michael

2014-02-01

We propose a new approach to differentiate between insight and noninsight problem solving, by introducing magic tricks as problem solving domain. We argue that magic tricks are ideally suited to investigate representational change, the key mechanism that yields sudden insight into the solution of a problem, because in order to gain insight into the magicians' secret method, observers must overcome implicit constraints and thus change their problem representation. In Experiment 1, 50 participants were exposed to 34 different magic tricks, asking them to find out how the trick was accomplished. Upon solving a trick, participants indicated if they had reached the solution either with or without insight. Insight was reported in 41.1% of solutions. The new task domain revealed differences in solution accuracy, time course and solution confidence with insight solutions being more likely to be true, reached earlier, and obtaining higher confidence ratings. In Experiment 2, we explored which role self-imposed constraints actually play in magic tricks. 62 participants were presented with 12 magic tricks. One group received verbal cues, providing solution relevant information without giving the solution away. The control group received no informative cue. Experiment 2 showed that participants' constraints were suggestible to verbal cues, resulting in higher solution rates. Thus, magic tricks provide more detailed information about the differences between insightful and noninsightful problem solving, and the underlying mechanisms that are necessary to have an insight. Copyright © 2013 Elsevier B.V. All rights reserved.

Design Principles for the Atomic and Electronic Structure of Halide Perovskite Photovoltaic Materials: Insights from Computation.

PubMed

Berger, Robert F

2018-02-09

In the current decade, perovskite solar cell research has emerged as a remarkably active, promising, and rapidly developing field. Alongside breakthroughs in synthesis and device engineering, halide perovskite photovoltaic materials have been the subject of predictive and explanatory computational work. In this Minireview, we focus on a subset of this computation: density functional theory (DFT)-based work highlighting the ways in which the electronic structure and band gap of this class of materials can be tuned via changes in atomic structure. We distill this body of computational literature into a set of underlying design principles for the band gap engineering of these materials, and rationalize these principles from the viewpoint of band-edge orbital character. We hope that this perspective provides guidance and insight toward the rational design and continued improvement of perovskite photovoltaics. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

New insights into the mechanism of interaction between CO2 and polymers from thermodynamic parameters obtained by in situ ATR-FTIR spectroscopy.

PubMed

Gabrienko, Anton A; Ewing, Andrew V; Chibiryaev, Andrey M; Agafontsev, Alexander M; Dubkov, Konstantin A; Kazarian, Sergei G

2016-03-07

This work reports new physical insights of the thermodynamic parameters and mechanisms of possible interactions occurring in polymers subjected to high-pressure CO2. ATR-FTIR spectroscopy has been used in situ to determine the thermodynamic parameters of the intermolecular interactions between CO2 and different functional groups of the polymers capable of specific interactions with sorbed CO2 molecules. Based on the measured ATR-FTIR spectra of the polymer samples subjected to high-pressure CO2 (30 bar) at different temperatures (300-340 K), it was possible to characterize polymer-polymer and CO2-polymer interactions. Particularly, the enthalpy and entropy of the formation of the specific non-covalent complexes between CO2 and the hydroxy (-OH), carbonyl (C[double bond, length as m-dash]O) and hydroxyimino ([double bond, length as m-dash]N-OH) functional groups of the polymer samples have been measured. Furthermore, the obtained spectroscopic results have provided an opportunity for the structure of these complexes to be proposed. An interesting phenomenon regarding the behavior of CO2/polymer systems has also been observed. It has been found that only for the polyketone, the value of enthalpy was negative indicating an exothermic process during the formation of the CO2-polymer non-covalent complexes. Conversely, for the polyoxime and polyalcohol samples there is a positive enthalpy determined. This is a result of the initial polymer-polymer interactions requiring more energy to break than is released during the formation of the CO2-polymer complex. The effect of increasing temperature to facilitate the breaking of the polymer-polymer interactions has also been observed. Hence, a mechanism for the formation of CO2-polymer complexes was suggested based on these results, which occurs via a two-step process: (1) the breaking of the existing polymer-polymer interactions followed by (2) the formation of new CO2-polymer non-covalent interactions.

Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A

PubMed Central

Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K.

2017-01-01

Abstract In the canonical DNA double helix, Watson–Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02–0.4%) and short-lived (lifetimes ∼0.2–2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. PMID:28369571

Closer insight into the structure of moderate to densely branched comb polymers by combining modelling and linear rheological measurements.

PubMed

Ahmadi, Mostafa; Pioge, Sandie; Fustin, Charles-Andre; Gohy, Jean-Francois; van Ruymbeke, Evelyne

2017-02-07

Synthesis of combs with well-entangled backbones and long branches with high densities has always been a challenge. Steric hindrance frequently leads to coupling of chains and structural imperfections that cannot be easily distinguished by traditional characterization methods. Research studies have therefore tried to use a combination of different methods to obtain more information on the actual microstructures. In this work, a grafting-from approach is used to synthesize poly(n-butyl acrylate) combs using atom transfer radical polymerization (ATRP) in three steps including the synthesis of a backbone, cleavage of protecting groups and growth of side branches. We have compared the linear viscoelastic properties theoretically predicted by a time marching algorithm (TMA) tube based model with the measured rheological behaviour to provide a better insight into the actual microstructure formed during synthesis. For combs with branches smaller than an entanglement, no discernible hierarchical relaxation can be distinguished, while for those with longer branches, a high frequency plateau made by entangled branches can be separated from backbone's relaxation. Dilution of the backbone, after relaxation of side branches, may accelerate the final relaxation, while extra friction can delay it especially for longer branches. Such a comparison provides a better assessment of the microstructure formed in combs.

Insight into the biological effects of acupuncture points by X-ray absorption fine structure.

PubMed

Liu, Chenglin; Liu, Qinghua; Zhang, Dongming; Liu, Wei; Yan, Xiaohui; Zhang, Xinyi; Oyanagi, Hiroyuki; Pan, Zhiyun; Hu, Fengchun; Wei, Shiqiang

2018-06-02

Exploration of the biological effects of transition metal ions in acupuncture points is essential to clarify the functional mechanism of acupuncture treatment. Here we show that in the SP6 acupuncture point (Sanyinjiao) the Fe ions are in a high-spin state of approximately t 2g 4.5 e g 1.5 in an Fe-N(O) octahedral crystal field. The Fe K-edge synchrotron radiation X-ray absorption fine structure results reveal that the Fe-N and Fe-O bond lengths in the SP6 acupuncture point are 2.05 and 2.13 Å, respectively, and are 0.05-0.10 Å longer than those in the surrounding tissue. The distorted atomic structure reduces the octahedral symmetry and weakens the crystal field around the Fe ions by approximately 0.3 eV, leading to the high-spin configuration of the Fe ions, which is favorable for strengthening the magnetotransport and oxygen transportation properties in the acupuncture point by the enhanced spin coherence. This finding might provide some insight into the microscopic effect of the atomic and electronic interactions of transition metal ions in the acupuncture point. Graphical Abstract ᅟ.

Insights into the role of protein molecule size and structure on interfacial properties using designed sequences

PubMed Central

Dwyer, Mirjana Dimitrijev; He, Lizhong; James, Michael; Nelson, Andrew; Middelberg, Anton P. J.

2013-01-01

Mixtures of a large, structured protein with a smaller, unstructured component are inherently complex and hard to characterize at interfaces, leading to difficulties in understanding their interfacial behaviours and, therefore, formulation optimization. Here, we investigated interfacial properties of such a mixed system. Simplicity was achieved using designed sequences in which chemical differences had been eliminated to isolate the effect of molecular size and structure, namely a short unstructured peptide (DAMP1) and its longer structured protein concatamer (DAMP4). Interfacial tension measurements suggested that the size and bulk structuring of the larger molecule led to much slower adsorption kinetics. Neutron reflectometry at equilibrium revealed that both molecules adsorbed as a monolayer to the air–water interface (indicating unfolding of DAMP4 to give a chain of four connected DAMP1 molecules), with a concentration ratio equal to that in the bulk. This suggests the overall free energy of adsorption is equal despite differences in size and bulk structure. At small interfacial extensional strains, only molecule packing influenced the stress response. At larger strains, the effect of size became apparent, with DAMP4 registering a higher stress response and interfacial elasticity. When both components were present at the interface, most stress-dissipating movement was achieved by DAMP1. This work thus provides insights into the role of proteins' molecular size and structure on their interfacial properties, and the designed sequences introduced here can serve as effective tools for interfacial studies of proteins and polymers. PMID:23303222

Crystal structure of Manduca sexta prophenoloxidase provides insights into the mechanism of type 3 copper enzymes

PubMed Central

Li, Yongchao; Wang, Yang; Jiang, Haobo; Deng, Junpeng

2009-01-01

Arthropod phenoloxidase (PO) generates quinones and other toxic compounds to sequester and kill pathogens during innate immune responses. It is also involved in wound healing and other physiological processes. Insect PO is activated from its inactive precursor, prophenoloxidase (PPO), by specific proteolysis via a serine protease cascade. Here, we report the crystal structure of PPO from a lepidopteran insect at a resolution of 1.97 Å, which is the initial structure for a PPO from the type 3 copper protein family. Manduca sexta PPO is a heterodimer consisting of 2 homologous polypeptide chains, PPO1 and PPO2. The active site of each subunit contains a canonical type 3 di-nuclear copper center, with each copper ion coordinated with 3 structurally conserved histidines. The acidic residue Glu-395 located at the active site of PPO2 may serve as a general base for deprotonation of monophenolic substrates, which is key to the ortho-hydroxylase activity of PO. The structure provides unique insights into the mechanism by which type 3 copper proteins differ in their enzymatic activities, albeit sharing a common active center. A drastic change in electrostatic surface induced on cleavage at Arg-51 allows us to propose a model for localized PPO activation in insects. PMID:19805072

Structural insights into selective agonist actions of tamoxifen on human estrogen receptor alpha.

PubMed

Chakraborty, Sandipan; Biswas, Pradip Kumar

2014-08-01

Tamoxifen-an anti-estrogenic ligand in breast tissues used as a first-line treatment in estrogen receptor (ER)-positive breast cancers-is associated with the development of resistance followed by resumption of tumor growth in about 30 % of cases. Whether tamoxifen assists in proliferation in such cases or whether any ligand-independent pathway to transcription exists is not fully understood; also, no ERα mutants have been detected so far that could lead to tamoxifen resistance. Using in silico conformational analysis of the ERα ligand binding domain (LBD), in the absence and presence of selective agonist (diethylstilbestrol; DES), antagonist (Faslodex; ICI), and selective estrogen receptor modulator (SERM; 4-hydroxy tamoxifen; 4-OHT) ligands, we have elucidated ligand-responsive structural modulations of the ERα-LBD dimer in its agonist and antagonist complexes to address the issue of "tamoxifen resistance". DES and ICI were found to stabilize the dimer in their agonist and antagonist conformations, respectively. The ERα-LBD dimer without the presence of any bound ligand also led to a stable structure in agonist conformation. However, binding of 4-OHT to the antagonist structure led to a flexible conformation allowing the protein to visit conformations populated by agonists as was evident from principal component analysis and radius of gyration plots. Further, the relaxed conformations of the 4-OHT bound protein exhibited a diminished size of the co-repressor binding pocket in the LBD, thus signaling a partial blockage of the co-repressor binding motif. Thus, the ability of 4-OHT-bound ERα-LBD to assume flexible conformations visited by agonists and reduced co-repressor binding surface at the LBD provide crucial structural insights into tamoxifen-resistance that complement our existing understanding.

Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution

PubMed Central

Zeng, Qinghong; Langereis, Martijn A.; van Vliet, Arno L. W.; Huizinga, Eric G.; de Groot, Raoul J.

2008-01-01

The hemagglutinin-esterases (HEs) are a family of viral envelope glycoproteins that mediate reversible attachment to O-acetylated sialic acids by acting both as lectins and as receptor-destroying enzymes (RDEs). Related HEs occur in influenza C, toro-, and coronaviruses, apparently as a result of relatively recent lateral gene transfer events. Here, we report the crystal structure of a coronavirus (CoV) HE in complex with its receptor. We show that CoV HE arose from an influenza C-like HE fusion protein (HEF). In the process, HE was transformed from a trimer into a dimer, whereas remnants of the fusion domain were adapted to establish novel monomer–monomer contacts. Whereas the structural design of the RDE-acetylesterase domain remained unaltered, the HE receptor-binding domain underwent remodeling to such extent that the ligand is now bound in opposite orientation. This is surprising, because the architecture of the HEF site was preserved in influenza A HA over a much larger evolutionary distance, a switch in receptor specificity and extensive antigenic variation notwithstanding. Apparently, HA and HEF are under more stringent selective constraints than HE, limiting their exploration of alternative binding-site topologies. We attribute the plasticity of the CoV HE receptor-binding site to evolutionary flexibility conferred by functional redundancy between HE and its companion spike protein S. Our findings offer unique insights into the structural and functional consequences of independent protein evolution after interviral gene exchange and open potential avenues to broad-spectrum antiviral drug design. PMID:18550812

Structural dynamic model obtained from flight use with piloted simulation and handling qualities analysis

NASA Technical Reports Server (NTRS)

Powers, Bruce G.

1996-01-01

The ability to use flight data to determine an aircraft model with structural dynamic effects suitable for piloted simulation. and handling qualities analysis has been developed. This technique was demonstrated using SR-71 flight test data. For the SR-71 aircraft, the most significant structural response is the longitudinal first-bending mode. This mode was modeled as a second-order system, and the other higher order modes were modeled as a time delay. The distribution of the modal response at various fuselage locations was developed using a uniform beam solution, which can be calibrated using flight data. This approach was compared to the mode shape obtained from the ground vibration test, and the general form of the uniform beam solution was found to be a good representation of the mode shape in the areas of interest. To calibrate the solution, pitch-rate and normal-acceleration instrumentation is required for at least two locations. With the resulting structural model incorporated into the simulation, a good representation of the flight characteristics was provided for handling qualities analysis and piloted simulation.

Structural insights into human heme oxygenase-1 inhibition by potent and selective azole-based compounds

PubMed Central

Rahman, Mona N.; Vukomanovic, Dragic; Vlahakis, Jason Z.; Szarek, Walter A.; Nakatsu, Kanji; Jia, Zongchao

2013-01-01

The development of heme oxygenase (HO) inhibitors, especially those that are isozyme-selective, promises powerful pharmacological tools to elucidate the regulatory characteristics of the HO system. It is already known that HO has cytoprotective properties and may play a role in several disease states, making it an enticing therapeutic target. Traditionally, the metalloporphyrins have been used as competitive HO inhibitors owing to their structural similarity with the substrate, heme. However, given heme's important role in several other proteins (e.g. cytochromes P450, nitric oxide synthase), non-selectivity is an unfortunate side-effect. Reports that azalanstat and other non-porphyrin molecules inhibited HO led to a multi-faceted effort to develop novel compounds as potent, selective inhibitors of HO. This resulted in the creation of non-competitive inhibitors with selectivity for HO, including a subset with isozyme selectivity for HO-1. Using X-ray crystallography, the structures of several complexes of HO-1 with novel inhibitors have been elucidated, which provided insightful information regarding the salient features required for inhibitor binding. This included the structural basis for non-competitive inhibition, flexibility and adaptability of the inhibitor binding pocket, and multiple, potential interaction subsites, all of which can be exploited in future drug-design strategies. PMID:23097500

Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems

PubMed Central

Phan, Isabelle Q. H.; Scheib, Holger; Subramanian, Sandhya; Edwards, Thomas E.; Lehman, Stephanie S.; Piitulainen, Hanna; Sayeedur Rahman, M.; Rennoll-Bankert, Kristen E.; Staker, Bart L.; Taira, Suvi; Stacy, Robin; Myler, Peter J.; Azad, Abdu F.

2015-01-01

ABSTRACT Prokaryotes use type IV secretion systems (T4SSs) to translocate substrates (e.g., nucleoprotein, DNA, and protein) and/or elaborate surface structures (i.e., pili or adhesins). Bacterial genomes may encode multiple T4SSs, e.g., there are three functionally divergent T4SSs in some Bartonella species (vir, vbh, and trw). In a unique case, most rickettsial species encode a T4SS (rvh) enriched with gene duplication. Within single genomes, the evolutionary and functional implications of cross-system interchangeability of analogous T4SS protein components remains poorly understood. To lend insight into cross-system interchangeability, we analyzed the VirB8 family of T4SS channel proteins. Crystal structures of three VirB8 and two TrwG Bartonella proteins revealed highly conserved C-terminal periplasmic domain folds and dimerization interfaces, despite tremendous sequence divergence. This implies remarkable structural constraints for VirB8 components in the assembly of a functional T4SS. VirB8/TrwG heterodimers, determined via bacterial two-hybrid assays and molecular modeling, indicate that differential expression of trw and vir systems is the likely barrier to VirB8-TrwG interchangeability. We also determined the crystal structure of Rickettsia typhi RvhB8-II and modeled its coexpressed divergent paralog RvhB8-I. Remarkably, while RvhB8-I dimerizes and is structurally similar to other VirB8 proteins, the RvhB8-II dimer interface deviates substantially from other VirB8 structures, potentially preventing RvhB8-I/RvhB8-II heterodimerization. For the rvh T4SS, the evolution of divergent VirB8 paralogs implies a functional diversification that is unknown in other T4SSs. Collectively, our data identify two different constraints (spatiotemporal for Bartonella trw and vir T4SSs and structural for rvh T4SSs) that mediate the functionality of multiple divergent T4SSs within a single bacterium. PMID:26646013

New structural phase obtained by exerting high pressure on (Br2)n@AFI composite material

NASA Astrophysics Data System (ADS)

Yao, Zhen; Lv, Jia-Yin; Liu, Bo; Liu, Bing-Bing; Yang, Bai

2018-06-01

In this paper, we present a theoretical study on the high-pressure behaviors of a (Br2)n@AlPO4-5 (AFI) peapod structure. The influence of the encapsulated Br2 molecule on the structural deformation of AFI crystal is analyzed using the volume-pressure function. The bonding process of the linearly arrayed Br2 molecule transferring to the bromine atomic chain is analyzed by the electron density distribution. A new high-pressure phase with P2 point group symmetry is obtained as the pressure increases to 34 GPa. In addition, electron density difference calculations are used to study the systematic charge transformation. Further analysis indicates that the encapsulated Br2 molecules can significantly modify the electronic structure of the AFI crystal. The band gap of the (Br2)n@AFI decreases with pressure and closes at 9 GPa. Moreover, the calculated bulk modulus and electronic properties indicate that the new structural phase is metallic with a high hardness, providing a new strategy for exploring novel nanomaterials.

Structural Insights into Drug Processing by Human Carboxylesterase 1: Tamoxifen, Mevastatin, and Inhibition by Benzil

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

Fleming, Christopher D.; Bencharit, Sompop; Edwards, Carol C.

2010-07-19

Human carboxylesterase 1 (hCE1) exhibits broad substrate specificity and is involved in xenobiotic processing and endobiotic metabolism. We present and analyze crystal structures of hCE1 in complexes with the cholesterol-lowering drug mevastatin, the breast cancer drug tamoxifen, the fatty acyl ethyl ester (FAEE) analogue ethyl acetate, and the novel hCE1 inhibitor benzil. We find that mevastatin does not appear to be a substrate for hCE1, and instead acts as a partially non-competitive inhibitor of the enzyme. Similarly, we show that tamoxifen is a low micromolar, partially non-competitive inhibitor of hCE1. Further, we describe the structural basis for the inhibition ofmore » hCE1 by the nanomolar-affinity dione benzil, which acts by forming both covalent and non-covalent complexes with the enzyme. Our results provide detailed insights into the catalytic and non-catalytic processing of small molecules by hCE1, and suggest that the efficacy of clinical drugs may be modulated by targeted hCE1 inhibitors.« less

Structural insights into drug processing by human carboxylesterase 1: tamoxifen, mevastatin, and inhibition by benzil.

PubMed

Fleming, Christopher D; Bencharit, Sompop; Edwards, Carol C; Hyatt, Janice L; Tsurkan, Lyudmila; Bai, Feng; Fraga, Charles; Morton, Christopher L; Howard-Williams, Escher L; Potter, Philip M; Redinbo, Matthew R

2005-09-09

Human carboxylesterase 1 (hCE1) exhibits broad substrate specificity and is involved in xenobiotic processing and endobiotic metabolism. We present and analyze crystal structures of hCE1 in complexes with the cholesterol-lowering drug mevastatin, the breast cancer drug tamoxifen, the fatty acyl ethyl ester (FAEE) analogue ethyl acetate, and the novel hCE1 inhibitor benzil. We find that mevastatin does not appear to be a substrate for hCE1, and instead acts as a partially non-competitive inhibitor of the enzyme. Similarly, we show that tamoxifen is a low micromolar, partially non-competitive inhibitor of hCE1. Further, we describe the structural basis for the inhibition of hCE1 by the nanomolar-affinity dione benzil, which acts by forming both covalent and non-covalent complexes with the enzyme. Our results provide detailed insights into the catalytic and non-catalytic processing of small molecules by hCE1, and suggest that the efficacy of clinical drugs may be modulated by targeted hCE1 inhibitors.

Insights into sleep's role for insight: Studies with the number reduction task

PubMed Central

Verleger, Rolf; Rose, Michael; Wagner, Ullrich; Yordanova, Juliana; Kolev, Vasil

2013-01-01

In recent years, vibrant research has developed on “consolidation” during sleep: To what extent are newly experienced impressions reprocessed or even restructured during sleep? We used the number reduction task (NRT) to study if and how sleep does not only reiterate new experiences but may even lead to new insights. In the NRT, covert regularities may speed responses. This implicit acquisition of regularities may become explicitly conscious at some point, leading to a qualitative change in behavior which reflects this insight. By applying the NRT at two consecutive sessions separated by an interval, we investigated the role of sleep in this interval for attaining insight at the second session. In the first study, a night of sleep was shown to triple the number of participants attaining insight above the base rate of about 20%. In the second study, this hard core of 20% discoverers differed from other participants in their task-related EEG potentials from the very beginning already. In the third study, the additional role of sleep was specified as an effect of the deep-sleep phase of slow-wave sleep on participants who had implicitly acquired the covert regularity before sleep. It was in these participants that a specific increase of EEG during slow-wave sleep in the 10-12 Hz band was obtained. These results support the view that neuronal memory reprocessing during slow-wave sleep restructures task-related representations in the brain, and that such restructuring promotes the gain of explicit knowledge. PMID:24605175

Insight into the structural requirements of proton pump inhibitors based on CoMFA and CoMSIA studies.

PubMed

Nayana, M Ravi Shashi; Sekhar, Y Nataraja; Nandyala, Haritha; Muttineni, Ravikumar; Bairy, Santosh Kumar; Singh, Kriti; Mahmood, S K

2008-10-01

In the present study, a series of 179 quinoline and quinazoline heterocyclic analogues exhibiting inhibitory activity against Gastric (H+/K+)-ATPase were investigated using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices (CoMSIA) methods. Both the models exhibited good correlation between the calculated 3D-QSAR fields and the observed biological activity for the respective training set compounds. The most optimal CoMFA and CoMSIA models yielded significant leave-one-out cross-validation coefficient, q(2) of 0.777, 0.744 and conventional cross-validation coefficient, r(2) of 0.927, 0.914 respectively. The predictive ability of generated models was tested on a set of 52 compounds having broad range of activity. CoMFA and CoMSIA yielded predicted activities for test set compounds with r(pred)(2) of 0.893 and 0.917 respectively. These validation tests not only revealed the robustness of the models but also demonstrated that for our models r(pred)(2) based on the mean activity of test set compounds can accurately estimate external predictivity. The factors affecting activity were analyzed carefully according to standard coefficient contour maps of steric, electrostatic, hydrophobic, acceptor and donor fields derived from the CoMFA and CoMSIA. These contour plots identified several key features which explain the wide range of activities. The results obtained from models offer important structural insight into designing novel peptic-ulcer inhibitors prior to their synthesis.

Crystal Structures of Human and Staphylococcus aureus Pyruvate Carboxylase and Molecular Insights into the Carboxyltransfer Reaction

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

Xiang,S.; Tong, L.

2008-01-01

Pyruvate carboxylase (PC) catalyzes the biotin-dependent production of oxaloacetate and has important roles in gluconeogenesis, lipogenesis, insulin secretion and other cellular processes. PC contains the biotin carboxylase (BC), carboxyltransferase (CT) and biotin-carboxyl carrier protein (BCCP) domains. We report here the crystal structures at 2.8-Angstroms resolution of full-length PC from Staphylococcus aureus and the C-terminal region (missing only the BC domain) of human PC. A conserved tetrameric association is observed for both enzymes, and our structural and mutagenesis studies reveal a previously uncharacterized domain, the PC tetramerization (PT) domain, which is important for oligomerization. A BCCP domain is located in themore » active site of the CT domain, providing the first molecular insights into how biotin participates in the carboxyltransfer reaction. There are dramatic differences in domain positions in the monomer and the organization of the tetramer between these enzymes and the PC from Rhizobium etli.« less

Structure of the oligomers obtained by enzymatic hydrolysis of the glucomannan produced by the plant Amorphophallus konjac.

PubMed

Cescutti, Paola; Campa, Cristiana; Delben, Franco; Rizzo, Roberto

2002-11-29

Dimers and trimers obtained by enzymatic hydrolysis of the glucomannan produced by the plant Amorphophallus konjac were analysed in order to obtain information on the saccharidic sequences present in the polymer. The polysaccharide was digested with cellulase and beta-mannanase and the oligomers produced were isolated by means of size-exclusion chromatography. They were structurally characterised using electrospray mass spectrometry, capillary electrophoresis, and NMR. The investigation revealed that many possible sequences were present in the polymer backbone suggesting a Bernoulli-type chain.

Structure of EspB from the ESX-1 type VII secretion system and insights into its export mechanism.

PubMed

Solomonson, Matthew; Setiaputra, Dheva; Makepeace, Karl A T; Lameignere, Emilie; Petrotchenko, Evgeniy V; Conrady, Deborah G; Bergeron, Julien R; Vuckovic, Marija; DiMaio, Frank; Borchers, Christoph H; Yip, Calvin K; Strynadka, Natalie C J

2015-03-03

Mycobacterium tuberculosis (Mtb) uses the ESX-1 type VII secretion system to export virulence proteins across its lipid-rich cell wall, which helps permeabilize the host's macrophage phagosomal membrane, facilitating the escape and cell-to-cell spread of Mtb. ESX-1 membranolytic activity depends on a set of specialized secreted Esp proteins, the structure and specific roles of which are not currently understood. Here, we report the X-ray and electron microscopic structures of the ESX-1-secreted EspB. We demonstrate that EspB adopts a PE/PPE-like fold that mediates oligomerization with apparent heptameric symmetry, generating a barrel-shaped structure with a central pore that we propose contributes to the macrophage killing functions of EspB. Our structural data also reveal unexpected direct interactions between the EspB bipartite secretion signal sequence elements that form a unified aromatic surface. These findings provide insight into how specialized proteins encoded within the ESX-1 locus are targeted for secretion, and for the first time indicate an oligomerization-dependent role for Esp virulence factors. Copyright © 2015 Elsevier Ltd. All rights reserved.

Algorithm for repairing the damaged images of grain structures obtained from the cellular automata and measurement of grain size

NASA Astrophysics Data System (ADS)

Ramírez-López, A.; Romero-Romo, M. A.; Muñoz-Negron, D.; López-Ramírez, S.; Escarela-Pérez, R.; Duran-Valencia, C.

2012-10-01

Computational models are developed to create grain structures using mathematical algorithms based on the chaos theory such as cellular automaton, geometrical models, fractals, and stochastic methods. Because of the chaotic nature of grain structures, some of the most popular routines are based on the Monte Carlo method, statistical distributions, and random walk methods, which can be easily programmed and included in nested loops. Nevertheless, grain structures are not well defined as the results of computational errors and numerical inconsistencies on mathematical methods. Due to the finite definition of numbers or the numerical restrictions during the simulation of solidification, damaged images appear on the screen. These images must be repaired to obtain a good measurement of grain geometrical properties. Some mathematical algorithms were developed to repair, measure, and characterize grain structures obtained from cellular automata in the present work. An appropriate measurement of grain size and the corrected identification of interfaces and length are very important topics in materials science because they are the representation and validation of mathematical models with real samples. As a result, the developed algorithms are tested and proved to be appropriate and efficient to eliminate the errors and characterize the grain structures.

InSight Planetary Protection Status

NASA Astrophysics Data System (ADS)

Benardini, James; La Duc, Myron; Willis, Jason

The NASA Discovery Program’s next mission, Interior Exploration using Seismic Investigations, Geodesy and Heat Transport (InSIght), consists of a single spacecraft that will be launched aboard an Atlas V 401 rocket from Vandenberg Air Force Base (Space Launch Complex 3E) during the March 2016 timeframe. The overarching mission goal is to illuminate the fundamentals of formation and evolution of terrestrial planets by investigating the interior structure and processes of Mars. The flight system consists of a heritage cruise stage, aeroshell (heatshield and backshell), and Lander from the 2008 Phoenix mission. Included in the lander payload are various cameras, a seismometer, an auxiliary sensor suite to measure wind, temperature, and pressure, and a mole to penetrate the regolith (<5 meters) and assess the subsurface geothermal gradient of Mars. Being a Mars lander mission without life detection instruments, InSight has been designated a PP Category Iva mission. As such, planetary protection bioburden requirements apply which require microbial reduction procedures and biological burden reporting. The InSight project is current with required PP documentation, having completed an approved Planetary Protection Plan, Subsidiary PP Plans, and a PP Implementation Plan. The InSight mission’s early planetary protection campaign has commenced, coinciding with the fabrication and assembly of payload and flight system hardware and the baseline analysis of existing flight spares. A report on the status of InSight PP activities will be provided.

Crystal structures of spleen tyrosine kinase in complex with novel inhibitors: structural insights for design of anticancer drugs.

PubMed

Lee, Sang Jae; Choi, Jang-Sik; Han, Byeong-Gu; Kim, Hyoun Sook; Song, Ho-Juhn; Lee, Jaekyoo; Nam, Seungyoon; Goh, Sung-Ho; Kim, Jung-Ho; Koh, Jong Sung; Lee, Byung Il

2016-10-01

Spleen tyrosine kinase (SYK) is a cytosolic nonreceptor protein tyrosine kinase that mediates key signal transduction pathways following the activation of immune cell receptors. SYK regulates cellular events induced by the B-cell receptor and Fc receptors with high intrinsic activity. Furthermore, SYK has been regarded as an attractive target for the treatment of autoimmune diseases and cancers. Here, we report the crystal structures of SYK in complex with seven newly developed inhibitors (G206, G207, O178, O194, O259, O272, and O282) to provide structural insights into which substituents of the inhibitors and binding regions of SYK are essential for lead compound optimization. Our kinase inhibitors exhibited high inhibitory activities against SYK, with half-maximal inhibitory concentrations (IC 50 ) of approximately 0.7-33 nm, but they showed dissimilar inhibitory activities against KDR, RET, JAK2, JAK3, and FLT3. Among the seven SYK inhibitors, O272 and O282 exhibited highly specific inhibitions against SYK, whereas O194 exhibited strong inhibition of both SYK and FLT3. Three inhibitors (G206, G207, and O178) more efficiently inhibited FLT3 while still substantially inhibiting SYK activity. The binding mode analysis suggested that a highly selective SYK inhibitor can be developed by optimizing the functional groups that facilitate direct interactions with Asn499. The atomic coordinates and structure factors for human SYK are in the Protein Data Bank under accession codes 4XG2 (inhibitor-free form), 4XG3 (G206), 4XG4 (G207), 5GHV (O178), 4XG6 (O194), 4XG7 (O259), 4XG8 (O272), and 4XG9 (O282). © 2016 Federation of European Biochemical Societies.

Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9)

PubMed Central

Fu, Qinqin; Yuan, Y. Adam

2013-01-01

Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA processing and RNA-mediated gene silencing, is largely unknown. Human RNA helicase A (DHX9) was reported to function as an RISC-loading factor, and such function is mediated mainly by its dsRNA-binding domains (dsRBDs). Here, we report the crystal structures of human RNA helicase A (RHA) dsRBD1 and dsRBD2 domains in complex with dsRNAs, respectively. Structural analysis not only reveals higher siRNA duplex-binding affinity displayed by dsRBD1, but also identifies a crystallographic dsRBD1 pair of physiological significance in cooperatively recognizing dsRNAs. Structural observations are further validated by isothermal titration calorimetric (ITC) assay. Moreover, co-immunoprecipitation (co-IP) assay coupled with mutagenesis demonstrated that both dsRBDs are required for RISC association, and such association is mediated by dsRNA. Hence, our structural and functional efforts have revealed a potential working model for siRNA recognition by RHA tandem dsRBDs, and together they provide direct structural insights into RISC assembly facilitated by RHA. PMID:23361462

Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9).

PubMed

Fu, Qinqin; Yuan, Y Adam

2013-03-01

Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA processing and RNA-mediated gene silencing, is largely unknown. Human RNA helicase A (DHX9) was reported to function as an RISC-loading factor, and such function is mediated mainly by its dsRNA-binding domains (dsRBDs). Here, we report the crystal structures of human RNA helicase A (RHA) dsRBD1 and dsRBD2 domains in complex with dsRNAs, respectively. Structural analysis not only reveals higher siRNA duplex-binding affinity displayed by dsRBD1, but also identifies a crystallographic dsRBD1 pair of physiological significance in cooperatively recognizing dsRNAs. Structural observations are further validated by isothermal titration calorimetric (ITC) assay. Moreover, co-immunoprecipitation (co-IP) assay coupled with mutagenesis demonstrated that both dsRBDs are required for RISC association, and such association is mediated by dsRNA. Hence, our structural and functional efforts have revealed a potential working model for siRNA recognition by RHA tandem dsRBDs, and together they provide direct structural insights into RISC assembly facilitated by RHA.

Insight and neurocognitive functioning in bipolar subjects.

PubMed

Shad, Mujeeb U; Prasad, Konasale; Forman, Steven D; Haas, Gretchen L; Walker, Jon D; Pisarov, Liubomir A; Goldstein, Gerald

2015-01-01

Insight concerning having a mental illness has been found to influence outcome and effectiveness of treatment. It has been studied mainly in the area of schizophrenia with few studies addressing other disorders. This study evaluates insight in individuals with bipolar disorder using the Scale to Assess Unawareness of Mental Disorder (SUMD), a comprehensive interview for evaluation of awareness of illness and attribution of symptoms. The hypothesis was that in bipolar disorder level of awareness may be associated with numerous factors including neurocognitive function, structural changes in the frontal lobes and hippocampus evaluated by MRI, neurocognitive status, severity of mania and other psychiatric symptoms and comorbid alcoholism. In order to evaluate this hypothesis 33 individuals with DSM-IV diagnosed bipolar disorder, some with and some without comorbid alcoholism, were administered the SUMD and a number of other procedures including a quantitative MRI measuring volume of the frontal lobes and hippocampus, a brief battery of neurocognitive tests, the Brief Psychiatric Rating Scale, and the Young Mania Rating Scale. The data were analyzed by comparing participants with and without alcoholism on these procedures using t tests and by linear multiple regression, with SUMD ratings of awareness and attribution as the dependent variables and variable sets from the other procedures administered as multivariate independent variables. The median score obtained from the SUMD for current awareness was in a range between full awareness and uncertainty concerning presence of a mental disorder. For attribution, the median score indicated that attribution was usually made to the illness itself. None of the differences between participants with and without comorbid alcoholism were significant for the SUMD awareness and attribution scores, neurocognitive or MRI variables. The multiple regression analyses only showed a significant degree of association between the SUMD

Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.

PubMed

Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K; Al-Hashimi, Hashim M

2017-05-19

In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02-0.4%) and short-lived (lifetimes ∼0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Electrochemical insights into the mechanism of NiFe membrane-bound hydrogenases

PubMed Central

Flanagan, Lindsey A.; Parkin, Alison

2016-01-01

Hydrogenases are enzymes of great biotechnological relevance because they catalyse the interconversion of H2, water (protons) and electricity using non-precious metal catalytic active sites. Electrochemical studies into the reactivity of NiFe membrane-bound hydrogenases (MBH) have provided a particularly detailed insight into the reactivity and mechanism of this group of enzymes. Significantly, the control centre for enabling O2 tolerance has been revealed as the electron-transfer relay of FeS clusters, rather than the NiFe bimetallic active site. The present review paper will discuss how electrochemistry results have complemented those obtained from structural and spectroscopic studies, to present a complete picture of our current understanding of NiFe MBH. PMID:26862221

Enhanced dewaterability of sludge during anaerobic digestion with thermal hydrolysis pretreatment: New insights through structure evolution.

PubMed

Zhang, Jingsi; Li, Ning; Dai, Xiaohu; Tao, Wenquan; Jenkinson, Ian R; Li, Zhuo

2017-12-19

Comprehensive insights into the sludge digestate dewaterability were gained through porous network structure of sludge. We measured the evolution of digestate dewaterability, represented by the solid content of centrifugally dewatered cake, in high-solids sequencing batch digesters with and without thermal hydrolysis pretreatment (THP). The results show that the dewaterability of the sludge after digestion was improved by 3.5% (±0.5%) for unpretreated sludge and 5.1% (±0.4%) for thermally hydrolyzed sludge. Compared to the unpretreated sludge digestate, thermal hydrolysis pretreatment eventually resulted in an improvement of dewaterability by 4.6% (±0.5%). Smaller particle size and larger surface area of sludge were induced by thermal hydrolysis and anaerobic digestion treatments. The structure strength and compactness of sludge, represented by elastic modulus and fractal dimension respectively, decreased with increase of digestion time. The porous network structure was broken up by thermal hydrolysis pretreatment and was further weakened during anaerobic digestion, which correspondingly improved the dewaterability of digestates. The logarithm of elastic modulus increased linearly with fractal dimension regardless of the pretreatment. Both fractal dimension and elastic modulus showed linear relationship with dewaterability. The rheological characterization combined with the analysis of fractal dimension of sewage sludge porous network structure was found applicable in quantitative evaluation of sludge dewaterability, which depended positively on both thermal hydrolysis and anaerobic digestion. Copyright © 2017 Elsevier Ltd. All rights reserved.

Insight into the Dzyaloshinskii-Moriya interaction through first-principles study of chiral magnetic structures

NASA Astrophysics Data System (ADS)

Sandratskii, L. M.

2017-07-01

The purpose of the paper is to gain deeper insight into microscopic formation of the Dzyaloshinskii-Moriya interaction (DMI). The paper aims at the development of the physical picture able to address apparently contradicting conclusions of recent studies concerning the location of the DMI energy in the real and reciprocal spaces as well as the relation between values of the atomic moments and the DMI strength. The main tools of our study are the first-principles calculations of the energies of the spiral magnetic states with opposite chiralities. We suggest a method of the calculation of the spiral structures with account for the spin-orbit coupling (SOC). It is based on the application of the generalized Bloch theorem and generalized Bloch functions and allows to reduce the consideration of arbitrary incommensurate spiral to small chemical unit cell. The method neglects the anisotropy in the plane orthogonal to the rotation axis of the spirals that does not influence importantly the DMI energy. For comparison, the supercell calculation with full account for the SOC is performed. The concrete calculations are performed for the Co/Pt bilayer. We consider the distribution of the DMI energy in both real and reciprocal spaces and the dependence of the DMI on the number of electrons. The results of the calculations reveal a number of energy compensations in the formation of the DMI. Thus, the partial atomic contributions as functions of the spiral wave vector q are nonmonotonic and have strongly varying slopes. However, in the total DMI energy these atom-related features compensate each other, resulting in a smooth q dependence. The reason for the peculiar form of the partial DMI contributions is a q -dependent difference in the charge distribution between q and -q spirals. The strongly q -dependent relation between atomic contributions shows that the real-space distribution of the DMI energy obtained for a selected q value cannot be considered as a general

Structures of parasite calreticulins provide insights into their flexibility and dual carbohydrate/peptide-binding properties.

PubMed

Moreau, Christophe; Cioci, Gianluca; Iannello, Marina; Laffly, Emmanuelle; Chouquet, Anne; Ferreira, Arturo; Thielens, Nicole M; Gaboriaud, Christine

2016-11-01

Calreticulin (CRT) is a multifaceted protein, initially discovered as an endoplasmic reticulum (ER) chaperone protein, that is essential in calcium metabolism. Various implications in cancer, early development and immunology have been discovered more recently for CRT, as well as its role as a dominant 'eat-me' prophagocytic signal. Intriguingly, cell-surface exposure/secretion of CRT is among the infective strategies used by parasites such as Trypanosoma cruzi , Entamoeba histolytica , Taenia solium , Leishmania donovani and Schistosoma mansoni . Because of the inherent flexibility of CRTs, their analysis by X-ray crystallography requires the design of recombinant constructs suitable for crystallization, and thus only the structures of two very similar mammalian CRT lectin domains are known. With the X-ray structures of two distant parasite CRTs, insights into species structural determinants that might be harnessed to fight against the parasites without affecting the functions of the host CRT are now provided. Moreover, although the hypothesis that CRT can exhibit both open and closed conformations has been proposed in relation to its chaperone function, only the open conformation has so far been observed in crystal structures. The first evidence is now provided of a complex conformational transition with the junction reoriented towards P-domain closure. SAXS experiments also provided additional information about the flexibility of T. cruzi CRT in solution, thus complementing crystallographic data on the open conformation. Finally, regarding the conserved lectin-domain structure and chaperone function, evidence is provided of its dual carbohydrate/protein specificity and a new scheme is proposed to interpret such unusual substrate-binding properties. These fascinating features are fully consistent with previous experimental observations, as discussed considering the broad spectrum of CRT sequence conservations and differences.

Structure of the apoptosome: mechanistic insights into activation of an initiator caspase from Drosophila

PubMed Central

Pang, Yuxuan; Bai, Xiao-chen; Yan, Chuangye; Hao, Qi; Chen, Zheqin; Wang, Jia-Wei

2015-01-01

Apoptosis is executed by a cascade of caspase activation. The autocatalytic activation of an initiator caspase, exemplified by caspase-9 in mammals or its ortholog, Dronc, in fruit flies, is facilitated by a multimeric adaptor complex known as the apoptosome. The underlying mechanism by which caspase-9 or Dronc is activated by the apoptosome remains unknown. Here we report the electron cryomicroscopic (cryo-EM) structure of the intact apoptosome from Drosophila melanogaster at 4.0 Å resolution. Analysis of the Drosophila apoptosome, which comprises 16 molecules of the Dark protein (Apaf-1 ortholog), reveals molecular determinants that support the assembly of the 2.5-MDa complex. In the absence of dATP or ATP, Dronc zymogen potently induces formation of the Dark apoptosome, within which Dronc is efficiently activated. At 4.1 Å resolution, the cryo-EM structure of the Dark apoptosome bound to the caspase recruitment domain (CARD) of Dronc (Dronc-CARD) reveals two stacked rings of Dronc-CARD that are sandwiched between two octameric rings of the Dark protein. The specific interactions between Dronc-CARD and both the CARD and the WD40 repeats of a nearby Dark protomer are indispensable for Dronc activation. These findings reveal important mechanistic insights into the activation of initiator caspase by the apoptosome. PMID:25644603

Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.

PubMed

Kuznetsova, Ekaterina; Nocek, Boguslaw; Brown, Greg; Makarova, Kira S; Flick, Robert; Wolf, Yuri I; Khusnutdinova, Anna; Evdokimova, Elena; Jin, Ke; Tan, Kemin; Hanson, Andrew D; Hasnain, Ghulam; Zallot, Rémi; de Crécy-Lagard, Valérie; Babu, Mohan; Savchenko, Alexei; Joachimiak, Andrzej; Edwards, Aled M; Koonin, Eugene V; Yakunin, Alexander F

2015-07-24

The haloacid dehalogenase (HAD)-like enzymes comprise a large superfamily of phosphohydrolases present in all organisms. The Saccharomyces cerevisiae genome encodes at least 19 soluble HADs, including 10 uncharacterized proteins. Here, we biochemically characterized 13 yeast phosphatases from the HAD superfamily, which includes both specific and promiscuous enzymes active against various phosphorylated metabolites and peptides with several HADs implicated in detoxification of phosphorylated compounds and pseudouridine. The crystal structures of four yeast HADs provided insight into their active sites, whereas the structure of the YKR070W dimer in complex with substrate revealed a composite substrate-binding site. Although the S. cerevisiae and Escherichia coli HADs share low sequence similarities, the comparison of their substrate profiles revealed seven phosphatases with common preferred substrates. The cluster of secondary substrates supporting significant activity of both S. cerevisiae and E. coli HADs includes 28 common metabolites that appear to represent the pool of potential activities for the evolution of novel HAD phosphatases. Evolution of novel substrate specificities of HAD phosphatases shows no strict correlation with sequence divergence. Thus, evolution of the HAD superfamily combines the conservation of the overall substrate pool and the substrate profiles of some enzymes with remarkable biochemical and structural flexibility of other superfamily members. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Damage identification of beam structures using free response shapes obtained by use of a continuously scanning laser Doppler vibrometer system

NASA Astrophysics Data System (ADS)

Xu, Y. F.; Chen, Da-Ming; Zhu, W. D.

2017-08-01

Spatially dense operating deflection shapes and mode shapes can be rapidly obtained by use of a continuously scanning laser Doppler vibrometer (CSLDV) system, which sweeps its laser spot over a vibrating structure surface. This paper introduces a new type of vibration shapes called a free response shape (FRS) that can be obtained by use of a CSLDV system, and a new damage identification methodology using FRSs is developed for beam structures. An analytical expression of FRSs of a damped beam structure is derived, and FRSs from the analytical expression compare well with those from a finite element model. In the damage identification methodology, a free-response damage index (FRDI) is proposed, and damage regions can be identified near neighborhoods with consistently high values of FRDIs associated with different modes; an auxiliary FRDI is defined to assist identification of the neighborhoods. A FRDI associated with a mode consists of differences between curvatures of FRSs associated with the mode in a number of half-scan periods of a CSLDV system and those from polynomials that fit the FRSs with properly determined orders. A convergence index is proposed to determine the proper order of a polynomial fit. One advantage of the methodology is that the FRDI does not require any baseline information of an undamaged beam structure, if it is geometrically smooth and made of materials that have no stiffness and mass discontinuities. Another advantage is that FRDIs associated with multiple modes can be obtained using free response of a beam structure measured by a CSLDV system in one scan. The number of half-scan periods for calculation of the FRDI associated with a mode can be determined by use of the short-time Fourier transform. The proposed methodology was numerically and experimentally applied to identify damage in beam structures; effects of the scan frequency of a CSLDV system on qualities of obtained FRSs were experimentally investigated.

Insights into Silicate and Oxide Melt Structure from Amorphous, Non-Glass-Forming Materials

NASA Astrophysics Data System (ADS)

Stebbins, J. F.

2015-12-01

Many silicate and oxide liquids of interest in the Earth sciences and in technology cannot readily be quenched to glasses, either because of low silica contents (and hence low viscosity at the melting point and accompanying liquid 'fragility') or because of liquid-liquid unmixing at high temperature. Although in-situ, high temperature structural tools have been in use for decades and are rapidly developing, many methods are still most informative for glass samples quenched to ambient pressure and temperature, e.g. high-resolution solid-state NMR. Amorphous oxides, including alumina and silicate compositions, have widespread technological applications. These are generally deposited by a variety of high-energy sputtering methods, as films of thicknesses of 10's to 100's of nm. Using Al-27, Si-29, and O-17 NMR, we have recently shown that for such films, very similar short-range structure is seen in materials made by very different kinetic pathways, such as sol-gel synthesis vs. ion-beam sputtering. This path-independent structure suggests that these materials pass through transient equilibrium states during their formation, probably that of deeply supercooled liquids just above glass transition temperatures. In the HfO2-SiO2 and ZrO2-SiO2 systems, for example, samples have well-resolved O-17 NMR spectra, allowing quantitation of O sites with only Hf(Zr) neighbors (so-called "free" oxide ions), with mixed Hf(Zr) and Si neighbors, and Si only. The observed oxygen speciation agrees well with a simple thermodynamic model of one of the most fundamental equilibria in silicate systems, namely the reaction of bridging (Si-O-Si) and "free" (e.g. OHf3 and OHf4) oxide ions to produce "non-bridging" oxygens (e.g. Si-OHf2). This new approach to sampling such structural equilibria in compositions far outside the range of normal glass-forming liquids may provide new insights into more geological compositions as well, as well as in more general models of silicate melt chemistry.

Structural and Depositional Evolution of the Stevenson Basin, a Gulf of Alaska Forearc Basin: Insights from Legacy Seismic and Borehole Data

NASA Astrophysics Data System (ADS)

Bhattacharya, R.; Liberty, L. M.; Almeida, R. V.; Hubbard, J.

2016-12-01

We explore the structural and depositional evolution of the Stevenson Basin, Gulf of Alaska from a dense network of 2-D marine seismic profiles that span the Gulf of Alaska continental margin. The grid of 71 seismic profiles was acquired as part of a 1975 Mineral Management Services (MMS) exploration project to assess basin architecture along the Alaska continental shelf. We obtained unmigrated and stacked seismic profiles in TIFF format. We converted the data to SEGY format and migrated each profile. Within the Stevenson Basin, we identify key seismic horizons, including the regional Eocene-Miocene unconformity, that provide insights into its depositional and structural history. Using these observations combined with stacking velocities, sonic logs from wells, and refraction velocities from the Edge profile of Ye et al. (1997), we develop a local 3D velocity model that we use to depth-convert the seismic reflection profiles. By using ties to >2.5 km deep exploration wells, we note the Stevenson Basin is one of many Eocene and younger depocenters that span the forearc between Kodiak and Prince William Sound. Well logs and seismic data suggest basal strata consist of Eocene sediments than are unconformably overlain by Neogene and younger strata. Faults that breach the sea floor suggest active deformation within and at the bounds of this basin, including on new faults that do not follow any pre-existing structural trends. This assessment is consistent with slip models that place tsunamigenic faults that ruptured during the 1964 Great Alaska earthquake in the vicinity of the basin. The catalog of faults, their slip history and the depositional evolution of the Stevenson Basin, all suggest that the basin evolution may be controlled by heterogeneities along the incoming plate.

Structural insights into a key carotenogenesis related enzyme phytoene synthase of P. falciparum: a novel drug target for malaria.

PubMed

Agarwal, Shalini; Sharma, Vijeta; Phulera, Swastik; Abdin, M Z; Ayana, R; Singh, Shailja

2015-12-01

Carotenoids represent a diverse group of pigments derived from the common isoprenoid precursors and fulfill a variety of critical functions in plants and animals. Phytoene synthase (PSY), a transferase enzyme that catalyzes the first specific step in carotenoid biosynthesis plays a central role in the regulation of a number of essential functions mediated via carotenoids. PSYs have been deeply investigated in plants, bacteria and algae however in apicomplexans it is poorly studied. In an effort to characterize PSY in apicomplexans especially the malaria parasite Plasmodium falciparum (P. falciparum), a detailed bioinformatics analysis is undertaken. We have analysed the Phylogenetic relationship of PSY also referred to as octaprenyl pyrophosphate synthase (OPPS) in P. falciparum with other taxonomic groups. Further, we in silico characterized the secondary and tertiary structures of P. falciparum PSY/OPPS and compared the tertiary structures with crystal structure of Thermotoga maritima (T. maritima) OPPS. Our results evidenced the resemblance of P. falciparum PSY with the active site of T. maritima OPPS. Interestingly, the comparative structural analysis revealed an unconserved unique loop in P. falciparum OPPS/PSY. Such structural insights might contribute novel accessory functions to the protein thus, offering potential drug targets.

Chemical, structural and combustion characteristics of carbonaceous products obtained by hydrothermal carbonization of palm empty fruit bunches.

PubMed

Parshetti, Ganesh K; Kent Hoekman, S; Balasubramanian, Rajasekhar

2013-05-01

A carbon-rich solid product, denoted as hydrochar, was synthesized by hydrothermal carbonization (HTC) of palm oil empty fruit bunch (EFB), at different pre-treatment temperatures of 150, 250 and 350 °C. The conversion of the raw biomass to its hydrochar occurred via dehydration and decarboxylation processes. The hydrochar produced at 350 °C had the maximum energy-density (>27 MJ kg(-1)) with 68.52% of raw EFB energy retained in the char. To gain a detailed insight into the chemical and structural properties, carbonaceous hydrochar materials were characterized by FE-SEM, FT-IR, XRD and Brunauer-Emmett-Teller (BET) analyses. This work also investigated the influence of hydrothermally treated hydrochars on the co-combustion characteristics of low rank Indonesian coal. Conventional thermal gravimetric analysis (TGA) parameters, kinetics and activation energy of different hydrochar and coal blends were estimated. Our results show that solid hydrochars improve the combustion of low rank coals for energy generation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Studying dyadic structure-function relationships: a review of current modeling approaches and new insights into Ca2+ (mis)handling.

PubMed

Maleckar, Mary M; Edwards, Andrew G; Louch, William E; Lines, Glenn T

2017-01-01

Excitation-contraction coupling in cardiac myocytes requires calcium influx through L-type calcium channels in the sarcolemma, which gates calcium release through sarcoplasmic reticulum ryanodine receptors in a process known as calcium-induced calcium release, producing a myoplasmic calcium transient and enabling cardiomyocyte contraction. The spatio-temporal dynamics of calcium release, buffering, and reuptake into the sarcoplasmic reticulum play a central role in excitation-contraction coupling in both normal and diseased cardiac myocytes. However, further quantitative understanding of these cells' calcium machinery and the study of mechanisms that underlie both normal cardiac function and calcium-dependent etiologies in heart disease requires accurate knowledge of cardiac ultrastructure, protein distribution and subcellular function. As current imaging techniques are limited in spatial resolution, limiting insight into changes in calcium handling, computational models of excitation-contraction coupling have been increasingly employed to probe these structure-function relationships. This review will focus on the development of structural models of cardiac calcium dynamics at the subcellular level, orienting the reader broadly towards the development of models of subcellular calcium handling in cardiomyocytes. Specific focus will be given to progress in recent years in terms of multi-scale modeling employing resolved spatial models of subcellular calcium machinery. A review of the state-of-the-art will be followed by a review of emergent insights into calcium-dependent etiologies in heart disease and, finally, we will offer a perspective on future directions for related computational modeling and simulation efforts.

Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana.

PubMed

Wu, Baixing; Zhang, Mengmeng; Su, Shichen; Liu, Hehua; Gan, Jianhua; Ma, Jinbiao

2018-06-22

Vernalization is a pivotal stage for some plants involving many epigenetic changes during cold exposure. In Arabidopsis, an essential step in vernalization for further flowering is successful silence the potent floral repressor Flowering Locus C (FLC) by repressing histone mark. AtVal1 is a multi-function protein containing five domains that participate into many recognition processes and is validated to recruit the repress histone modifier PHD-PRC2 complex and interact with components of the ASAP complex target to the FLC nucleation region through recognizing a cis element known as CME (cold memory element) by its plant-specific B3 domain. Here, we determine the crystal structure of the B3 domain in complex with Sph/RY motif in CME. Our structural analysis reveals the specific DNA recognition by B3 domain, combined with our in vitro experiments, we provide the structural insight into the important implication of AtVAL1-B3 domain in flowering process. Copyright © 2018 Elsevier Inc. All rights reserved.

Paclitaxel-Loaded pH-Sensitive Liposome: New Insights on Structural and Physicochemical Characterization.

PubMed

Monteiro, Liziane O F; Malachias, Ângelo; Pound-Lana, Gwenaelle; Magalhães-Paniago, Rogério; Mosqueira, Vanessa C F; Oliveira, Mônica C; de Barros, André Luís B; Leite, Elaine A

2018-05-22

A long-circulating and pH-sensitive liposome containing paclitaxel (SpHL-PTX) was recently developed by our group. Once in an acidic environment, for example, tumors, these liposomes undergo destabilization, releasing the encapsulated drug. In this way, the aim of this study was to evaluate the molecular and supramolecular interactions between the lipid bilayer and PTX in similar biological environment conditions. High-sensitivity analyses of SpHL-PTX structures were obtained by the small-angle X-ray scattering technique combined with other techniques such as dynamic light scattering, asymmetric flow field-flow fractionation, transmission electron microscopy, and high-performance liquid chromatography. The results showed that PTX incorporation in the liposomal bilayer clearly leads to changes in supramolecular organization of dioleoylphosphatidylethanolamine (DOPE) molecules, inducing the formation of more ordered structures. Changes in supramolecular organization were observed at lower pH, indicating that pH sensitivity was preserved even in the presence of fetal bovine serum proteins. Furthermore, morphological and physicochemical characterization of SpHL-PTX evidenced the formation of nanosized dispersion suitable for intravenous administration. In conclusion, a stable nanosized dispersion of PTX was obtained at pH 7.4 with suitable parameters for intravenous administration. At lower pH conditions, the pH sensitivity of the system was clearly evidenced by changes in the supramolecular organization of DOPE molecules, which is crucial for the delivery of PTX into the cytoplasm of the targeted cells. In this way, the results obtained by different techniques confirm the feasibility of SpHL as a promising tool to PTX delivery in acidic environments, such as tumors.

Analysis of simple sequence repeat (SSR) structure and sequence within Epichloë endophyte genomes reveals impacts on gene structure and insights into ancestral hybridization events.

PubMed

Clayton, William; Eaton, Carla Jane; Dupont, Pierre-Yves; Gillanders, Tim; Cameron, Nick; Saikia, Sanjay; Scott, Barry

2017-01-01

Epichloë grass endophytes comprise a group of filamentous fungi of both sexual and asexual species. Known for the beneficial characteristics they endow upon their grass hosts, the identification of these endophyte species has been of great interest agronomically and scientifically. The use of simple sequence repeat loci and the variation in repeat elements has been used to rapidly identify endophyte species and strains, however, little is known of how the structure of repeat elements changes between species and strains, and where these repeat elements are located in the fungal genome. We report on an in-depth analysis of the structure and genomic location of the simple sequence repeat locus B10, commonly used for Epichloë endophyte species identification. The B10 repeat was found to be located within an exon of a putative bZIP transcription factor, suggesting possible impacts on polypeptide sequence and thus protein function. Analysis of this repeat in the asexual endophyte hybrid Epichloë uncinata revealed that the structure of B10 alleles reflects the ancestral species that hybridized to give rise to this species. Understanding the structure and sequence of these simple sequence repeats provides a useful set of tools for readily distinguishing strains and for gaining insights into the ancestral species that have undergone hybridization events.

Investigation of the structure and properties of boron-containing coatings obtained by electron-beam treatment

NASA Astrophysics Data System (ADS)

Krivezhenko, Dina S.; Drobyaz, Ekaterina A.; Bataev, Ivan A.; Chuchkova, Lyubov V.

2015-10-01

An investigation of surface-hardened materials obtained by cladding with an electron beam injected into the air atmosphere was carried out. Structural investigations of coatings revealed that an increase in boron carbide concentration in a saturating mixture contributed to a rise of a volume fraction of iron borides in coatings. The maximum hardened depth reached 2 mm. Hardened layers were characterized by the formation of heterogeneous structure which consisted of iron borides and titanium carbides distributed uniformly in the eutectic matrix. Areas of titanium boride conglomerations were detected. It was found that an increase in the boron carbide content led to an enhancement in hardness of the investigated materials. Friction testing against loosely fixed abrasive particles showed that electron-beam cladding of powder mixtures containing boron carbides, titanium, and iron in air atmosphere allowed enhancing a resistance of materials hardened in two times.

A procedure obtaining stiffnesses and masses of a structure from vibration modes and substructure static test data

NASA Technical Reports Server (NTRS)

Edighoffer, H. H.

1979-01-01

A component mode desynthesis procedure is developed for determining the unknown vibration characteristics of a structural component (i.e., a launch vehicle) given the vibration characteristics of a structural system composed of that component combined with a known one (i.e., a payload). At least one component static test has to be performed. These data are used in conjunction with the system measured frequencies and mode shapes to obtain the vibration characteristics of each component. The flight dynamics of an empty launch vehicle can be determined from measurements made on a vehicle/payload combination in conjunction with a static test on the payload.

Insights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein Fold

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

Tan, Kemin; Cao, Nan; Cheng, Bokun

The DNA topoisomerase I enzyme of Mycobacterium tuberculosis (MtTOP1) is essential for the viability of the organism and survival in a murine model. This topoisomerase is being pursued as a novel target for the discovery of new therapeutic agents for the treatment of drug-resistant tuberculosis. In this study, we succeeded in obtaining a structure of MtTOP1 by first predicting that the C-terminal region of MtTOP1 contains four repeated domains that do not involve the Zn-binding tetracysteine motifs seen in the C-terminal domains of Escherichia coli topoisomerase I. A construct (amino acids A2-T704), MtTOP1-704t, that includes the N-terminal domains (D1-D4) andmore » the first predicted C-terminal domain (D5) of MtTOP1 was expressed and found to retain DNA cleavage-religation activity and catalyze single-stranded DNA catenation. MtTOP1-704t was crystallized, and a structure of 2.52 angstrom resolution limit was obtained. The structure of the MtTOP1 N-terminal domains has features that have not been observed in other previously available bacterial topoisomerase I crystal structures. The first C-terminal domain D5 forms a novel protein fold of a four-stranded antiparallel beta-sheet stabilized by a crossing-over alpha-helix. Since there is only one type IA topoisomerase present in Mycobacteriaceae and related Actinobacteria, this subfamily of type IA topoisomerase may be required for multiple functions in DNA replication, transcription, recombination, and repair. The unique structural features observed for MtTOP1 may allow these topoisomerase I enzymes to carry out physiological functions associated with topoisomerase III enzyme in other bacteria.« less

Structural insights into the metabolism of 2-chlorodibenzofuran by an evolved biphenyl dioxygenase

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

Kumar, Pravindra; Mohammadi, Mahmood; Dhindwal, Sonali

2012-06-28

The biphenyl dioxygenase of Burkholderia xenovorans LB400 (BphAE{sub LB400}) is a Rieske-type oxygenase that catalyzes the stereospecific oxygenation of many heterocyclic aromatics including dibenzofuran. In a previous work, we evolved BphAE{sub LB400} and obtained BphAE{sub RR41}. This variant metabolizes dibenzofuran and 2-chlorodibenzofuran more efficiently than BphAE{sub LB400}. However, the regiospecificity of BphAE{sub RR41} toward these substrates differs. Dibenzofuran is metabolized principally through a lateral dioxygenation whereas 2-chlorodibenzofuran is metabolized principally through an angular dioxygenation. In order to explain this difference, we examined the crystal structures of both substrate-bound forms of BphAE{sub RR41} obtained under anaerobic conditions. This structure analysis, inmore » combination with biochemical data for a Ser283Gly mutant provided evidences that the substrate is compelled to move after oxygen-binding in BphAE{sub RR41}:dibenzofuran. In BphAE{sub RR41}:2-chlorodibenzofuran, the chlorine atom is close to the side chain of Ser283. This contact is missing in the BphAE{sub RR41}:dibenzofuran, and strong enough in the BphAE{sub RR41}:2-chlorodibenzofuran to help prevent substrate movement during the catalytic reaction.« less

Partial rupture of the Achilles tendon during a simulated fire ground task: insights obtained from a case report for the prevention and reporting of musculoskeletal injury.

PubMed

Gooyers, Chad E; Frost, David M; McGill, Stuart M; Callaghan, Jack P

2013-04-01

In this case report an incumbent firefighter partially ruptured his right Achilles tendon during a study of the physical demands of firefighting. Kinematics and kinetics of the lower limbs and trunk were collected while the firefighter performed two simulated fire ground tasks. From this unexpected event, two insights were obtained that should be considered in all future injury prevention and reporting efforts. (i) Consider the full anatomical linkage--the right ankle and knee kinematics leading up to the onset of injury trial were comparable to all preceding repetitions. However, there was a notable difference in the left knee starting position before the initiation of movement of the 37th hose-advance trial. (ii) Consider the cumulative load--the task in question comprised forward and backward phases. A marked difference was observed in the frontal-plane ankle moment during the return phase of the trial preceding the injury. Additionally, the magnitude of the left side vertical ground reaction force was comparable across all trials, suggesting that loads experienced by the right limb were also similar. This would indicate that the tolerance of the Achilles tendon and not the magnitude of the loading was altered. The unfortunate injury captured in this work provides insight into the complexity of characterizing the pathways of injury. It is recommended that future injury prevention and reporting efforts consider individuals' physical demands (at work and in life) and document the nature of loading (i.e., frequency, duration, magnitude, type) when considering the mechanism for injury. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Diverse Actions and Target-Site Selectivity of Neonicotinoids: Structural Insights

PubMed Central

Matsuda, Kazuhiko; Kanaoka, Satoshi; Akamatsu, Miki; Sattelle, David B.

2009-01-01

The nicotinic acetylcholine receptors (nAChRs) are targets for human and veterinary medicines as well as insecticides. Subtype-selectivity among the diverse nAChR family members is important for medicines targeting particular disorders, and pest-insect selectivity is essential for the development of safer, environmentally acceptable insecticides. Neonicotinoid insecticides selectively targeting insect nAChRs have important applications in crop protection and animal health. Members of this class exhibit strikingly diverse actions on their nAChR targets. Here we review the chemistry and diverse actions of neonicotinoids on insect and mammalian nAChRs. Electrophysiological studies on native nAChRs and on wild-type and mutagenized recombinant nAChRs have shown that basic residues particular to loop D of insect nAChRs are likely to interact electrostatically with the nitro group of neonicotinoids. In 2008, the crystal structures were published showing neonicotinoids docking into the acetylcholine binding site of molluscan acetylcholine binding proteins with homology to the ligand binding domain (LBD) of nAChRs. The crystal structures showed that 1) glutamine in loop D, corresponding to the basic residues of insect nAChRs, hydrogen bonds with the NO2 group of imidacloprid and 2) neonicotinoid-unique stacking and CH-π bonds at the LBD. A neonicotinoid-resistant strain obtained by laboratory-screening has been found to result from target site mutations, and possible reasons for this are also suggested by the crystal structures. The prospects of designing neonicotinoids that are safe not only for mammals but also for beneficial insects such as honey bees (Apis mellifera) are discussed in terms of interactions with non-α nAChR subunits. PMID:19321668

Structural Insight into Nucleoprotein Conformation Change Chaperoned by VP35 Peptide in Marburg Virus.

PubMed

Liu, Baocheng; Dong, Shishang; Li, Guobang; Wang, Wenming; Liu, Xiang; Wang, Yantong; Yang, Cheng; Rao, Zihe; Guo, Yu

2017-08-15

Marburg virus (MARV) encodes a nucleoprotein (NP) to encapsidate its genome by oligomerization and form a ribonucleoprotein complex (RNP). According to previous investigation on nonsegmented negative-sense RNA viruses (nsNSV), the newly synthesized NPs must be prevented from indiscriminately binding to noncognate RNAs. During the viral RNA synthesis process, the RNPs undergo a transition from an RNA-bound form to a template-free form, to open access for the interaction between the viral polymerase and the RNA template. In filoviruses, this transition is regulated by VP35 peptide and other viral components. To further understand the dynamic process of filovirus RNP formation, we report here the structure of MARV NP core , both in the apo form and in the VP35 peptide-chaperoned form. These structures reveal a typical bilobed structure, with a positive-charged RNA binding groove between two lobes. In the apo form, the MARV NP exists in an interesting hexameric state formed by the hydrophobic interaction within the long helix of the NP core C-terminal region, which shows high structural flexibility among filoviruses and may imply critical function during RNP formation. Moreover, the VP35 peptide-chaperoned NP core remains in a monomeric state and completely loses its affinity for single-stranded RNA (ssRNA). The structural comparison reveals that the RNA binding groove undergoes a transition from closed state to open state, chaperoned by VP35 peptide, thus preventing the interaction for viral RNA. Our investigation provides considerable structural insight into the filovirus RNP working mechanism and may support the development of antiviral therapies targeting the RNP formation of filovirus. IMPORTANCE Marburg virus is one of the most dangerous viruses, with high morbidity and mortality. A recent outbreak in Angola in 2005 caused the deaths of 272 persons. NP is one of the most essential proteins, as it encapsidates and protects the whole virus genome simultaneously

Structure of aryl O -demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

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

Kohler, Amanda C.; Mills, Matthew J. L.; Adams, Paul D.

Some strains of soil and marine bacteria have evolved intricate metabolic pathways for using environmentally derived aromatics as a carbon source. Many of these metabolic pathways go through intermediates such as vanillate, 3-O-methylgallate, and syringate. Demethylation of these compounds is essential for downstream aryl modification, ring opening, and subsequent assimilation of these compounds into the tricarboxylic acid (TCA) cycle, and, correspondingly, there are a variety of associated aryl demethylase systems that vary in complexity. Intriguingly, only a basic understanding of the least complex system, the tetrahydrofolate-dependent aryl demethylase LigM from Sphingomonas paucimobilis, a bacterial strain that metabolizes lignin-derived aromatics, wasmore » previously available. LigM-catalyzed demethylation enables further modification and rin g opening of the single-ring aromatics vanillate and 3-Omethylgallate, which are common byproducts of biofuel production. We characterize aryl O-demethylation by LigM and report its 1.81-Å crystal structure, revealing a unique demethylase fold and a canonical folate-binding domain. Structural homology and geometry optimization calculations enabled the identification of LigM's tetrahydrofolate-binding site and protein-folate interactions. Computationally guided mutagenesis and kinetic analyses allowed the identification of the enzyme's aryl-binding site location and determination of its unique, catalytic tyrosine-dependent reaction mechanism. This work defines LigM as a distinct demethylase, both structurally and functionally, and provides insight into demethylation and its reaction requirements. Our results afford the mechanistic details required for efficient utilization of LigM as a tool for aryl O-demethylation and as a component of synthetic biology efforts to valorize previously underused aromatic compounds.« less

Structure of aryl O -demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

DOE PAGES

Kohler, Amanda C.; Mills, Matthew J. L.; Adams, Paul D.; ...

2017-04-03

Some strains of soil and marine bacteria have evolved intricate metabolic pathways for using environmentally derived aromatics as a carbon source. Many of these metabolic pathways go through intermediates such as vanillate, 3-O-methylgallate, and syringate. Demethylation of these compounds is essential for downstream aryl modification, ring opening, and subsequent assimilation of these compounds into the tricarboxylic acid (TCA) cycle, and, correspondingly, there are a variety of associated aryl demethylase systems that vary in complexity. Intriguingly, only a basic understanding of the least complex system, the tetrahydrofolate-dependent aryl demethylase LigM from Sphingomonas paucimobilis, a bacterial strain that metabolizes lignin-derived aromatics, wasmore » previously available. LigM-catalyzed demethylation enables further modification and rin g opening of the single-ring aromatics vanillate and 3-Omethylgallate, which are common byproducts of biofuel production. We characterize aryl O-demethylation by LigM and report its 1.81-Å crystal structure, revealing a unique demethylase fold and a canonical folate-binding domain. Structural homology and geometry optimization calculations enabled the identification of LigM's tetrahydrofolate-binding site and protein-folate interactions. Computationally guided mutagenesis and kinetic analyses allowed the identification of the enzyme's aryl-binding site location and determination of its unique, catalytic tyrosine-dependent reaction mechanism. This work defines LigM as a distinct demethylase, both structurally and functionally, and provides insight into demethylation and its reaction requirements. Our results afford the mechanistic details required for efficient utilization of LigM as a tool for aryl O-demethylation and as a component of synthetic biology efforts to valorize previously underused aromatic compounds.« less

Structural, mechanistic and functional insight into gliotoxin bis-thiomethylation in Aspergillus fumigatus

PubMed Central

Dolan, Stephen K.; Bock, Tobias; Hering, Vanessa; Owens, Rebecca A.; Jones, Gary W.

2017-01-01

Gliotoxin is an epipolythiodioxopiperazine (ETP) class toxin, contains a disulfide bridge that mediates its toxic effects via redox cycling and is produced by the opportunistic fungal pathogen Aspergillus fumigatus. Self-resistance against gliotoxin is effected by the gliotoxin oxidase GliT, and attenuation of gliotoxin biosynthesis is catalysed by gliotoxin S-methyltransferase GtmA. Here we describe the X-ray crystal structures of GtmA-apo (1.66 Å), GtmA complexed to S-adenosylhomocysteine (1.33 Å) and GtmA complexed to S-adenosylmethionine (2.28 Å), providing mechanistic insights into this important biotransformation. We further reveal that simultaneous elimination of the ability of A. fumigatus to dissipate highly reactive dithiol gliotoxin, via deletion of GliT and GtmA, results in the most significant hypersensitivity to exogenous gliotoxin observed to date. Indeed, quantitative proteomic analysis of ΔgliT::ΔgtmA reveals an uncontrolled over-activation of the gli-cluster upon gliotoxin exposure. The data presented herein reveal, for the first time, the extreme risk associated with intracellular dithiol gliotoxin biosynthesis—in the absence of an efficient dismutation capacity. Significantly, a previously concealed protective role for GtmA and functionality of ETP bis-thiomethylation as an ancestral protection strategy against dithiol compounds is now evident. PMID:28179499

Structural, mechanistic and functional insight into gliotoxin bis-thiomethylation in Aspergillus fumigatus.

PubMed

Dolan, Stephen K; Bock, Tobias; Hering, Vanessa; Owens, Rebecca A; Jones, Gary W; Blankenfeldt, Wulf; Doyle, Sean

2017-02-01

Gliotoxin is an epipolythiodioxopiperazine (ETP) class toxin, contains a disulfide bridge that mediates its toxic effects via redox cycling and is produced by the opportunistic fungal pathogen Aspergillus fumigatus Self-resistance against gliotoxin is effected by the gliotoxin oxidase GliT, and attenuation of gliotoxin biosynthesis is catalysed by gliotoxin S -methyltransferase GtmA. Here we describe the X-ray crystal structures of GtmA-apo (1.66 Å), GtmA complexed to S -adenosylhomocysteine (1.33 Å) and GtmA complexed to S -adenosylmethionine (2.28 Å), providing mechanistic insights into this important biotransformation. We further reveal that simultaneous elimination of the ability of A. fumigatus to dissipate highly reactive dithiol gliotoxin, via deletion of GliT and GtmA, results in the most significant hypersensitivity to exogenous gliotoxin observed to date. Indeed, quantitative proteomic analysis of Δ gliT ::Δ gtmA reveals an uncontrolled over-activation of the gli -cluster upon gliotoxin exposure. The data presented herein reveal, for the first time, the extreme risk associated with intracellular dithiol gliotoxin biosynthesis-in the absence of an efficient dismutation capacity. Significantly, a previously concealed protective role for GtmA and functionality of ETP bis -thiomethylation as an ancestral protection strategy against dithiol compounds is now evident. © 2017 The Authors.

Structural insights into translational fidelity.

PubMed

Ogle, James M; Ramakrishnan, V

2005-01-01

The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigation. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75 A away. The ribosome recognizes the geometry of codon-anticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, among other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting.

Investigation of the structure and properties of boron-containing coatings obtained by electron-beam treatment

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

Krivezhenko, Dina S., E-mail: dinylkaa@yandex.ru; Drobyaz, Ekaterina A., E-mail: ekaterina.drobyaz@yandex.ru; Bataev, Ivan A., E-mail: ivanbataev@ngs.ru

2015-10-27

An investigation of surface-hardened materials obtained by cladding with an electron beam injected into the air atmosphere was carried out. Structural investigations of coatings revealed that an increase in boron carbide concentration in a saturating mixture contributed to a rise of a volume fraction of iron borides in coatings. The maximum hardened depth reached 2 mm. Hardened layers were characterized by the formation of heterogeneous structure which consisted of iron borides and titanium carbides distributed uniformly in the eutectic matrix. Areas of titanium boride conglomerations were detected. It was found that an increase in the boron carbide content led to anmore » enhancement in hardness of the investigated materials. Friction testing against loosely fixed abrasive particles showed that electron-beam cladding of powder mixtures containing boron carbides, titanium, and iron in air atmosphere allowed enhancing a resistance of materials hardened in two times.« less

The structure of human tripeptidyl peptidase II as determined by a hybrid approach.

PubMed

Schönegge, Anne-Marie; Villa, Elizabeth; Förster, Friedrich; Hegerl, Reiner; Peters, Jürgen; Baumeister, Wolfgang; Rockel, Beate

2012-04-04

Tripeptidyl-peptidase II (TPPII) is a high molecular mass (∼5 MDa) serine protease, which is thought to act downstream of the 26S proteasome, cleaving peptides released by the latter. Here, the structure of human TPPII (HsTPPII) has been determined to subnanometer resolution by cryoelectron microscopy and single-particle analysis. The complex is built from two strands forming a quasihelical structure harboring a complex system of inner cavities. HsTPPII particles exhibit some polymorphism resulting in complexes consisting of nine or of eight dimers per strand. To obtain deeper insights into the architecture and function of HsTPPII, we have created a pseudoatomic structure of the HsTPPII spindle using a comparative model of HsTPPII dimers and molecular dynamics flexible fitting. Analyses of the resulting hybrid structure of the HsTPPII holocomplex provide new insights into the mechanism of maturation and activation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Insights into biodegradation through depth-resolved microbial community functional and structural profiling of a crude-oil contaminant plume

USGS Publications Warehouse

Fahrenfeld, Nicole; Cozzarelli, Isabelle M.; Bailey, Zach; Pruden, Amy

2014-01-01

Small-scale geochemical gradients are a key feature of aquifer contaminant plumes, highlighting the need for functional and structural profiling of corresponding microbial communities on a similar scale. The purpose of this study was to characterize the microbial functional and structural diversity with depth across representative redox zones of a hydrocarbon plume and an adjacent wetland, at the Bemidji Oil Spill site. A combination of quantitative PCR, denaturing gradient gel electrophoresis, and pyrosequencing were applied to vertically sampled sediment cores. Levels of the methanogenic marker gene, methyl coenzyme-M reductase A (mcrA), increased with depth near the oil body center, but were variable with depth further downgradient. Benzoate degradation N (bzdN) hydrocarbon-degradation gene, common to facultatively anaerobic Azoarcus spp., was found at all locations, but was highest near the oil body center. Microbial community structural differences were observed across sediment cores, and bacterial classes containing known hydrocarbon degraders were found to be low in relative abundance. Depth-resolved functional and structural profiling revealed the strongest gradients in the iron-reducing zone, displaying the greatest variability with depth. This study provides important insight into biogeochemical characteristics in different regions of contaminant plumes, which will aid in improving models of contaminant fate and natural attenuation rates.

Mentalization, insightfulness, and therapeutic action. The importance of mental organization.

PubMed

Sugarman, Alan

2006-08-01

Continuing debates over the relative importance of the role of interpretation leading to insight versus the relationship with the analyst as contributing to structural change are based on traditional definitions of insight as gaining knowledge of unconscious content. This definition inevitably privileges verbal interpretation as self-knowledge becomes equated with understanding the contents of the mind. It is suggested that a way out of this debate is to redefine insight as a process, one that is called insightfulness. This term builds on concepts such as mentalization, or theory of mind, and suggests that patients present with difficulties being able to fully mentalize. Awareness of repudiated content will usually accompany the attainment of insightfulness. But the point of insightfulness is to regain access to inhibited or repudiated mentalization, not to specific content, per se. Emphasizing the process of insightfulness integrates the importance of the relationship with the analyst with the facilitation of insightfulness. A variety of interventions help patients gain the capacity to reflect upon and become aware of the intricate workings of their minds, of which verbal interpretation is only one. For example, often it seems less important to focus on a particular conflict than to show interest in our patients' minds. Furthermore, analysands develop insightfulness by becoming interested in and observing our minds in action. Because the mind originates in bodily experience, mental functioning will always fluctuate between action modes of experiencing and expressing and verbal, symbolic modes. The analyst's role becomes making the patient aware of regressions to action modes, understanding the reasons for doing so, and subordinating this tendency to the verbal, symbolic mode. All mental functions work better and facilitate greater self-regulation when they work in abstract, symbolic ways. Psychopathology can be understood as failing to develop or losing the

Structural insight into the active site of mushroom tyrosinase using phenylbenzoic acid derivatives.

PubMed

Oyama, Takahiro; Yoshimori, Atsushi; Takahashi, Satoshi; Yamamoto, Tetsuya; Sato, Akira; Kamiya, Takanori; Abe, Hideaki; Abe, Takehiko; Tanuma, Sei-Ichi

2017-07-01

So far, many inhibitors of tyrosinase have been discovered for cosmetic and clinical agents. However, the molecular mechanisms underlying the inhibition in the active site of tyrosinase have not been well understood. To explore this problem, we examined here the inhibitory effects of 4'-hydroxylation and methoxylation of phenylbenzoic acid (PBA) isomers, which have a unique scaffold to inhibit mushroom tyrosinase. The inhibitory effect of 3-PBA, which has the most potent inhibitory activity among the isomers, was slightly decreased by 4'-hydroxylation and further decreased by 4'-methoxylation against mushroom tyrosinase. Surprisingly, 4'-hydroxylation but not methoxylation of 2-PBA appeared inhibitory activity. On the other hand, both 4'-hydroxylation and methoxylation of 4-PBA increased the inhibitory activity against mushroom tyrosinase. In silico docking analyses using the crystallographic structure of mushroom tyrosinase indicated that the carboxylic acid or 4'-hydroxyl group of PBA derivatives could chelate with cupric ions in the active site of mushroom tyrosinase, and that the interactions of Asn260 and Phe264 in the active site with the adequate-angled biphenyl group are involved in the inhibitory activities of the modified PBAs, by parallel and T-shaped π-π interactions, respectively. Furthermore, Arg268 could fix the angle of the aromatic ring of Phe264, and Val248 is supposed to interact with the inhibitors as a hydrophobic manner. These results may enhance the structural insight into mushroom tyrosinase for the creation of novel tyrosinase inhibitors. Copyright © 2017 Elsevier Ltd. All rights reserved.

Electric Field Effects on the Intermolecular Interactions in Water Whiskers: Insight from Structures, Energetics, and Properties

DOE PAGES

Bai, Yang; He, Hui-Min; Li, Ying; ...

2015-02-19

Modulation of intermolecular interactions in response to external electric fields could be fundamental to the formation of unusual forms of water, such as water whiskers. However, a detailed understanding of the nature of intermolecular interactions in such systems is lacking. In this study, we present novel theoretical results based on electron correlation calculations regarding the nature of H-bonds in water whiskers, which is revealed by studying their evolution under external electric fields with various field strengths. We find that the water whiskers consisting of 2-7 water molecules all have a chain-length dependent critical electric field. Under the critical electric field,more » the most compact chain structures are obtained, featuring very strong H-bonds, herein referred to as covalent H-bonds. In the case of a water dimer whisker, the bond length of the novel covalent H-bond shortens by 25%, the covalent bond order increases by 9 times, and accordingly the H-bond energy is strengthened by 5 times compared to the normal H-bond in a (H 2O) 2 cluster. Below the critical electric field, it is observed that with increasing field strength, H-bonding orbitals display gradual evolutions in the orbital energy, orbital ordering, and orbital nature (i.e., from typical -style orbital to unusual -style double H-bonding orbital). We also show that beyond the critical electric field, a single water whisker may disintegrate to form a loosely bound zwitterionic chain due to a relay-style proton transfer, whereas two water whiskers may undergo intermolecular cross-linking to form a quasi-two-dimensional water network. In conclusion, these results help shed new insight on the effects of electric fields on water whisker formation.« less

Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations.

PubMed

Presti, Davide; Pedone, Alfonso; Mancini, Giordano; Duce, Celia; Tiné, Maria Rosaria; Barone, Vincenzo

2016-01-21

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water-clay interfaces, which are of fundamental importance for both natural processes and industrial applications.

Molecular details of secretory phospholipase A2 from flax (Linum usitatissimum L.) provide insight into its structure and function.

PubMed

Gupta, Payal; Dash, Prasanta K

2017-09-11

Secretory phospholipase A 2 (sPLA 2 ) are low molecular weight proteins (12-18 kDa) involved in a suite of plant cellular processes imparting growth and development. With myriad roles in physiological and biochemical processes in plants, detailed analysis of sPLA 2 in flax/linseed is meagre. The present work, first in flax, embodies cloning, expression, purification and molecular characterisation of two distinct sPLA 2 s (I and II) from flax. PLA 2 activity of the cloned sPLA 2 s were biochemically assayed authenticating them as bona fide phospholipase A 2 . Physiochemical properties of both the sPLA 2 s revealed they are thermostable proteins requiring di-valent cations for optimum activity.While, structural analysis of both the proteins revealed deviations in the amino acid sequence at C- & N-terminal regions; hydropathic study revealed LusPLA 2 I as a hydrophobic protein and LusPLA 2 II as a hydrophilic protein. Structural analysis of flax sPLA 2 s revealed that secondary structure of both the proteins are dominated by α-helix followed by random coils. Modular superimposition of LusPLA 2 isoforms with rice sPLA 2 confirmed monomeric structural preservation among plant phospholipase A 2 and provided insight into structure of folded flax sPLA 2 s.

Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes

PubMed Central

Jiménez, Diego Javier; Andreote, Fernando Dini; Chaves, Diego; Montaña, José Salvador; Osorio-Forero, Cesar; Junca, Howard; Zambrano, María Mercedes; Baena, Sandra

2012-01-01

A taxonomic and annotated functional description of microbial life was deduced from 53 Mb of metagenomic sequence retrieved from a planktonic fraction of the Neotropical high Andean (3,973 meters above sea level) acidic hot spring El Coquito (EC). A classification of unassembled metagenomic reads using different databases showed a high proportion of Gammaproteobacteria and Alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16S rRNA gene fragments we observed the presence of Proteobacteria, micro-algae chloroplast and Firmicutes. Reads mapped against the genomes Acidiphilium cryptum JF-5, Legionella pneumophila str. Corby and Acidithiobacillus caldus revealed the presence of transposase-like sequences, potentially involved in horizontal gene transfer. Functional annotation and hierarchical comparison with different datasets obtained by pyrosequencing in different ecosystems showed that the microbial community also contained extensive DNA repair systems, possibly to cope with ultraviolet radiation at such high altitudes. Analysis of genes involved in the nitrogen cycle indicated the presence of dissimilatory nitrate reduction to N2 (narGHI, nirS, norBCDQ and nosZ), associated with Proteobacteria-like sequences. Genes involved in the sulfur cycle (cysDN, cysNC and aprA) indicated adenylsulfate and sulfite production that were affiliated to several bacterial species. In summary, metagenomic sequence data provided insight regarding the structure and possible functions of this hot spring microbial community, describing some groups potentially involved in the nitrogen and sulfur cycling in this environment. PMID:23251687

Flexural strength and reliability of monolithic and trilayer ceramic structures obtained by the CAD-on technique.

PubMed

Basso, G R; Moraes, R R; Borba, M; Griggs, J A; Della Bona, A

2015-12-01

To evaluate the flexural strength, Weibull modulus, fracture toughness, and failure behavior of ceramic structures obtained by the CAD-on technique, testing the null hypothesis that trilayer structures show similar properties to monolithic structures. Bar-shaped (1.8mm×4mm×16mm) monolithic specimens of zirconia (IPS e.max ZirCAD - Ivoclar Vivadent) and trilayer specimens of zirconia/fusion ceramic/lithium dissilicate (IPS e.max ZirCAD/IPS e.max CAD Crystall./Connect/IPS e.max CAD, Ivoclar Vivadent) were fabricated (n=30). Specimens were tested in flexure in 37°C deionized water using a universal testing machine at a crosshead speed of 0.5mm/min. Failure loads were recorded, and the flexural strength values were calculated. Fractography principles were used to examine the fracture surfaces under optical and scanning electron microscopy. Data were statistically analyzed using Student's t-test and Weibull statistics (α=0.05). Monolithic and trilayer specimens showed similar mean flexural strengths, characteristic strengths, and Weibull moduli. Trilayer structures showed greater mean critical flaw and fracture toughness values than monolithic specimens (p<0.001). Most critical flaws in the trilayer groups were located on the Y-TZP surface subjected to tension and propagated catastrophically. Trilayer structures showed no flaw deflection at the interface. Considering the CAD-on technique, the trilayer structures showed greater fracture toughness than the monolithic zirconia specimens. Copyright © 2015 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Structural insights into the metabolism of 2-chlorodibenzofuran by an evolved biphenyl dioxygenase

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

Kumar, Pravindra; Department of Biotechnology, Indian Institute of Technology, Roorkee 247667; Mohammadi, Mahmood

2012-05-18

Highlights: Black-Right-Pointing-Pointer Regiospecificity of BphAE{sub RR41} toward dibenzofuran and 2-chlorodibenzofuran differs. Black-Right-Pointing-Pointer We compared the structures of the substrate-bound forms of the enzyme with both substrates. Black-Right-Pointing-Pointer Dibenzofuran is compelled to move during the catalytic reaction. Black-Right-Pointing-Pointer Ser283 contact with 2-chlorodibenzofuran helps prevent substrate movement during the reaction. -- Abstract: The biphenyl dioxygenase of Burkholderia xenovorans LB400 (BphAE{sub LB400}) is a Rieske-type oxygenase that catalyzes the stereospecific oxygenation of many heterocyclic aromatics including dibenzofuran. In a previous work, we evolved BphAE{sub LB400} and obtained BphAE{sub RR41}. This variant metabolizes dibenzofuran and 2-chlorodibenzofuran more efficiently than BphAE{sub LB400}. However, the regiospecificitymore » of BphAE{sub RR41} toward these substrates differs. Dibenzofuran is metabolized principally through a lateral dioxygenation whereas 2-chlorodibenzofuran is metabolized principally through an angular dioxygenation. In order to explain this difference, we examined the crystal structures of both substrate-bound forms of BphAE{sub RR41} obtained under anaerobic conditions. This structure analysis, in combination with biochemical data for a Ser283Gly mutant provided evidences that the substrate is compelled to move after oxygen-binding in BphAE{sub RR41}:dibenzofuran. In BphAE{sub RR41}:2-chlorodibenzofuran, the chlorine atom is close to the side chain of Ser283. This contact is missing in the BphAE{sub RR41}:dibenzofuran, and strong enough in the BphAE{sub RR41}:2-chlorodibenzofuran to help prevent substrate movement during the catalytic reaction.« less

Probing the interaction of anticancer drug temsirolimus with human serum albumin: molecular docking and spectroscopic insight.

PubMed

Shamsi, Anas; Ahmed, Azaj; Bano, Bilqees

2018-05-01

The binding interaction between temsirolimus, an important antirenal cancer drug, and HSA, an important carrier protein was scrutinized making use of UV and fluorescence spectroscopy. Hyper chromaticity observed in UV spectroscopy in the presence of temsirolimus as compared to free HSA suggests the formation of complex between HSA and temsirolimus. Fluorescence quenching experiments clearly showed quenching in the fluorescence of HSA in the presence of temsirolimus confirming the complex formation and also confirmed that static mode of interaction is operative for this binding process. Binding constant values obtained through UV and fluorescence spectroscopy reveal strong interaction; temsirolimus binds to HSA at 298 K with a binding constant of 2.9 × 10 4  M -1 implying the strength of interaction. The negative Gibbs free energy obtained through Isothermal titration calorimetry as well as quenching experiments suggests that binding process is spontaneous. Molecular docking further provides an insight of various residues that are involved in this binding process; showing the binding energy to be -12.9 kcal/mol. CD spectroscopy was retorted to analyze changes in secondary structure of HSA; increased intensity in presence of temsirolimus showing changes in secondary structure of HSA induced by temsirolimus. This study is of importance as it provides an insight into the binding mechanism of an important antirenal cancer drug with an important carrier protein. Once temsirolimus binds to HSA, it changes conformation of HSA which in turn can alter the functionality of this important carrier protein and this altered functionality of HSA can be highlighted in variety of diseases.

Oxidation-induced water-solubilization and chemical functionalization of fullerenes C60, Gd@C60 and Gd@C82: atomistic insights into the formation mechanisms and structures of fullerenols synthesized by different methods.

PubMed

Wang, Zhenzhen; Lu, Zhanghui; Zhao, Yuliang; Gao, Xingfa

2015-02-21

Water-solubilization is the prerequisite to endow the pristinely hydrophobic fullerenes with biocompatibility and biofunctionality, which has been widely applied to derive fullerene-based nanomaterials for biomedical applications. Oxidation reactions using O2 and H2O2 are the most commonly used approaches to this end, through which fullerenols with different structural features can be obtained. Despite the progress in the syntheses and bioapplications of fullerenols, their formation mechanisms and structures at the atomic level, which substantialize their physical properties and biofunctions, have been little understood. Using density functional theory calculations, we comparatively study the mechanisms and product structures for the oxidations of C60, Gd@C60 and Gd@C82 using both O2 and H2O2 as oxidizing agents under both neutral and alkaline aqueous conditions. We predict the formation mechanisms and product structures corresponding to the different synthetic conditions. Briefly, the H2O2 oxidations of C60, Gd@C60 and Gd@C82 under neutral conditions do not occur readily at room temperature because of the high energy barriers, whereas the H2O2 oxidations can readily proceed under alkaline conditions. The oxygen-containing groups of the fullerenols obtained under these conditions include hydroxyl, carbonyl, hemiacetal and deprotonated vic-diol. In contrast, through O2 oxidation under alkaline conditions, the most probable oxygen-containing groups for C60 fullerenols are epoxide and deprotonated vic-diol, and those for Gd@C60 and Gd@C82 fullerenols are hydroxyls and carbonyls. The results explain a wide range of experimental findings reported before. More importantly, they provide atomistic-level insights into the formation mechanisms and structures for various fullerenols, which are of fundamental interest for understanding their biomedical applications in the future.

Emerging structural insights into glycoprotein quality control coupled with N-glycan processing in the endoplasmic reticulum.

PubMed

Satoh, Tadashi; Yamaguchi, Takumi; Kato, Koichi

2015-01-30

In the endoplasmic reticulum (ER), the sugar chain is initially introduced onto newly synthesized proteins as a triantennary tetradecasaccharide (Glc3Man9GlcNAc2). The attached oligosaccharide chain is subjected to stepwise trimming by the actions of specific glucosidases and mannosidases. In these processes, the transiently expressed N-glycans, as processing intermediates, function as signals for the determination of glycoprotein fates, i.e., folding, transport, or degradation through interactions of a series of intracellular lectins. The monoglucosylated glycoforms are hallmarks of incompletely folded states of glycoproteins in this system, whereas the outer mannose trimming leads to ER-associated glycoprotein degradation. This review outlines the recently emerging evidence regarding the molecular and structural basis of this glycoprotein quality control system, which is regulated through dynamic interplay among intracellular lectins, glycosidases, and glycosyltransferase. Structural snapshots of carbohydrate-lectin interactions have been provided at the atomic level using X-ray crystallographic analyses. Conformational ensembles of uncomplexed triantennary high-mannose-type oligosaccharides have been characterized in a quantitative manner using molecular dynamics simulation in conjunction with nuclear magnetic resonance spectroscopy. These complementary views provide new insights into glycoprotein recognition in quality control coupled with N-glycan processing.

The evolution of insight, paranoia and depression during early schizophrenia.

PubMed

Drake, R J; Pickles, A; Bentall, R P; Kinderman, P; Haddock, G; Tarrier, N; Lewis, S W

2004-02-01

How insight, paranoia and depression evolve in relation to each other during and after the first episode of schizophrenia is poorly understood but of clinical importance. Serial assessments over 18 months were made using multiple instruments in a consecutive sample of 257 patients with first episode DSM-IV non-affective psychosis. Repeated measures of paranoia, insight, depression and self-esteem were analysed using structural equation modelling, to examine the direction of relationships over time after controlling for confounds. Depression was predicted directly by greater insight, particularly at baseline, and by greater paranoia at every stage of follow-up. Neither relationship was mediated by self-esteem, although there was a weak association of lower self-esteem with greater depression and better insight. Paranoia was not strongly associated with insight. Duration of untreated psychosis and substance use at baseline predicted depression at 18 months. In first-episode psychosis, good insight predicts depression. Subsequently, paranoia is the strongest predictor. Neither effect is mediated by low self-esteem. Effective treatment of positive symptoms is important in preventing and treating low mood in early schizophrenia.

Modeling the human Nav1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade

PubMed Central

Ahmed, Marawan; Jalily Hasani, Horia; Ganesan, Aravindhan; Houghton, Michael; Barakat, Khaled

2017-01-01

Abnormalities in the human Nav1.5 (hNav1.5) voltage-gated sodium ion channel (VGSC) are associated with a wide range of cardiac problems and diseases in humans. Current structural models of hNav1.5 are still far from complete and, consequently, their ability to study atomistic interactions of this channel is very limited. Here, we report a comprehensive atomistic model of the hNav1.5 ion channel, constructed using homology modeling technique and refined through long molecular dynamics simulations (680 ns) in the lipid membrane bilayer. Our model was comprehensively validated by using reported mutagenesis data, comparisons with previous models, and binding to a panel of known hNav1.5 blockers. The relatively long classical MD simulation was sufficient to observe a natural sodium permeation event across the channel’s selectivity filters to reach the channel’s central cavity, together with the identification of a unique role of the lysine residue. Electrostatic potential calculations revealed the existence of two potential binding sites for the sodium ion at the outer selectivity filters. To obtain further mechanistic insight into the permeation event from the central cavity to the intracellular region of the channel, we further employed “state-of-the-art” steered molecular dynamics (SMD) simulations. Our SMD simulations revealed two different pathways through which a sodium ion can be expelled from the channel. Further, the SMD simulations identified the key residues that are likely to control these processes. Finally, we discuss the potential binding modes of a panel of known hNav1.5 blockers to our structural model of hNav1.5. We believe that the data presented here will enhance our understanding of the structure–property relationships of the hNav1.5 ion channel and the underlying molecular mechanisms in sodium ion permeation and drug interactions. The results presented here could be useful for designing safer drugs that do not block the hNav1.5 channel

Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis.

PubMed

Houston, Simon; Lithgow, Karen Vivien; Osbak, Kara Krista; Kenyon, Chris Richard; Cameron, Caroline E

2018-05-16

Syphilis continues to be a major global health threat with 11 million new infections each year, and a global burden of 36 million cases. The causative agent of syphilis, Treponema pallidum subspecies pallidum, is a highly virulent bacterium, however the molecular mechanisms underlying T. pallidum pathogenesis remain to be definitively identified. This is due to the fact that T. pallidum is currently uncultivatable, inherently fragile and thus difficult to work with, and phylogenetically distinct with no conventional virulence factor homologs found in other pathogens. In fact, approximately 30% of its predicted protein-coding genes have no known orthologs or assigned functions. Here we employed a structural bioinformatics approach using Phyre2-based tertiary structure modeling to improve our understanding of T. pallidum protein function on a proteome-wide scale. Phyre2-based tertiary structure modeling generated high-confidence predictions for 80% of the T. pallidum proteome (780/978 predicted proteins). Tertiary structure modeling also inferred the same function as primary structure-based annotations from genome sequencing pipelines for 525/605 proteins (87%), which represents 54% (525/978) of all T. pallidum proteins. Of the 175 T. pallidum proteins modeled with high confidence that were not assigned functions in the previously annotated published proteome, 167 (95%) were able to be assigned predicted functions. Twenty-one of the 175 hypothetical proteins modeled with high confidence were also predicted to exhibit significant structural similarity with proteins experimentally confirmed to be required for virulence in other pathogens. Phyre2-based structural modeling is a powerful bioinformatics tool that has provided insight into the potential structure and function of the majority of T. pallidum proteins and helped validate the primary structure-based annotation of more than 50% of all T. pallidum proteins with high confidence. This work represents the first T

Structure of the 26S proteasome with ATP-γS bound provides insights into the mechanism of nucleotide-dependent substrate translocation

PubMed Central

Śledź, Paweł; Unverdorben, Pia; Beck, Florian; Pfeifer, Günter; Schweitzer, Andreas; Förster, Friedrich; Baumeister, Wolfgang

2013-01-01

The 26S proteasome is a 2.5-MDa, ATP-dependent multisubunit proteolytic complex that processively destroys proteins carrying a degradation signal. The proteasomal ATPase heterohexamer is a key module of the 19S regulatory particle; it unfolds substrates and translocates them into the 20S core particle where degradation takes place. We used cryoelectron microscopy single-particle analysis to obtain insights into the structural changes of 26S proteasome upon the binding and hydrolysis of ATP. The ATPase ring adopts at least two distinct helical staircase conformations dependent on the nucleotide state. The transition from the conformation observed in the presence of ATP to the predominant conformation in the presence of ATP-γS induces a sliding motion of the ATPase ring over the 20S core particle ring leading to an alignment of the translocation channels of the ATPase and the core particle gate, a conformational state likely to facilitate substrate translocation. Two types of intersubunit modules formed by the large ATPase domain of one ATPase subunit and the small ATPase domain of its neighbor exist. They resemble the contacts observed in the crystal structures of ClpX and proteasome-activating nucleotidase, respectively. The ClpX-like contacts are positioned consecutively and give rise to helical shape in the hexamer, whereas the proteasome-activating nucleotidase-like contact is required to close the ring. Conformational switching between these forms allows adopting different helical conformations in different nucleotide states. We postulate that ATP hydrolysis by the regulatory particle ATPase (Rpt) 5 subunit initiates a cascade of conformational changes, leading to pulling of the substrate, which is primarily executed by Rpt1, Rpt2, and Rpt6. PMID:23589842

Rate Constants for Fine-Structure Excitations in O - H Collisions with Error Bars Obtained by Machine Learning

NASA Astrophysics Data System (ADS)

Vieira, Daniel; Krems, Roman

2017-04-01

Fine-structure transitions in collisions of O(3Pj) with atomic hydrogen are an important cooling mechanism in the interstellar medium; knowledge of the rate coefficients for these transitions has a wide range of astrophysical applications. The accuracy of the theoretical calculation is limited by inaccuracy in the ab initio interaction potentials used in the coupled-channel quantum scattering calculations from which the rate coefficients can be obtained. In this work we use the latest ab initio results for the O(3Pj) + H interaction potentials to improve on previous calculations of the rate coefficients. We further present a machine-learning technique based on Gaussian Process regression to determine the sensitivity of the rate coefficients to variations of the underlying adiabatic interaction potentials. To account for the inaccuracy inherent in the ab initio calculations we compute error bars for the rate coefficients corresponding to 20% variation in each of the interaction potentials. We obtain these error bars by fitting a Gaussian Process model to a data set of potential curves and rate constants. We use the fitted model to do sensitivity analysis, determining the relative importance of individual adiabatic potential curves to a given fine-structure transition. NSERC.

Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei

PubMed Central

Lopez-Zavala, Alonso A.; Carrasco-Miranda, Jesus S.; Ramirez-Aguirre, Claudia D.; López-Hidalgo, Marisol; Benitez-Cardoza, Claudia G.; Ochoa-Leyva, Adrian; Cardona-Felix, Cesar S.; Diaz-Quezada, Corina; Rudiño-Piñera, Enrique; Sotelo-Mundo, Rogerio R.; Brieba, Luis G.

2016-01-01

Triosephosphate isomerase (TIM; EC 5.3.1.1) is a key enzyme involved in glycolysis and gluconeogenesis. Glycolysis is one of the most regulated metabolic pathways, however little is known about the structural mechanisms for its regulation in non-model organisms, like crustaceans. To understand the structure and function of this enzyme in invertebrates, we obtained the crystal structure of triosephosphate isomerase from the marine Pacific whiteleg shrimp (Litopenaeus vannamei, LvTIM) in complex with its inhibitor 2-phosphogyceric acid (2-PG) at 1.7 Å resolution. LvTIM assembles as a homodimer with residues 166-176 covering the active site and residue Glu166 interacting with the inhibitor. We found that LvTIM is the least stable TIM characterized to date, with the lowest range of melting temperatures, and with the lowest activation enthalpy associated with the thermal unfolding process reported. In TIMs dimer stabilization is maintained by an interaction of loop 3 by a set of hydrophobic contacts between subunits. Within these contacts, the side chain of a hydrophobic residue of one subunit fits into a cavity created by a set of hydrophobic residues in the neighboring subunit, via a "ball and socket" interaction. LvTIM presents a Cys47 at the "ball" inter-subunit contact indicating that the character of this residue is responsible for the decrease in dimer stability. Mutational studies show that this residue plays a role in dimer stability but is not a solely determinant for dimer formation. PMID:27614148

Crystal structure of chiral gammaPNA with complementary DNA strand: insights into the stability and specificity of recognition and conformational preorganization.

PubMed

Yeh, Joanne I; Shivachev, Boris; Rapireddy, Srinivas; Crawford, Matthew J; Gil, Roberto R; Du, Shoucheng; Madrid, Marcela; Ly, Danith H

2010-08-11

We have determined the structure of a PNA-DNA duplex to 1.7 A resolution by multiple-wavelength anomalous diffraction phasing method on a zinc derivative. This structure represents the first high-resolution 3D view of a hybrid duplex containing a contiguous chiral PNA strand with complete gamma-backbone modification ("gammaPNA"). Unlike the achiral counterpart, which adopts a random-fold, this particular gammaPNA is already preorganized into a right-handed helix as a single strand. The new structure illustrates the unique characteristics of this modified PNA, possessing conformational flexibility while maintaining sufficient structural integrity to ultimately adopt the preferred P-helical conformation upon hybridization with DNA. The unusual structural adaptability found in the gammaPNA strand is crucial for enabling the accommodation of backbone modifications while constraining conformational states. In conjunction with NMR analysis characterizing the structures and substructures of the individual building blocks, these results provide unprecedented insights into how this new class of chiral gammaPNA is preorganized and stabilized, before and after hybridization with a cDNA strand. Such knowledge is crucial for the future design and development of PNA for applications in biology, biotechnology, and medicine.

A study of poor insight in social anxiety disorder.

PubMed

Vigne, Paula; de Menezes, Gabriela B; Harrison, Ben J; Fontenelle, Leonardo F

2014-11-30

We investigated levels of insight among patients with Social Anxiety Disorder (SAD) as compared to patients with Obsessive-Compulsive Disorder (OCD) and evaluated whether levels of insight in SAD were related to specific sociodemographic and/or clinical features. Thirty-seven SAD patients and 51 OCD patients attending a tertiary obsessive-compulsive and anxiety disorders clinic were assessed with a sociodemographic and clinical questionnaire, a structured diagnostic interview, the Brown Assessment of Beliefs Scale (BABS), the Social Phobia Inventory (SPIN), the Beck Depression Inventory (BDI), the Sheehan Disability Scale (SDS), and the Treatment Adherence Survey-patient version (TAS-P). According to the BABS, SAD patients exhibited insight levels that were as low as those exhibited by OCD patients, with up to 29.7% of them being described as "poor insight" SAD. Although poor insight SAD patients were more frequently married, less depressed and displayed a statistical trend towards greater rates of early drop-out from cognitive-behavioral therapy, their insight levels were not associated with other variables of interest, including sex, age, employment, age at onset, duration of illness, associated psychiatric disorders, SPIN and SDS scores. Patients with poor insight SAD might perceive their symptoms as being less distressful and thus report fewer depressive symptoms and high rates of treatment non-adherence. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Genetic Population Structure in the Antarctic Benthos: Insights from the Widespread Amphipod, Orchomenella franklini

PubMed Central

Baird, Helena Phoenix; Miller, Karen Joy; Stark, Jonathan Sean

2012-01-01

Currently there is very limited understanding of genetic population structure in the Antarctic benthos. We conducted one of the first studies of microsatellite variation in an Antarctic benthic invertebrate, using the ubiquitous amphipod Orchomenella franklini (Walker, 1903). Seven microsatellite loci were used to assess genetic structure on three spatial scales: sites (100 s of metres), locations (1–10 kilometres) and regions (1000 s of kilometres) sampled in East Antarctica at Casey and Davis stations. Considerable genetic diversity was revealed, which varied between the two regions and also between polluted and unpolluted sites. Genetic differentiation among all populations was highly significant (F ST = 0.086, R ST = 0.139, p<0.001) consistent with the brooding mode of development in O. franklini. Hierarchical AMOVA revealed that the majority of the genetic subdivision occurred across the largest geographical scale, with Nem≈1 suggesting insufficient gene flow to prevent independent evolution of the two regions, i.e., Casey and Davis are effectively isolated. Isolation by distance was detected at smaller scales and indicates that gene flow in O. franklini occurs primarily through stepping-stone dispersal. Three of the microsatellite loci showed signs of selection, providing evidence that localised adaptation may occur within the Antarctic benthos. These results provide insights into processes of speciation in Antarctic brooders, and will help inform the design of spatial management initiatives recently endorsed for the Antarctic benthos. PMID:22479613

The structural flexibility of the human copper chaperone Atox1: Insights from combined pulsed EPR studies and computations.

PubMed

Levy, Ariel R; Turgeman, Meital; Gevorkyan-Aiapetov, Lada; Ruthstein, Sharon

2017-08-01

Metallochaperones are responsible for shuttling metal ions to target proteins. Thus, a metallochaperone's structure must be sufficiently flexible both to hold onto its ion while traversing the cytoplasm and to transfer the ion to or from a partner protein. Here, we sought to shed light on the structure of Atox1, a metallochaperone involved in the human copper regulation system. Atox1 shuttles copper ions from the main copper transporter, Ctr1, to the ATP7b transporter in the Golgi apparatus. Conventional biophysical tools such as X-ray or NMR cannot always target the various conformational states of metallochaperones, owing to a requirement for crystallography or low sensitivity and resolution. Electron paramagnetic resonance (EPR) spectroscopy has recently emerged as a powerful tool for resolving biological reactions and mechanisms in solution. When coupled with computational methods, EPR with site-directed spin labeling and nanoscale distance measurements can provide structural information on a protein or protein complex in solution. We use these methods to show that Atox1 can accommodate at least four different conformations in the apo state (unbound to copper), and two different conformations in the holo state (bound to copper). We also demonstrate that the structure of Atox1 in the holo form is more compact than in the apo form. Our data provide insight regarding the structural mechanisms through which Atox1 can fulfill its dual role of copper binding and transfer. © 2017 The Protein Society.

Correlation Between Chain Architecture and Hydration Water Structure in Polysaccharides.

PubMed

Grossutti, Michael; Dutcher, John R

2016-03-14

The physical properties of confined water can differ dramatically from those of bulk water. Hydration water associated with polysaccharides provides a particularly interesting example of confined water, because differences in polysaccharide structure provide different spatially confined environments for water sorption. We have used attenuated total reflection infrared (ATR-IR) spectroscopy to investigate the structure of hydration water in films of three different polysaccharides under controlled relative humidity (RH) conditions. We compare the results obtained for films of highly branched, dendrimer-like phytoglycogen nanoparticles to those obtained for two unbranched polysaccharides, hyaluronic acid (HA), and chitosan. We find similarities between the water structuring in the two linear polysaccharides and significant differences for phytoglycogen. In particular, the results suggest that the high degree of branching in phytoglycogen leads to a much more well-ordered water structure (low density, high connectivity network water), indicating the strong influence of chain architecture on the structuring of water. These measurements provide unique insight into the relationship between the structure and hydration of polysaccharides, which is important for understanding and exploiting these sustainable nanomaterials in a wide range of applications.

Correlation Between Chain Architecture and Hydration Water Structure in Polysaccharides

NASA Astrophysics Data System (ADS)

Grossutti, Michael; Dutcher, John

The physical properties of confined water can differ dramatically from those of bulk water. Hydration water associated with polysaccharides provides a particularly important example of confined water, with differences in polysaccharide structure providing different spatially confined environments for water adsorption. We have used attenuated total reflection infrared (ATR-IR) spectroscopy to investigate the structure of hydration water in films of three different polysaccharides under controlled relative humidity (RH) conditions. We compare the results obtained for films of highly branched, monodisperse phytoglycogen nanoparticles to those obtained for two unbranched polysaccharides, hyaluronic acid (HA) and chitosan. We find similarities between water structuring in the two linear polysaccharides, and significant differences for phytoglycogen. In particular, the phytoglycogen nanoparticles exhibited high network water connectivity, and a large increase in the fraction of multimer water clusters with increasing RH, whereas the water structure for HA and chitosan was found to be insensitive to changes in RH. These measurements provide unique insight into the relationship between the chain architecture and hydration of polysaccharides.

Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights

PubMed Central

Kumar, Amitha Sampath; Sowpati, Divya Tej; Mishra, Rakesh K.

2016-01-01

Microsatellites or simple sequence repeats (SSR) are abundant, highly diverse stretches of short DNA repeats present in all genomes. Tandem mono/tri/hexanucleotide repeats in the coding regions contribute to single amino acids repeats (SAARs) in the proteome. While SSRs in the coding region always result in amino acid repeats, a majority of SAARs arise due to a combination of various codons representing the same amino acid and not as a consequence of SSR events. Certain amino acids are abundant in repeat regions indicating a positive selection pressure behind the accumulation of SAARs. By analysing 22 proteomes including the human proteome, we explored the functional and structural relationship of amino acid repeats in an evolutionary context. Only ~15% of repeats are present in any known functional domain, while ~74% of repeats are present in the disordered regions, suggesting that SAARs add to the functionality of proteins by providing flexibility, stability and act as linker elements between domains. Comparison of SAAR containing proteins across species reveals that while shorter repeats are conserved among orthologs, proteins with longer repeats, >15 amino acids, are unique to the respective organism. Lysine repeats are well conserved among orthologs with respect to their length and number of occurrences in a protein. Other amino acids such as glutamic acid, proline, serine and alanine repeats are generally conserved among the orthologs with varying repeat lengths. These findings suggest that SAARs have accumulated in the proteome under positive selection pressure and that they provide flexibility for optimal folding of functional/structural domains of proteins. The insights gained from our observations can help in effective designing and engineering of proteins with novel features. PMID:27893794

Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function

DOE PAGES

Sun, Jingchuan; Li, Huilin; Fernandez-Cid, Alejandra; ...

2014-10-15

Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2–7 (minichromosome maintenance proteins 2–7) double hexamer. During S phase, each Mcm2–7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC–Cdc6 function to recruit a single Cdt1–Mcm2–7 heptamer to replication origins prior to Cdt1 release and ORC–Cdc6–Mcm2–7 complex formation, but how the second Mcm2–7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC–Cdc6–Mcm2–7 complex andmore » an ORC–Cdc6–Mcm2–7–Mcm2–7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2–7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2–7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability.« less

Do People Really Have Insights in the Shower? The When, Where and Who of the Aha! Moment

ERIC Educational Resources Information Center

Ovington, Linda A.; Saliba, Anthony J.; Moran, Carmen C.; Goldring, Jeremy; MacDonald, Jasmine B.

2018-01-01

While there are well-known anecdotes and documented insight cases by renowned scientists and inventors, little is known about the experiences of insight in the general population. The present study aimed to determine peoples' self-reported experience of insight in their daily lives. Using an online questionnaire, responses were obtained from 1,114…

Insights into the structure of covalently bound fatty acid monolayers on a simplified model of the hair epicuticle from molecular dynamics simulations.

PubMed

Cheong, Daniel W; Lim, Freda C H; Zhang, Liping

2012-09-11

The epicuticle is the outermost layer of the human hair, and consists of a monolayer of fatty acids that is predominantly 18-methyleicosanoic acid (18-MEA) covalently bound to a protein matrix. Surprisingly, despite the clear scientific and industrial importance, the detailed molecular structure of this fatty acid layer is still poorly understood. In this work, we aim to gain insight into the structure of this so-called F-layer by performing molecular dynamics simulations on a simplified hair surface model consisting of a monolayer of 18-MEA covalently attached to graphene sheets at various separation distances. The relative free energy of the fatty acid layer was calculated as a function of separation distance in order to obtain the optimal packing density of the fatty acids. Conformational properties such as the thickness, tilt angle, and order parameter of the fatty acid layers were also calculated to characterize the structure of the F-layer. Simulations of the structurally similar eicosanoic acid (EA) were also performed as a comparison and to investigate the role of the anteiso-methyl side chain at the 18th position of 18-MEA. The degree of water penetration into the fatty acid layer at the various separation distances was also investigated. Our simulations suggest that the optimal spacing for the fatty acids is between 0.492 and 0.651 nm, in contrast to the generally accepted literature value of around 0.9-1.0 nm. This results in a packing density of between 0.21 and 0.37 nm(2) per fatty acid molecule and a thickness of around 2.01-2.64 nm. We also show that, at larger separation distances, the 18-MEA fatty acid provides a slightly better hydrophobic layer than the EA fatty acid, suggesting that the 18-MEA fatty acid may have been naturally selected to provide better protection for the hair when it loses some of the fatty acids due to daily wear and tear. To our knowledge, this is the first attempt to systematically investigate the hair surface structure and

Fractal analysis and its impact factors on pore structure of artificial cores based on the images obtained using magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Wang, Heming; Liu, Yu; Song, Yongchen; Zhao, Yuechao; Zhao, Jiafei; Wang, Dayong

2012-11-01

Pore structure is one of important factors affecting the properties of porous media, but it is difficult to describe the complexity of pore structure exactly. Fractal theory is an effective and available method for quantifying the complex and irregular pore structure. In this paper, the fractal dimension calculated by box-counting method based on fractal theory was applied to characterize the pore structure of artificial cores. The microstructure or pore distribution in the porous material was obtained using the nuclear magnetic resonance imaging (MRI). Three classical fractals and one sand packed bed model were selected as the experimental material to investigate the influence of box sizes, threshold value, and the image resolution when performing fractal analysis. To avoid the influence of box sizes, a sequence of divisors of the image was proposed and compared with other two algorithms (geometric sequence and arithmetic sequence) with its performance of partitioning the image completely and bringing the least fitted error. Threshold value selected manually and automatically showed that it plays an important role during the image binary processing and the minimum-error method can be used to obtain an appropriate or reasonable one. Images obtained under different pixel matrices in MRI were used to analyze the influence of image resolution. Higher image resolution can detect more quantity of pore structure and increase its irregularity. With benefits of those influence factors, fractal analysis on four kinds of artificial cores showed the fractal dimension can be used to distinguish the different kinds of artificial cores and the relationship between fractal dimension and porosity or permeability can be expressed by the model of D = a - bln(x + c).

IR investigation on silicon oxycarbide structure obtained from precursors with 1:1 silicon to carbon atoms ratio and various carbon atoms distribution

NASA Astrophysics Data System (ADS)

Niemiec, Wiktor; Szczygieł, Przemysław; Jeleń, Piotr; Handke, Mirosław

2018-07-01

Silicon oxycarbide is a material with a number of advantageous properties that strongly depend on its structure. The most common approach to its tailoring is based on varying the silicon to carbon atoms ratio in the preceramic polymeric precursor. This work is the first comparison of the materials obtained from precursors with the same Si to C atoms ratio, but with various distribution of these atoms in the preceramic polymer. In addition to standard mixtures of monomers containing single silicon atom, a number of monomers with high molar masses and well defined structure was used. The IR was used to investigate the structure of the precursors and materials obtained after their annealing in 800 °C. The results show, that not only the distribution of carbon containing groups among the monomers is important, but also the (in)ability of these groups to end up in each other vicinity in the precursor as well as the degree of condensation of each structural unit.

Structure and characteristics of functional powder composite materials obtained by spark plasma sintering

NASA Astrophysics Data System (ADS)

Oglezneva, S. A.; Kachenyuk, M. N.; Kulmeteva, V. B.; Ogleznev, N. B.

2017-07-01

The article describes the results of spark plasma sintering of ceramic materials based on titanium carbide, titanium carbosilicide, ceramic composite materials based on zirconium oxide, strengthened by carbon nanostructures and composite materials of electrotechnical purpose based on copper with addition of carbon structures and titanium carbosilicide. The research shows that the spark plasma sintering can achieve relative density of the material up to 98%. The effect of sintering temperature on the phase composition, density and porosity of the final product has been studied. It was found that with addition of carbon nanostructures the relative density and hardness decrease, but the fracture strength of ZrO2 increases up to times 2. The relative erosion resistance of the electrodes made of composite copper-based powder materials, obtained by spark plasma sintering during electroerosion treatment of tool steel exceeds that parameter of pure copper up to times 15.

Development of the insight scale for affective disorders (ISAD): modification from the scale to assess unawareness of mental disorder.

PubMed

Olaya, Beatriz; Marsà, Ferran; Ochoa, Susana; Balanzá-Martínez, Vicent; Barbeito, Sara; García-Portilla, Mari Paz; González-Pinto, Ana; Lobo, Antonio; López-Antón, Raúl; Usall, Judith; Arranz, Belén; Haro, Josep Maria

2012-12-15

Research on insight in patients with mood disorders has grown in recent years. Several instruments to assess insight have been used, but most of them have been specifically designed for psychosis and may not appear relevant to mood disorders. The aim of the present study is to develop a short, multidimensional, reliable and valid scale to measure insight in patients with mood disorders, based on the Amador's Scale to Assess Unawareness of Mental Disorders (SUMD). A Delphi method was used to facilitate expert participation and ensure face and content validity. The SUMD structure and items were used as a reference in the scale development. A new scale with 17 items was obtained. Internal consistency, test-retest and inter-rater reliability and validity were studied in a sample of 76 outpatients with a DSM-IV diagnosis of major depression or bipolar disorder (type I or II). Internal consistency of the general items was moderate, and high for the symptoms awareness subscale. Scores on ISAD correlated with other measures of insight and with some clinical measures, thus supporting its validity. The majority of the sample came from community services. Future studies should use inpatients or patients with severe symptoms to broaden the range of responses. Moreover, the rating of insight and other measures by the same clinician might introduce a methodological bias. The ISAD, with a multidimensional approach, appears as a short, reliable and valid measure of insight in mood disorders. Expert consensus ensures its face and content validity. Copyright © 2012 Elsevier B.V. All rights reserved.

Effect of structural distortion on the electronic band structure of NaOsO3 studied within density functional theory and a three-orbital model

NASA Astrophysics Data System (ADS)

Mohapatra, Shubhajyoti; Bhandari, Churna; Satpathy, Sashi; Singh, Avinash

2018-04-01

Effects of the structural distortion associated with the OsO6 octahedral rotation and tilting on the electronic band structure and magnetic anisotropy energy for the 5 d3 compound NaOsO3 are investigated using the density functional theory (DFT) and within a three-orbital model. Comparison of the essential features of the DFT band structures with the three-orbital model for both the undistorted and distorted structures provides insight into the orbital and directional asymmetry in the electron hopping terms resulting from the structural distortion. The orbital mixing terms obtained in the transformed hopping Hamiltonian resulting from the octahedral rotations are shown to account for the fine features in the DFT band structure. Staggered magnetization and the magnetic character of states near the Fermi energy indicate weak coupling behavior.

Structural Insights into the Functional Role of the Hcn Sub-domain of the Receptor-Binding Domain of the Botulinum Neurotoxin Mosaic Serotype C/D

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

Zhang, Yanfeng; Gardberg, Anna; Edwards, Tom E.

Botulinum neurotoxin (BoNT), the causative agent of the deadly neuroparalytic disease botulism, is the most poisonous protein known for humans. Produced by different strains of the anaerobic bacterium Clostridium botulinum, BoNT effects cellular intoxication via a multistep mechanism executed by the three modules of the activated protein. Endocytosis, the first step of cellular intoxication, is triggered by the ~50 kDa, heavy-chain receptor-binding module (HCR) that is specific for a ganglioside and a protein receptor on neuronal cell surfaces. This dual receptor recognition mechanism between BoNT and the host cell’s membrane is well documented and occurs via specific intermolecular interactions withmore » the C-terminal sub-domain, Hcc, of BoNT-HCR. The N-terminal sub-domain of BoNT-HCR, Hcn, comprises ~50% of BoNT-HCR and adopts a B-sheet jelly roll fold. While suspected in assisting cell surface recognition, no unambiguous function for the Hcn sub-domain in BoNT has been indentified. To obtain insights into the potential function of the Hcn sub-domain in BoNT, the first crystal structure of a BoNT with an organic ligand bound to the Hcn sub-domain has been obtained. Here, we describe the crystal structure of BoNT/CD-HCR determined at 1.70 Å resolution with a tetraethylene glycol (PG4) molecule bound in an hydrophobic cleft between B-strands in the B-sheet jelly fold roll of the Hcn sub-domain. The molecule is completely engulfed in the cleft, making numerous hydrophobic (Y932, S959, W966, and D1042) and hydrophilic (S935, W977, L979, N1013, and I1066) contacts with the protein’s side chain and backbone that may mimic in vivo interactions with the phospholipid membranes on neuronal cell surfaces. A sulfate ion was also observed bound to residues T1176, D1177, K1196, and R1243 in the Hcc sub-domain of BoNT/CD-HCR. In the crystal structure of a similar protein, BoNT/D-HCR, a sialic acid« less

Obtaining source current density related to irregularly structured electromagnetic target field inside human body using hybrid inverse/FDTD method.

PubMed

Han, Jijun; Yang, Deqiang; Sun, Houjun; Xin, Sherman Xuegang

2017-01-01

Inverse method is inherently suitable for calculating the distribution of source current density related with an irregularly structured electromagnetic target field. However, the present form of inverse method cannot calculate complex field-tissue interactions. A novel hybrid inverse/finite-difference time domain (FDTD) method that can calculate the complex field-tissue interactions for the inverse design of source current density related with an irregularly structured electromagnetic target field is proposed. A Huygens' equivalent surface is established as a bridge to combine the inverse and FDTD method. Distribution of the radiofrequency (RF) magnetic field on the Huygens' equivalent surface is obtained using the FDTD method by considering the complex field-tissue interactions within the human body model. The obtained magnetic field distributed on the Huygens' equivalent surface is regarded as the next target. The current density on the designated source surface is derived using the inverse method. The homogeneity of target magnetic field and specific energy absorption rate are calculated to verify the proposed method.

Structure of Pneumococcal Peptidoglycan Hydrolase LytB Reveals Insights into the Bacterial Cell Wall Remodeling and Pathogenesis*

PubMed Central

Bai, Xiao-Hui; Chen, Hui-Jie; Jiang, Yong-Liang; Wen, Zhensong; Huang, Yubin; Cheng, Wang; Li, Qiong; Qi, Lei; Zhang, Jing-Ren; Chen, Yuxing; Zhou, Cong-Zhao

2014-01-01

Streptococcus pneumoniae causes a series of devastating infections in humans. Previous studies have shown that the endo-β-N-acetylglucosaminidase LytB is critical for pneumococcal cell division and nasal colonization, but the biochemical mechanism of LytB action remains unknown. Here we report the 1.65 Å crystal structure of the catalytic domain (residues Lys-375–Asp-658) of LytB (termed LytBCAT), excluding the choline binding domain. LytBCAT consists of three structurally independent modules: SH3b, WW, and GH73. These modules form a “T-shaped” pocket that accommodates a putative tetrasaccharide-pentapeptide substrate of peptidoglycan. Structural comparison and simulation revealed that the GH73 module of LytB harbors the active site, including the catalytic residue Glu-564. In vitro assays of hydrolytic activity indicated that LytB prefers the peptidoglycan from the lytB-deficient pneumococci, suggesting the existence of a specific substrate of LytB in the immature peptidoglycan. Combined with in vitro cell-dispersing and in vivo cell separation assays, we demonstrated that all three modules are necessary for the optimal activity of LytB. Further functional analysis showed that the full catalytic activity of LytB is required for pneumococcal adhesion to and invasion into human lung epithelial cells. Structure-based alignment indicated that the unique modular organization of LytB is highly conserved in its orthologs from Streptococcus mitis group and Gemella species. These findings provided structural insights into the pneumococcal cell wall remodeling and novel hints for the rational design of therapeutic agents against pneumococcal growth and thereby the related diseases. PMID:25002590

Crystal Structures of the β2-Adrenergic Receptor

NASA Astrophysics Data System (ADS)

Weis, William I.; Rosenbaum, Daniel M.; Rasmussen, Søren G. F.; Choi, Hee-Jung; Thian, Foon Sun; Kobilka, Tong Sun; Yao, Xiao-Jie; Day, Peter W.; Parnot, Charles; Fung, Juan J.; Ratnala, Venkata R. P.; Kobilka, Brian K.; Cherezov, Vadim; Hanson, Michael A.; Kuhn, Peter; Stevens, Raymond C.; Edwards, Patricia C.; Schertler, Gebhard F. X.; Burghammer, Manfred; Sanishvili, Ruslan; Fischetti, Robert F.; Masood, Asna; Rohrer, Daniel K.

G protein coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome, and are responsible for the majority of signal transduction events involving hormones and neuro-transmitters across the cell membrane. GPCRs that bind to diffusible ligands have low natural abundance, are relatively unstable in detergents, and display basal G protein activation even in the absence of ligands. To overcome these problems two approaches were taken to obtain crystal structures of the β2-adrenergic receptor (β2AR), a well-characterized GPCR that binds cate-cholamine hormones. The receptor was bound to the partial inverse agonist carazolol and co-crystallized with a Fab made to a three-dimensional epitope formed by the third intracellular loop (ICL3), or by replacement of ICL3 with T4 lysozyme. Small crystals were obtained in lipid bicelles (β2AR-Fab) or lipidic cubic phase (β2AR-T4 lysozyme), and diffraction data were obtained using microfocus technology. The structures provide insights into the basal activity of the receptor, the structural features that enable binding of diffusible ligands, and the coupling between ligand binding and G-protein activation.

Structuration of lipid bases with fully hydrogenated crambe oil and sorbitan monostearate for obtaining zero-trans/low sat fats.

PubMed

Stahl, Marcella Aparecida; Buscato, Monise Helen Masuchi; Grimaldi, Renato; Cardoso, Lisandro Pavie; Ribeiro, Ana Paula Badan

2018-05-01

Several studies have shown that excessive intake of trans and saturated fatty acids is associated with an increased risk of cardiovascular disease. In this context, the food industry has sought alternatives for the development of healthy lipid bases, with higher levels of unsaturated fatty acids, adapting to current legislation. The incorporation of structuring agents into liquid oils has proven to be a potential alternative for obtaining semi-plastic lipid bases with reduced levels of saturated fatty acids. Thus, the objective of this study was to produce zero trans fat bases with lower saturated fatty acids levels. Palm oil (PO) was used as a zero trans-lipid base reference because of its technological functionality. Blends containing different proportions of high oleic sunflower oil (HOSO) and PO were prepared as follows: control 100: 0; 80:20; 60:40; 40:60; 20:80; and 100: 0 PO: HOSO (w/w%), respectively. Then, 3% of fully hydrogenated crambe oil (FHCO) and 3% sorbitan monostearate (SMS) were added to the blends as structuring agents, forming the structured (S) blends. The addition of HOSO to the PO decreased the saturated fatty acids by up to 30.6%, with consequent increase of unsaturated fatty acids, especially oleic acid. The joint action of the SMS and the FCHO allowed for obtaining structured blends with plastic and spreadability characteristics, as well as modifications throughout the crystallization process of the original blends. Copyright © 2018 Elsevier Ltd. All rights reserved.

Insights into RNA binding by the anticancer drug cisplatin from the crystal structure of cisplatin-modified ribosome

PubMed Central

Melnikov, Sergey V.; Söll, Dieter; Steitz, Thomas A.

2016-01-01

Abstract Cisplatin is a widely prescribed anticancer drug, which triggers cell death by covalent binding to a broad range of biological molecules. Among cisplatin targets, cellular RNAs remain the most poorly characterized molecules. Although cisplatin was shown to inactivate essential RNAs, including ribosomal, spliceosomal and telomeric RNAs, cisplatin binding sites in most RNA molecules are unknown, and therefore it remains challenging to study how modifications of RNA by cisplatin contributes to its toxicity. Here we report a 2.6Å-resolution X-ray structure of cisplatin-modified 70S ribosome, which describes cisplatin binding to the ribosome and provides the first nearly atomic model of cisplatin–RNA complex. We observe nine cisplatin molecules bound to the ribosome and reveal consensus structural features of the cisplatin-binding sites. Two of the cisplatin molecules modify conserved functional centers of the ribosome—the mRNA-channel and the GTPase center. In the mRNA-channel, cisplatin intercalates between the ribosome and the messenger RNA, suggesting that the observed inhibition of protein synthesis by cisplatin is caused by impaired mRNA-translocation. Our structure provides an insight into RNA targeting and inhibition by cisplatin, which can help predict cisplatin-binding sites in other cellular RNAs and design studies to elucidate a link between RNA modifications by cisplatin and cisplatin toxicity. PMID:27079977

Small-angle X-Ray analysis of macromolecular structure: the structure of protein NS2 (NEP) in solution

NASA Astrophysics Data System (ADS)

Shtykova, E. V.; Bogacheva, E. N.; Dadinova, L. A.; Jeffries, C. M.; Fedorova, N. V.; Golovko, A. O.; Baratova, L. A.; Batishchev, O. V.

2017-11-01

A complex structural analysis of nuclear export protein NS2 (NEP) of influenza virus A has been performed using bioinformatics predictive methods and small-angle X-ray scattering data. The behavior of NEP molecules in a solution (their aggregation, oligomerization, and dissociation, depending on the buffer composition) has been investigated. It was shown that stable associates are formed even in a conventional aqueous salt solution at physiological pH value. For the first time we have managed to get NEP dimers in solution, to analyze their structure, and to compare the models obtained using the method of the molecular tectonics with the spatial protein structure predicted by us using the bioinformatics methods. The results of the study provide a new insight into the structural features of nuclear export protein NS2 (NEP) of the influenza virus A, which is very important for viral infection development.

Insights into nuclear dynamics using live-cell imaging approaches.

PubMed

Bigley, Rachel B; Payumo, Alexander Y; Alexander, Jeffrey M; Huang, Guo N

2017-03-01

The nucleus contains the genetic blueprint of the cell and myriad interactions within this subcellular structure are required for gene regulation. In the current scientific era, characterization of these gene regulatory networks through biochemical techniques coupled with systems-wide 'omic' approaches has become commonplace. However, these strategies are limited because they represent a mere snapshot of the cellular state. To obtain a holistic understanding of nuclear dynamics, relevant molecules must be studied in their native contexts in living systems. Live-cell imaging approaches are capable of providing quantitative assessment of the dynamics of gene regulatory interactions within the nucleus. We survey recent insights into what live-cell imaging approaches have provided the field of nuclear dynamics. In this review, we focus on interactions of DNA with other DNA loci, proteins, RNA, and the nuclear envelope. WIREs Syst Biol Med 2017, 9:e1372. doi: 10.1002/wsbm.1372 For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.

Unraveling interrelationships among psychopathology symptoms, cognitive domains and insight dimensions in chronic schizophrenia.

PubMed

Xavier, Rose Mary; Pan, Wei; Dungan, Jennifer R; Keefe, Richard S E; Vorderstrasse, Allison

2018-03-01

Insight in schizophrenia is long known to have a complex relationship with psychopathology symptoms and cognition. However, very few studies have examined models that explain these interrelationships. In a large sample derived from the NIMH Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) schizophrenia trial (N=1391), we interrogated these interrelationships for potential causal pathways using structural equation modeling. Using the NIMH consensus model, latent variables were constructed for psychopathology symptom dimensions, including positive, negative, disorganized, excited and depressed from the Positive and Negative Syndrome Scale (PANSS) items. Neurocognitive variables were created from five predefined domains of working memory, verbal memory, reasoning, vigilance and processing speed. Illness insight and treatment insight were tested using latent variables constructed from the Illness and Treatment Attitude Questionnaire (ITAQ). Disorganized symptoms had the strongest effect on insight. Illness insight mediated the relationship of positive, depressed, and disorganized symptoms with treatment insight. Neurocognition mediated the relationship between disorganized and treatment insight and depressed symptoms and treatment insight. There was no effect of negative symptoms on either illness insight or treatment insight. Taken together, our results indicate overlapping and unique relational paths for illness and treatment insight dimensions, which could suggest differences in causal mechanisms and potential interventions to improve insight. Copyright © 2017 Elsevier B.V. All rights reserved.

On the temporality of creative insight: a psychological and phenomenological perspective

PubMed Central

Cosmelli, Diego; Preiss, David D.

2014-01-01

Research into creative insight has had a strong emphasis on the psychological processes underlying problem-solving situations as a standard model for the empirical study of this phenomenon. Although this model has produced significant advances in our scientific understanding of the nature of insight, we believe that a full comprehension of insight requires complementing cognitive and neuroscientific studies with a descriptive, first-person, phenomenological approach into how creative insight is experienced. Here we propose to take such first-person perspective while paying special attention to the temporal aspects of this experience. When this first-person perspective is taken into account, a dynamic past–future interplay can be identified at the core of the experience of creative insight, a structure that is compatible with both biological and biographical evidences. We believe this approach could complement and help bring together biological and psychological perspectives. Furthermore, we argue that because of its spontaneous but recurrent nature, creative insight could represent a relevant target for the phenomenological investigation of the flow of experience itself. PMID:25368595

Homogenization models for thin rigid structured surfaces and films.

PubMed

Marigo, Jean-Jacques; Maurel, Agnès

2016-07-01

A homogenization method for thin microstructured surfaces and films is presented. In both cases, sound hard materials are considered, associated with Neumann boundary conditions and the wave equation in the time domain is examined. For a structured surface, a boundary condition is obtained on an equivalent flat wall, which links the acoustic velocity to its normal and tangential derivatives (of the Myers type). For a structured film, jump conditions are obtained for the acoustic pressure and the normal velocity across an equivalent interface (of the Ventcels type). This interface homogenization is based on a matched asymptotic expansion technique, and differs slightly from the classical homogenization, which is known to fail for small structuration thicknesses. In order to get insight into what causes this failure, a two-step homogenization is proposed, mixing classical homogenization and matched asymptotic expansion. Results of the two homogenizations are analyzed in light of the associated elementary problems, which correspond to problems of fluid mechanics, namely, potential flows around rigid obstacles.

Association between insight, cognitive insight, positive symptoms and violence in patients with schizophrenia.

PubMed

Ekinci, Okan; Ekinci, Asli

2013-04-01

Violence is a significant clinical and public concern and is a frequent occurrence in patients with schizophrenia. The relationship between insight and violence remains controversial. In addition, there is a lack of research on insight, cognitive insight, demographic and psychopathologic variables in violent versus nonviolent schizophrenia patients. We aimed to compare insight, cognitive insight, psychopathological and demographic variables in violent and nonviolent subjects suffering from schizophrenia. In addition, we aimed to determine the demographic and clinical predictors of violent behaviour in patients with schizophrenia. We recruited 133 schizophrenic patients without concomitant substance abuse or axis II disorder. Diagnoses were based on the SCID-I and SCID-II. Violent behaviours were assessed using the Overt Aggression Scale. Insight and cognitive insight were assessed with the Scale to Assess Unawareness of Mental Disorder and the Beck Cognitive Insight Scale, respectively. We compared 47 patients with violent schizophrenia with 86 nonviolent patients. Non-violent patients had more severe depression, lower scores on positive symptoms, better clinical insight, more self-reflectivity and higher R-C index scores than did violent patients. In addition, history of violence, lower self-reflectiveness, worse clinical insight and delusion severity were significant predictors of violence in schizophrenia. The present study suggests that the inclusion of insight and cognitive insight may increase the prediction of violence in this population. In addition, clinicians should consider using non-pharmacological techniques that are based on cognitive behaviour therapy and enhance insight, particularly cognitive insight, among patients with schizophrenia who exhibit violent behaviour.

The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation

PubMed Central

Mueller-Dieckmann, Christoph; Kernstock, Stefan; Lisurek, Michael; von Kries, Jens Peter; Haag, Friedrich; Weiss, Manfred S.; Koch-Nolte, Friedrich

2006-01-01

Posttranslational modifications are used by cells from all kingdoms of life to control enzymatic activity and to regulate protein function. For many cellular processes, including DNA repair, spindle function, and apoptosis, reversible mono- and polyADP-ribosylation constitutes a very important regulatory mechanism. Moreover, many pathogenic bacteria secrete toxins which ADP-ribosylate human proteins, causing diseases such as whooping cough, cholera, and diphtheria. Whereas the 3D structures of numerous ADP-ribosylating toxins and related mammalian enzymes have been elucidated, virtually nothing is known about the structure of protein de-ADP-ribosylating enzymes. Here, we report the 3Dstructure of human ADP-ribosylhydrolase 3 (hARH3). The molecular architecture of hARH3 constitutes the archetype of an all-α-helical protein fold and provides insights into the reversibility of protein ADP-ribosylation. Two magnesium ions flanked by highly conserved amino acids pinpoint the active-site crevice. Recombinant hARH3 binds free ADP-ribose with micromolar affinity and efficiently de-ADP-ribosylates poly- but not monoADP-ribosylated proteins. Docking experiments indicate a possible binding mode for ADP-ribose polymers and suggest a reaction mechanism. Our results underscore the importance of endogenous ADP-ribosylation cycles and provide a basis for structure-based design of ADP-ribosylhydrolase inhibitors. PMID:17015823

Structural Insights into the Affinity of Cel7A Carbohydrate-binding Module for Lignin*

PubMed Central

Strobel, Kathryn L.; Pfeiffer, Katherine A.; Blanch, Harvey W.; Clark, Douglas S.

2015-01-01

The high cost of hydrolytic enzymes impedes the commercial production of lignocellulosic biofuels. High enzyme loadings are required in part due to their non-productive adsorption to lignin, a major component of biomass. Despite numerous studies documenting cellulase adsorption to lignin, few attempts have been made to engineer enzymes to reduce lignin binding. In this work, we used alanine-scanning mutagenesis to elucidate the structural basis for the lignin affinity of Trichoderma reesei Cel7A carbohydrate binding module (CBM). T. reesei Cel7A CBM mutants were produced with a Talaromyces emersonii Cel7A catalytic domain and screened for their binding to cellulose and lignin. Mutation of aromatic and polar residues on the planar face of the CBM greatly decreased binding to both cellulose and lignin, supporting the hypothesis that the cellulose-binding face is also responsible for lignin affinity. Cellulose and lignin affinity of the 31 mutants were highly correlated, although several mutants displayed selective reductions in lignin or cellulose affinity. Four mutants with increased cellulose selectivity (Q2A, H4A, V18A, and P30A) did not exhibit improved hydrolysis of cellulose in the presence of lignin. Further reduction in lignin affinity while maintaining a high level of cellulose affinity is thus necessary to generate an enzyme with improved hydrolysis capability. This work provides insights into the structural underpinnings of lignin affinity, identifies residues amenable to mutation without compromising cellulose affinity, and informs engineering strategies for family one CBMs. PMID:26209638

Structure-activity relationships of diphenyl-ether as protoporphyrinogen oxidase inhibitors: insights from computational simulations

NASA Astrophysics Data System (ADS)

Hao, Ge-Fei; Tan, Ying; Yu, Ning-Xi; Yang, Guang-Fu

2011-03-01

Protoporphyrinogen oxidase (PPO, EC 1.3.3.4), which has been identified as a significant target for a great family of herbicides with diverse chemical structures, is the last common enzyme responsible for the seventh step in the biosynthetic pathway to heme and chlorophyll. Among the existing PPO inhibitors, diphenyl-ether is the first commercial family of PPO inhibitors and used as agriculture herbicides for decades. Most importantly, diphenyl-ether inhibitors have been found recently to possess the potential in Photodynamic therapy (PDT) to treat cancer. Herein, molecular dynamics simulations, approximate free energy calculations and hydrogen bond energy calculations were integrated together to uncover the structure-activity relationships of this type of PPO inhibitors. The calculated binding free energies are correlated very well with the values derived from the experimental k i data. According to the established computational models and the results of approximate free energy calculation, the substitution effects at different position were rationalized from the view of binding free energy. Some outlier ( e.g. LS) in traditional QSAR study can also be explained reasonably. In addition, the hydrogen bond energy calculation and interaction analysis results indicated that the carbonyl oxygen on position-9 and the NO2 group at position-8 are both vital for the electrostatic interaction with Arg98, which made a great contribution to the binding free energy. These insights from computational simulations are not only helpful for understanding the molecular mechanism of PPO-inhibitor interactions, but also beneficial to the future rational design of novel promising PPO inhibitors.

Insights into Hsp70 Chaperone Activity from a Crystal Structure of the Yeast Hsp110 Sse1

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

Liu,Q.; Hendrickson, W.

2007-01-01

Classic Hsp70 chaperones assist in diverse processes of protein folding and translocation, and Hsp110s had seemed by sequence to be distant relatives within an Hsp70 superfamily. The 2.4 Angstroms resolution structure of Sse1 with ATP shows that Hsp110s are indeed Hsp70 relatives, and it provides insight into allosteric coupling between sites for ATP and polypeptide-substrate binding in Hsp70s. Subdomain structures are similar in intact Sse1(ATP) and in the separate Hsp70 domains, but conformational dispositions are radically different. Interfaces between Sse1 domains are extensive, intimate, and conservative in sequence with Hsp70s. We propose that Sse1(ATP) may be an evolutionary vestige ofmore » the Hsp70(ATP) state, and an analysis of 64 mutant variants in Sse1 and three Hsp70 homologs supports this hypothesis. An atomic-level understanding of Hsp70 communication between ATP and substrate-binding domains follows. Requirements on Sse1 for yeast viability are in keeping with the distinct function of Hsp110s as nucleotide exchange factors.« less

[Insight in schizophrenia: relationship to family history, and positive and negative symptoms].

PubMed

Danki, Demet; Dilbaz, Nesrin; Okay, Ihsan Tuncer; Telci, Sükran

2007-01-01

To determine the level of insight among patients with schizophrenia and to compare sociodemographic and clinical features. The study included 66 patients with schizophrenia based on DSM-IV criteria. A semi-structured sociodemographic instrument, the Positive and Negative Syndrome Scale (PANSS), and the Schedule for Assessing the Three Components of Insight (SATCI) were used for the study. Family history was significantly related to low-level insight in schizophrenic patients. Positive symptom scores in patients with a family history of schizophrenia were significantly higher than in patients without such a family history. Positive and general psychopathological symptoms were inversely related to level of insight in patients with schizophrenia. There was no significant relationship between the negative symptoms scores and level of insight. Family history of schizophrenia in schizophrenic patients was significantly related to low-level insight. Insight in the schizophrenic patients was affected by biological, psychological, and psychosociological factors. Family history of schizophrenia was one of these factors, which may affect the level of insight in numerous ways. Studies of patient family position and its relationship to insight have generally explored the effects of family situation on schizophrenia and insight, but not family history and its relationship to insight. In this study positive symptom severity was higher in patients with a family history of schizophrenia than in those without such a history. There was a positive relationship between low-level insight and both high positive and general psychopathology symptom levels in patients with schizophrenia.

Kohler's Insight Revisited.

ERIC Educational Resources Information Center

Windholtz, George

1985-01-01

Psychology textbooks frequently present Wolfgang Kohler's two-stick experiment with chimpanzees as having demonstrated insight in learning. Studies that replicated Kohler's work support his findings but not his interpretation in terms of insightful solution. The uncritical inclusion of Kohler's insight interpretation in texts is not warranted in…

Structural Color Tuning: Mixing Melanin-Like Particles with Different Diameters to Create Neutral Colors.

PubMed

Kawamura, Ayaka; Kohri, Michinari; Yoshioka, Shinya; Taniguchi, Tatsuo; Kishikawa, Keiki

2017-04-18

We present the ability to tune structural colors by mixing colloidal particles. To produce high-visibility structural colors, melanin-like core-shell particles composed of a polystyrene (PSt) core and a polydopamine (PDA) shell, were used as components. The results indicated that neutral structural colors could be successfully obtained by simply mixing two differently sized melanin-like PSt@PDA core-shell particles. In addition, the arrangements of the particles, which were important factors when forming structural colors, were investigated by mathematical processing using a 2D Fourier transform technique and Voronoi diagrams. These findings provide new insights for the development of structural color-based ink applications.

Structural Insight into the Assembly of TRPV Channels

PubMed Central

Huynh, Kevin W.; Cohen, Matthew R.; Chakrapani, Sudha; Holdaway, Heather A.; Stewart, Phoebe L.; Moiseenkova-Bell, Vera Y.

2017-01-01

SUMMARY Transient receptor potential (TRP) proteins are a large family of polymodal nonselective cation channels. The TRP vanilloid (TRPV) subfamily consists of six homologous members with diverse functions. TRPV1–TRPV4 are nonselective cation channels proposed to play a role in nociception, while TRPV5 and TRPV6 are involved in epithelial Ca2+ homeostasis. Here we present the cryo-electron microscopy (cryo-EM) structure of functional, full-length TRPV2 at 13.6 Å resolution. The map reveals that the TRPV2 cytoplasmic domain displays a 4-fold petal-like shape in which high-resolution N-terminal ankyrin repeat domain (ARD) structures can be unambiguously fitted. Fitting of the available ARD structures for other TRPV subfamily members into the TRPV2 EM map suggests that TRPV subfamily members have highly homologous structural topologies. These results allowed us to postulate a structural explanation for the functional diversity among TRPV channels and their differential regulation by proteins and ligands. PMID:24373766

Insight and analysis problem solving in microbes to machines.

PubMed

Clark, Kevin B

2015-11-01

A key feature for obtaining solutions to difficult problems, insight is oftentimes vaguely regarded as a special discontinuous intellectual process and/or a cognitive restructuring of problem representation or goal approach. However, this nearly century-old state of art devised by the Gestalt tradition to explain the non-analytical or non-trial-and-error, goal-seeking aptitude of primate mentality tends to neglect problem-solving capabilities of lower animal phyla, Kingdoms other than Animalia, and advancing smart computational technologies built from biological, artificial, and composite media. Attempting to provide an inclusive, precise definition of insight, two major criteria of insight, discontinuous processing and problem restructuring, are here reframed using terminology and statistical mechanical properties of computational complexity classes. Discontinuous processing becomes abrupt state transitions in algorithmic/heuristic outcomes or in types of algorithms/heuristics executed by agents using classical and/or quantum computational models. And problem restructuring becomes combinatorial reorganization of resources, problem-type substitution, and/or exchange of computational models. With insight bounded by computational complexity, humans, ciliated protozoa, and complex technological networks, for example, show insight when restructuring time requirements, combinatorial complexity, and problem type to solve polynomial and nondeterministic polynomial decision problems. Similar effects are expected from other problem types, supporting the idea that insight might be an epiphenomenon of analytical problem solving and consequently a larger information processing framework. Thus, this computational complexity definition of insight improves the power, external and internal validity, and reliability of operational parameters with which to classify, investigate, and produce the phenomenon for computational agents ranging from microbes to man-made devices. Copyright

Structural insights into the functions of the FANCM-FAAP24 complex in DNA repair

PubMed Central

Yang, Hui; Zhang, Tianlong; Tao, Ye; Wang, Fang; Tong, Liang; Ding, Jianping

2013-01-01

Fanconi anemia (FA) is a genetically heterogeneous disorder associated with deficiencies in the FA complementation group network. FA complementation group M (FANCM) and FA-associated protein 24 kDa (FAAP24) form a stable complex to anchor the FA core complex to chromatin in repairing DNA interstrand crosslinks. Here, we report the first crystal structure of the C-terminal segment of FANCM in complex with FAAP24. The C-terminal segment of FANCM and FAAP24 both consist of a nuclease domain at the N-terminus and a tandem helix-hairpin-helix (HhH)2 domain at the C-terminus. The FANCM-FAAP24 complex exhibits a similar architecture as that of ApXPF. However, the variations of several key residues and the electrostatic property at the active-site region render a catalytically inactive nuclease domain of FANCM, accounting for the lack of nuclease activity. We also show that the first HhH motif of FAAP24 is a potential binding site for DNA, which plays a critical role in targeting FANCM-FAAP24 to chromatin. These results reveal the mechanistic insights into the functions of FANCM-FAAP24 in DNA repair. PMID:24003026

Insight into the structure of photosynthetic LH2 aggregate from spectroscopy simulations.

PubMed

Rancova, Olga; Sulskus, Juozas; Abramavicius, Darius

2012-07-12

Using the electrostatic model of intermolecular interactions, we obtain the Frenkel exciton Hamiltonian parameters for the chlorophyll Qy band of a photosynthetic peripheral light harvesting complex LH2 of a purple bacteria Rhodopseudomonas acidophila from structural data. The intermolecular couplings are mostly determined by the chlorophyll relative positions, whereas the molecular transition energies are determined by the background charge distribution of the whole complex. The protonation pattern of titratable residues is used as a tunable parameter. By studying several protonation state scenarios for distinct protein groups and comparing the simulated absorption and circular dichroism spectra to experiment, we determine the most probable configuration of the protonation states of various side groups of the protein.

Structural, electronic, elastic, and thermal properties of CaNiH3 perovskite obtained from first-principles calculations

NASA Astrophysics Data System (ADS)

Benlamari, S.; Bendjeddou, H.; Boulechfar, R.; Amara Korba, S.; Meradji, H.; Ahmed, R.; Ghemid, S.; Khenata, R.; Omran, S. Bin

2018-03-01

A theoretical study of the structural, elastic, electronic, mechanical, and thermal properties of the perovskite-type hydride CaNiH3 is presented. This study is carried out via first-principles full potential (FP) linearized augmented plane wave plus local orbital (LAPW+lo) method designed within the density functional theory (DFT). To treat the exchange–correlation energy/potential for the total energy calculations, the local density approximation (LDA) of Perdew–Wang (PW) and the generalized gradient approximation (GGA) of Perdew–Burke–Ernzerhof (PBE) are used. The three independent elastic constants (C 11, C 12, and C 44) are calculated from the direct computation of the stresses generated by small strains. Besides, we report the variation of the elastic constants as a function of pressure as well. From the calculated elastic constants, the mechanical character of CaNiH3 is predicted. Pertaining to the thermal properties, the Debye temperature is estimated from the average sound velocity. To further comprehend this compound, the quasi-harmonic Debye model is used to analyze the thermal properties. From the calculations, we find that the obtained results of the lattice constant (a 0), bulk modulus (B 0), and its pressure derivative ({B}0^{\\prime }) are in good agreement with the available theoretical as well as experimental results. Similarly, the obtained electronic band structure demonstrates the metallic character of this perovskite-type hydride.

Structural, functional and immunogenic insights on Cu,Zn superoxide dismutase pathogenic virulence factors from Neisseria meningitidis and Brucella abortus

DOE PAGES

Pratt, Ashley J.; DiDonato, Michael; Shin, David S.; ...

2015-10-12

Bacterial pathogens Neisseria meningitidis and Brucella abortus pose threats to human and animal health worldwide, causing meningococcal disease and brucellosis, respectively. Mortality from acute N. meningitidis infections remains high despite antibiotics, and brucellosis presents alimentary and health consequences. Superoxide dismutases are master regulators of reactive oxygen, general pathogenicity factors and therefore therapeutic targets. Cu,Zn superoxide dismutases (SODs) localized to the periplasm promote survival by detoxifying superoxide radicals generated by major host antimicrobial immune responses. We discovered that passive immunization with an antibody directed at N. meningitidis SOD (NmSOD) was protective in a mouse infection model. To define the relevant atomicmore » details and solution assembly states of this important virulence factor, we report high-resolution and X-ray scattering analyses of NmSOD and SOD from B. abortus (BaSOD). The NmSOD structures revealed an auxiliary tetrahedral Cu-binding site bridging the dimer interface; mutational analyses suggested that this metal site contributes to protein stability, with implications for bacterial defense mechanisms. Biochemical and structural analyses informed us about electrostatic substrate guidance, dimer assembly and an exposed C-terminal epitope in the NmSOD dimer. In contrast, the monomeric BaSOD structure provided insights for extending immunogenic peptide epitopes derived from the protein. These collective results reveal unique contributions of SOD to pathogenic virulence, refine predictive motifs for distinguishing SOD classes and suggest general targets for anti-bacterial immune responses. The identified functional contributions, motifs, and targets distinguishing bacterial and eukaryotic SOD assemblies presented here provide a foundation for efforts to develop SOD-specific inhibitors or vaccines against these harmful pathogens. IMPORTANCE By protecting microbes against reactive oxygen

Structural, Functional, and Immunogenic Insights on Cu,Zn Superoxide Dismutase Pathogenic Virulence Factors from Neisseria meningitidis and Brucella abortus

PubMed Central

Pratt, Ashley J.; DiDonato, Michael; Shin, David S.; Cabelli, Diane E.; Bruns, Cami K.; Belzer, Carol A.; Gorringe, Andrew R.; Langford, Paul R.; Tabatabai, Louisa B.; Kroll, J. Simon; Tainer, John A.

2015-01-01

ABSTRACT Bacterial pathogens Neisseria meningitidis and Brucella abortus pose threats to human and animal health worldwide, causing meningococcal disease and brucellosis, respectively. Mortality from acute N. meningitidis infections remains high despite antibiotics, and brucellosis presents alimentary and health consequences. Superoxide dismutases are master regulators of reactive oxygen and general pathogenicity factors and are therefore therapeutic targets. Cu,Zn superoxide dismutases (SODs) localized to the periplasm promote survival by detoxifying superoxide radicals generated by major host antimicrobial immune responses. We discovered that passive immunization with an antibody directed at N. meningitidis SOD (NmSOD) was protective in a mouse infection model. To define the relevant atomic details and solution assembly states of this important virulence factor, we report high-resolution and X-ray scattering analyses of NmSOD and of SOD from B. abortus (BaSOD). The NmSOD structures revealed an auxiliary tetrahedral Cu-binding site bridging the dimer interface; mutational analyses suggested that this metal site contributes to protein stability, with implications for bacterial defense mechanisms. Biochemical and structural analyses informed us about electrostatic substrate guidance, dimer assembly, and an exposed C-terminal epitope in the NmSOD dimer. In contrast, the monomeric BaSOD structure provided insights for extending immunogenic peptide epitopes derived from the protein. These collective results reveal unique contributions of SOD to pathogenic virulence, refine predictive motifs for distinguishing SOD classes, and suggest general targets for antibacterial immune responses. The identified functional contributions, motifs, and targets distinguishing bacterial and eukaryotic SOD assemblies presented here provide a foundation for efforts to develop SOD-specific inhibitors of or vaccines against these harmful pathogens. IMPORTANCE By protecting microbes against

Structural, Functional, and Immunogenic Insights on Cu,Zn Superoxide Dismutase Pathogenic Virulence Factors from Neisseria meningitidis and Brucella abortus.

PubMed

Pratt, Ashley J; DiDonato, Michael; Shin, David S; Cabelli, Diane E; Bruns, Cami K; Belzer, Carol A; Gorringe, Andrew R; Langford, Paul R; Tabatabai, Louisa B; Kroll, J Simon; Tainer, John A; Getzoff, Elizabeth D

2015-12-01

Bacterial pathogens Neisseria meningitidis and Brucella abortus pose threats to human and animal health worldwide, causing meningococcal disease and brucellosis, respectively. Mortality from acute N. meningitidis infections remains high despite antibiotics, and brucellosis presents alimentary and health consequences. Superoxide dismutases are master regulators of reactive oxygen and general pathogenicity factors and are therefore therapeutic targets. Cu,Zn superoxide dismutases (SODs) localized to the periplasm promote survival by detoxifying superoxide radicals generated by major host antimicrobial immune responses. We discovered that passive immunization with an antibody directed at N. meningitidis SOD (NmSOD) was protective in a mouse infection model. To define the relevant atomic details and solution assembly states of this important virulence factor, we report high-resolution and X-ray scattering analyses of NmSOD and of SOD from B. abortus (BaSOD). The NmSOD structures revealed an auxiliary tetrahedral Cu-binding site bridging the dimer interface; mutational analyses suggested that this metal site contributes to protein stability, with implications for bacterial defense mechanisms. Biochemical and structural analyses informed us about electrostatic substrate guidance, dimer assembly, and an exposed C-terminal epitope in the NmSOD dimer. In contrast, the monomeric BaSOD structure provided insights for extending immunogenic peptide epitopes derived from the protein. These collective results reveal unique contributions of SOD to pathogenic virulence, refine predictive motifs for distinguishing SOD classes, and suggest general targets for antibacterial immune responses. The identified functional contributions, motifs, and targets distinguishing bacterial and eukaryotic SOD assemblies presented here provide a foundation for efforts to develop SOD-specific inhibitors of or vaccines against these harmful pathogens. By protecting microbes against reactive oxygen

Structural, functional and immunogenic insights on Cu,Zn superoxide dismutase pathogenic virulence factors from Neisseria meningitidis and Brucella abortus

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

Pratt, Ashley J.; DiDonato, Michael; Shin, David S.

Bacterial pathogens Neisseria meningitidis and Brucella abortus pose threats to human and animal health worldwide, causing meningococcal disease and brucellosis, respectively. Mortality from acute N. meningitidis infections remains high despite antibiotics, and brucellosis presents alimentary and health consequences. Superoxide dismutases are master regulators of reactive oxygen, general pathogenicity factors and therefore therapeutic targets. Cu,Zn superoxide dismutases (SODs) localized to the periplasm promote survival by detoxifying superoxide radicals generated by major host antimicrobial immune responses. We discovered that passive immunization with an antibody directed at N. meningitidis SOD (NmSOD) was protective in a mouse infection model. To define the relevant atomicmore » details and solution assembly states of this important virulence factor, we report high-resolution and X-ray scattering analyses of NmSOD and SOD from B. abortus (BaSOD). The NmSOD structures revealed an auxiliary tetrahedral Cu-binding site bridging the dimer interface; mutational analyses suggested that this metal site contributes to protein stability, with implications for bacterial defense mechanisms. Biochemical and structural analyses informed us about electrostatic substrate guidance, dimer assembly and an exposed C-terminal epitope in the NmSOD dimer. In contrast, the monomeric BaSOD structure provided insights for extending immunogenic peptide epitopes derived from the protein. These collective results reveal unique contributions of SOD to pathogenic virulence, refine predictive motifs for distinguishing SOD classes and suggest general targets for anti-bacterial immune responses. The identified functional contributions, motifs, and targets distinguishing bacterial and eukaryotic SOD assemblies presented here provide a foundation for efforts to develop SOD-specific inhibitors or vaccines against these harmful pathogens. IMPORTANCE By protecting microbes against reactive oxygen

Structural insight of the charge-ordering phenomena in manganites

NASA Astrophysics Data System (ADS)

Garcia, Joaquin

2005-03-01

Recent experiments using x-ray absorption spectroscopy (XAS) and x-ray resonant scattering (XRS) techniques show that the conventional description of the so-called charge ordering phases of manganites in terms of Mn^3+/Mn^4+ ionic ordering is far from reality. I present here the XRS study of the low temperature phase of Nd0.5Sr0.5MnO3 manganite. Strong resonances are observed in the energy dependent spectra of (300), (030) and (05/20) reflections. Their azimuthal and polarization dependencies are well explained by the anisotropy of the local geometrical structure. Two different Mn sites were found. One of them is surrounded by a tetragonal distorted oxygen octahedron, whereas the other site has a nearly regular octahedral environment. The charge separation between the intermediate valence states is less than 0.2 e-. The analysis performed resolves some of the apparent contradictions with previous XRS and XAS experiments in manganites. These results joined to those recently obtained on the Verwey transition in magnetite indicate that the electronic states in transition-metal oxides need to be described in terms of band states instead of localized ones. Colaborators: G. Sub'ias, J. Blasco, M. G. Proietti, M. S'anchez and J. Herrero-Martin

Insights in KIR2.1 channel structure and function by an evolutionary approach; cloning and functional characterization of the first reptilian inward rectifier channel KIR2.1, derived from the California kingsnake (Lampropeltis getula californiae).

PubMed

Houtman, Marien J C; Korte, Sanne M; Ji, Yuan; Kok, Bart; Vos, Marc A; Stary-Weinzinger, Anna; van der Heyden, Marcel A G

2014-10-03

Potassium inward rectifier KIR2.1 channels contribute to the stable resting membrane potential in a variety of muscle and neuronal cell-types. Mutations in the KIR2.1 gene KCNJ2 have been associated with human disease, such as cardiac arrhythmias and periodic paralysis. Crystal structure and homology modelling of KIR2.1 channels combined with functional current measurements provided valuable insights in mechanisms underlying channel function. KIR2.1 channels have been cloned and analyzed from all main vertebrate phyla, except reptilians. To address this lacuna, we set out to clone reptilian KIR2.1 channels. Using a degenerated primer set we cloned the KCNJ2 coding regions from muscle tissue of turtle, snake, bear, quail and bream, and compared their deduced amino acid sequences with those of KIR2.1 sequences from 26 different animal species obtained from Genbank. Furthermore, expression constructs were prepared for functional electrophysiological studies of ectopically expressed KIR2.1 ion channels. In general, KCNJ2 gene evolution followed normal phylogenetic patterns, however turtle KIR2.1 ion channel sequence is more homologues to avians than to snake. Alignment of all 31 KIR2.1 sequences showed that all disease causing KIR2.1 mutations, except V93I, V123G and N318S, are fully conserved. Homology models were built to provide structural insights into species specific amino acid substitutions. Snake KIR2.1 channels became expressed at the plasmamembrane and produced typical barium sensitive (IC50 ∼6μM) inward rectifier currents. Copyright © 2014 Elsevier Inc. All rights reserved.

Mechanistic insight into formation and changes of nanoparticles in MgF2 sols evidenced by liquid and solid state NMR.

PubMed

Karg, M; Scholz, G; König, R; Kemnitz, E

2012-02-28

The fluorolytic sol-gel reaction of magnesium methoxide with HF in methanol was studied by (19)F, (1)H and (13)C liquid and solid state NMR. In (19)F NMR five different species were identified, three of which belong to magnesium fluoride nanoparticles, i.e. NMR gave access to local structures of solid particles in suspensions. The long-term evolution of (19)F signals was followed and along with (19)F MAS NMR experiments of sols rotating at 13 kHz mechanistic insights into the ageing processes were obtained.

Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455.

PubMed

Wu, Daichao; Guo, Ming; Philips, Michael A; Qu, Lingzhi; Jiang, Longying; Li, Jun; Chen, Xiaojuan; Chen, Zhuchu; Chen, Lin; Chen, Yongheng

2016-01-01

Aberrant FGFR4 signaling has been documented abundantly in various human cancers. The majority of FGFR inhibitors display significantly reduced potency toward FGFR4 compared to FGFR1-3. However, LY2874455 has similar inhibition potency for FGFR1-4 with IC50 less than 6.4 nM. To date, there is no published crystal structure of LY2874455 in complex with any kinase. To better understand the pan-FGFR selectivity of LY2874455, we have determined the crystal structure of the FGFR4 kinase domain bound to LY2874455 at a resolution of 2.35 Å. LY2874455, a type I inhibitor for FGFR4, binds to the ATP-binding pocket of FGFR4 in a DFG-in active conformation with three hydrogen bonds and a number of van der Waals contacts. After alignment of the kinase domain sequence of 4 FGFRs, and superposition of the ATP binding pocket of 4 FGFRs, our structural analyses reveal that the interactions of LY2874455 to FGFR4 are largely conserved in 4 FGFRs, explaining at least partly, the broad inhibitory activity of LY2874455 toward 4 FGFRs. Consequently, our studies reveal new insights into the pan-FGFR selectivity of LY2874455 and provide a structural basis for developing novel FGFR inhibitors that target FGFR1-4 broadly.

Structural and functional insights into sorting nexin 5/6 interaction with bacterial effector IncE.

PubMed

Sun, Qingxiang; Yong, Xin; Sun, Xiaodong; Yang, Fan; Dai, Zhonghua; Gong, Yanqiu; Zhou, Liming; Zhang, Xia; Niu, Dawen; Dai, Lunzhi; Liu, Jia-Jia; Jia, Da

2017-01-01

The endosomal trafficking pathways are essential for many cellular activities. They are also important targets by many intracellular pathogens. Key regulators of the endosomal trafficking include the retromer complex and sorting nexins (SNXs). Chlamydia trachomatis effector protein IncE directly targets the retromer components SNX5 and SNX6 and suppresses retromer-mediated transport, but the exact mechanism has remained unclear. We present the crystal structure of the PX domain of SNX5 in complex with IncE, showing that IncE binds to a highly conserved hydrophobic groove of SNX5. The unique helical hairpin of SNX5/6 is essential for binding, explaining the specificity of SNX5/6 for IncE. The SNX5/6-IncE interaction is required for cellular localization of IncE and its inhibitory function. Mechanistically, IncE inhibits the association of CI-MPR cargo with retromer-containing endosomal subdomains. Our study provides new insights into the regulation of retromer-mediated transport and illustrates the intricate competition between host and pathogens in controlling cellular trafficking.

G protein-coupled odorant receptors: From sequence to structure.

PubMed

de March, Claire A; Kim, Soo-Kyung; Antonczak, Serge; Goddard, William A; Golebiowski, Jérôme

2015-09-01

Odorant receptors (ORs) are the largest subfamily within class A G protein-coupled receptors (GPCRs). No experimental structural data of any OR is available to date and atomic-level insights are likely to be obtained by means of molecular modeling. In this article, we critically align sequences of ORs with those GPCRs for which a structure is available. Here, an alignment consistent with available site-directed mutagenesis data on various ORs is proposed. Using this alignment, the choice of the template is deemed rather minor for identifying residues that constitute the wall of the binding cavity or those involved in G protein recognition. © 2015 The Protein Society.

G protein-coupled odorant receptors: From sequence to structure

PubMed Central

de March, Claire A; Kim, Soo-Kyung; Antonczak, Serge; Goddard, William A; Golebiowski, Jérôme

2015-01-01

Odorant receptors (ORs) are the largest subfamily within class A G protein-coupled receptors (GPCRs). No experimental structural data of any OR is available to date and atomic-level insights are likely to be obtained by means of molecular modeling. In this article, we critically align sequences of ORs with those GPCRs for which a structure is available. Here, an alignment consistent with available site-directed mutagenesis data on various ORs is proposed. Using this alignment, the choice of the template is deemed rather minor for identifying residues that constitute the wall of the binding cavity or those involved in G protein recognition. PMID:26044705

Call it a monster for lack of anything else: narrative insight in psychosis.

PubMed

Roe, David; Hasson-Ohayon, Ilanit; Kravetz, Shlomo; Yanos, Phil T; Lysaker, Paul H

2008-12-01

Individuals diagnosed with schizophrenia often appear to be unaware of having an illness or actively reject their diagnostic label. It is unclear, however, how this lack of awareness relates to important outcomes. Broadening the definition of awareness to include "narrative insight" may clarify this issue. The objective of this study was to identify profiles of narrative insight and test how these relate to standardized measure of insight. Sixty-five individuals with schizophrenia spectrum disorders participated in an assessment that included the Scale of Unawareness of Mental Disorder (SUMD) and an in-depth semi-structured interview. Qualitative analysis revealed 5 central themes related to insight on the basis of which each interview was then rated. Cluster analysis of these ratings resulted in 4 profiles of narrative insight: (1) accepts illness/rejects label, (2) rejects illness/searches for a name (3) passive insight of illness and label, and (4) integrative insight. The SUMD differentiated between individuals assigned to profile 2 who showed low insight to their illness and those assigned to the other profiles of narrative insight, but could not differentiate between them. Results support the claim that illness narratives are multifaceted and that traditional measures of insight may not be sensitive to different ways in which people understand their illness.

Theory of mind correlates with clinical insight but not cognitive insight in patients with schizophrenia.

PubMed

Zhang, Qi; Li, Xu; Parker, Giverny J; Hong, Xiao-Hong; Wang, Yi; Lui, Simon S Y; Neumann, David L; Cheung, Eric F C; Shum, David H K; Chan, Raymond C K

2016-03-30

Research on the relationship between insight and social cognition, in particular Theory of Mind (ToM), in schizophrenia has yielded mixed findings to date. Very few studies, however, have assessed both clinical insight and cognitive insight when examining their relationships with ToM in schizophrenia. The current study thus investigated the relationship between clinical insight, cognitive insight, and ToM in a sample of 56 patients with schizophrenia and 30 healthy controls. Twenty-seven patients were classified as low in clinical insight according to their scores on the 'insight' item (G12) of the Positive and Negative Syndrome Scale (PANSS). Moreover, cognitive insight and ToM were assessed with the Beck Cognitive Insight Scale (BCIS) and the Yoni task, respectively. The results indicated that patients with poor clinical insight performed worse on tasks of second-order cognitive and affective ToM, while the ToM performance of patients with high clinical insight was equivalent to that of healthy controls. Furthermore, while clinical insight was correlated with ToM and clinical symptoms, cognitive insight did not correlate with clinical insight, ToM, or clinical symptoms. Clinical insight thus appears to be an important factor related to ToM in schizophrenia. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

New Insights into Structure and Luminescence of Eu III and Sm III Complexes of the 3,4,3-LI(1,2-HOPO) Ligand

DOE PAGES

Daumann, Lena J.; Tatum, David S.; Snyder, Benjamin E. R.; ...

2015-01-21

We report the preparation and new insight into photophysical properties of luminescent hydroxypyridonate complexes [M IIIL] - (M = Eu or Sm) of the versatile 3,4,3-LI(1,2-HOPO) ligand (L). We report the crystal structure of this ligand with EuIII as well as insights into the coordination behavior and geometry in solution by using magnetic circular dichroism. In addition TD-DFT calculations were used to examine the excited states of the two different chromophores present in the 3,4,3-LI(1,2-HOPO) ligand. We find that the Eu III and Sm III complexes of this ligand undergo a transformation after in situ preparation to yield complexes withmore » higher quantum yield (QY) over time. We propose that the lower QY in the in situ complexes is not only due to water quenching but could also be due to a lower degree of f-orbital overlap (in a kinetic isomer) as indicated by magnetic circular dichroism measurements.« less

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

NASA Astrophysics Data System (ADS)

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-01

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics.

PubMed

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-14

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.

Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights.

PubMed

Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji

2016-12-13

Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

New insights into apoptosome structure and function.

PubMed

Dorstyn, Loretta; Akey, Christopher W; Kumar, Sharad

2018-05-15

The apoptosome is a platform that activates apical procaspases in response to intrinsic cell death signals. Biochemical and structural studies in the past two decades have extended our understanding of apoptosome composition and structure, while illuminating the requirements for initiator procaspase activation. A number of studies have now provided high-resolution structures for apoptosomes from C. elegans (CED-4), D. melanogaster (Dark), and H. sapiens (Apaf-1), which define critical protein interfaces, including intra and interdomain interactions. This work also reveals interactions of apoptosomes with their respective initiator caspases, CED-3, Dronc and procaspase-9. Structures of the human apoptosome have defined the requirements for cytochrome c binding, which triggers the conversion of inactive Apaf-1 molecules to an extended, assembly competent state. While recent data have provided a detailed understanding of apoptosome formation and procaspase activation, they also highlight important evolutionary differences with functional implications for caspase activation. CARD/CARD interactions in the CED-4, Dark and Apaf-1 apoptosomes. Type I, II and III interfaces that stabilize CARD-CARD interactions are indicated (left column). Note that the Type I interface appears to be unique to Apaf-1/pc-9 CARD interactions. Middle column shows cartoons of the active states of the CARD-CARD disks, illustrating the two CED-4 tetrameric ring layers (top) and the recruitment of 8 Dronc CARDs and between 3-4 pc-9 CARDs, to the Dark and Apaf-1 apoptosomes respectively (middle and lower panels). Ribbon diagrams of the CED-4, Dark and Apaf-1 apoptosomes are shown (right column).

An efficient and practical approach to obtain a better optimum solution for structural optimization

NASA Astrophysics Data System (ADS)

Chen, Ting-Yu; Huang, Jyun-Hao

2013-08-01

For many structural optimization problems, it is hard or even impossible to find the global optimum solution owing to unaffordable computational cost. An alternative and practical way of thinking is thus proposed in this research to obtain an optimum design which may not be global but is better than most local optimum solutions that can be found by gradient-based search methods. The way to reach this goal is to find a smaller search space for gradient-based search methods. It is found in this research that data mining can accomplish this goal easily. The activities of classification, association and clustering in data mining are employed to reduce the original design space. For unconstrained optimization problems, the data mining activities are used to find a smaller search region which contains the global or better local solutions. For constrained optimization problems, it is used to find the feasible region or the feasible region with better objective values. Numerical examples show that the optimum solutions found in the reduced design space by sequential quadratic programming (SQP) are indeed much better than those found by SQP in the original design space. The optimum solutions found in a reduced space by SQP sometimes are even better than the solution found using a hybrid global search method with approximate structural analyses.

Subsurface architecture of a strike-slip collapse structure: insights from Ilopango caldera, El Salvador

NASA Astrophysics Data System (ADS)

Saxby, Jennifer; Gottsmann, Joachim; Cashman, Katherine; Gutierrez, Eduardo

2016-04-01

While most calderas are created by roof collapse along ring-like faults into an emptying magma reservoir during a large and violent explosive eruption, an additional condition for caldera formation may be tectonically induced extensional stresses. Here we provide geophysical insights into the shallow sub-volcanic plumbing system of a collapse caldera in a major strike-slip tectonic setting by inverting Bouguer gravity data from the Ilopango caldera in El Salvador. Despite a long history of catastrophic eruptions with the most recent in 500 A.D., the internal architecture of the caldera has not been investigated, although studies of the most recent eruption have not identified the ring faults commonly associated with caldera collapse. The gravity data show that low-density material aligned along the principal stress orientations of the El Salvador Fault Zone (ESFZ) forms a pronounced gravity low beneath the caldera. Extending to around 6 km depth, the low density structure likely maps a complex stacked shallow plumbing system composed of magmatic and fractured hydrothermal reservoirs. A substantial volume of the plumbing system must be composed of a vapour phase to explain the modeled negative density contrasts. We use these constraints to map the possible multi-phase parameter space contributing to the subsurface architecture of the caldera and propose that the local extension along the complex ESFZ controls accumulation, ascent and eruption of magma at Ilopango. The data further suggest that future eruptions at Ilopango could be facilitated by rapid rise of magma along conjugate fault damage zones through a mechanically weak crust under tension. This may explain the absence of clear ring fault structures at the caldera.

Large-scale biochemical profiling of the Candida albicans biofilm matrix: new compositional, structural, and functional insights.

PubMed

Lopez-Ribot, Jose L

2014-09-09

Among pathogenic fungi, Candida albicans is most frequently associated with biofilm formation, a lifestyle that is entirely different from the planktonic state. One of the distinguishing features of these biofilms is the presence of extracellular material, commonly referred to as the "biofilm matrix." The fungal biofilm matrix embeds sessile cells within these communities and plays important structural and physiological functions, including antifungal drug resistance with important clinical repercussions. This matrix is mostly self-produced by the fungal cells themselves and is composed of different types of biopolymers. In C. albicans, the main components of the biofilm matrix are carbohydrates, proteins, lipids, and DNA, but many of them remain unidentified and/or poorly characterized. In their recent article, Zarnowski et al. [mBio 5(4):e01333-14, 2014, doi:10.1128/mBio.01333-14] used a variety of biochemical and state-of-the-art "omic" approaches (glycomics, proteomics, and lipidomics) to identify and characterize unique biopolymers present in the C. albicans biofilm matrix. Besides generating a true "encyclopedic" catalog of individual moieties from each of the different macromolecular categories, results also provide important insights into structural and functional aspects of the fungal biofilm matrix, particularly the interaction between different components and the contribution of multiple matrix constituents to biofilm antifungal drug resistance. Copyright © 2014 Lopez-Ribot.

The benefits of analysing complete mitochondrial genomes: Deep insights into the phylogeny and population structure of Echinococcus granulosus sensu lato genotypes G6 and G7.

PubMed

Laurimäe, Teivi; Kinkar, Liina; Romig, Thomas; Omer, Rihab A; Casulli, Adriano; Umhang, Gérald; Gasser, Robin B; Jabbar, Abdul; Sharbatkhori, Mitra; Mirhendi, Hossein; Ponce-Gordo, Francisco; Lazzarini, Lorena E; Soriano, Silvia V; Varcasia, Antonio; Nejad, Mohammad Rostami; Andresiuk, Vanessa; Maravilla, Pablo; González, Luis Miguel; Dybicz, Monika; Gawor, Jakub; Šarkūnas, Mindaugas; Šnábel, Viliam; Kuzmina, Tetiana; Saarma, Urmas

2018-06-12

Cystic echinococcosis (CE) is a zoonotic disease caused by the larval stage of the species complex Echinococcus granulosus sensu lato. Within this complex, genotypes G6 and G7 have been frequently associated with human CE worldwide. Previous studies exploring the genetic variability and phylogeography of genotypes G6 and G7 have been based on relatively short mtDNA sequences, and the resolution of these studies has often been low. Moreover, using short sequences, the distinction between G6 and G7 has in some cases remained challenging. The aim here was to sequence complete mitochondrial genomes (mitogenomes) to obtain deeper insight into the genetic diversity, phylogeny and population structure of genotypes G6 and G7. We sequenced complete mitogenomes of 94 samples collected from 15 different countries worldwide. The results demonstrated that (i) genotypes G6 and G7 can be clearly distinguished when mitogenome sequences are used; (ii) G7 is represented by two major haplogroups, G7a and G7b, the latter being specific to islands of Corsica and Sardinia; (iii) intensive animal trade, but also geographical isolation, have likely had the largest impact on shaping the genetic structure and distribution of genotypes G6 and G7. In addition, we found phylogenetically highly divergent haplotype from Mongolia (Gmon), which had a higher affinity to G6. Copyright © 2017. Published by Elsevier B.V.

Simultaneous Determination of Structure and Event Location Using Body and Surface Wave Measurements at a Single Station: Preparation for Mars Data from the InSight Mission

NASA Astrophysics Data System (ADS)

Panning, M. P.; Banerdt, W. B.; Beucler, E.; Blanchette-Guertin, J. F.; Boese, M.; Clinton, J. F.; Drilleau, M.; James, S. R.; Kawamura, T.; Khan, A.; Lognonne, P. H.; Mocquet, A.; van Driel, M.

2015-12-01

An important challenge for the upcoming InSight mission to Mars, which will deliver a broadband seismic station to Mars along with other geophysical instruments in 2016, is to accurately determine event locations with the use of a single station. Locations are critical for the primary objective of the mission, determining the internal structure of Mars, as well as a secondary objective of measuring the activity of distribution of seismic events. As part of the mission planning process, a variety of techniques have been explored for location of marsquakes and inversion of structure, and preliminary procedures and software are already under development as part of the InSight Mars Quake and Mars Structure Services. One proposed method, involving the use of recordings of multiple-orbit surface waves, has already been tested with synthetic data and Earth recordings. This method has the strength of not requiring an a priori velocity model of Mars for quake location, but will only be practical for larger events. For smaller events where only first orbit surface waves and body waves are observable, other methods are required. In this study, we implement a transdimensional Bayesian inversion approach to simultaneously invert for basic velocity structure and location parameters (epicentral distance and origin time) using only measurements of body wave arrival times and dispersion of first orbit surface waves. The method is tested with synthetic data with expected Mars noise and Earth data for single events and groups of events and evaluated for errors in both location and structural determination, as well as tradeoffs between resolvable parameters and the effect of 3D crustal variations.

Insights into Modern Human Prehistory Using Ancient Genomes.

PubMed

Yang, Melinda A; Fu, Qiaomei

2018-03-01

The genetic relationship of past modern humans to today's populations and each other was largely unknown until recently, when advances in ancient DNA sequencing allowed for unprecedented analysis of the genomes of these early people. These ancient genomes reveal new insights into human prehistory not always observed studying present-day populations, including greater details on the genetic diversity, population structure, and gene flow that characterized past human populations, particularly in early Eurasia, as well as increased insight on the relationship between archaic and modern humans. Here, we review genetic studies on ∼45000- to 7500-year-old individuals associated with mainly preagricultural cultures found in Eurasia, the Americas, and Africa. Copyright © 2017 Elsevier Ltd. All rights reserved.

Influence of heme environment structure on dioxygen affinity for the dual function Amphitrite ornata hemoglobin/dehaloperoxidase. Insights into the evolutional structure-function adaptations

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

Sun, Shengfang; Sono, Masanori; Wang, Chunxue

Sea worm, Amphitrite ornata, has evolved its globin (an O 2 carrier) also to serves as a dehaloperoxidase (DHP) to detoxify haloaromatic pollutants generated by competing species. A previous mutagenesis study by our groups on both DHP and sperm whale myoglobin (SW Mb) revealed some structural factors that influence the dehaloperoxidase activities (significantly lower for Mb) of both proteins. Using an isocyanide/O 2 partition constant measurement method in this study, we have examined the effects of these structural factors on the O 2 equilibrium constants (K O2) of DHP, SW Mb, and their mutants. A clear trend of decreasing Omore » 2 affinity and increasing catalytic activity along with the increase in the distal His N ε–heme iron distance is observed. An H93K/T95H Mb double mutant mimicking the DHP proximal His positioning exhibited markedly enhanced O 2 affinity, confirming the essential effect of proximal His rotation on the globin function of DHP. For DHP, the L100F, T56G and M86E variants showed the effects of distal volume, distal His flexibility and proximal electronic push, respectively, on the O 2 affinity. This study provides insights into how DHP has evolved its heme environment to gain significantly enhanced peroxidase capability without compromising its primary function as an O 2 carrier.« less

New insights into the structure and energetics of the Martian ionosphere

NASA Astrophysics Data System (ADS)

Fowler, Christopher M.

Understanding the formation and evolution of planetary bodies is of great interest and importance to humankind. Mars, being the closest analogue to Earth in our solar system, has been of particular importance. Having studied the red planet for many decades using landers and orbiting spacecraft, we are now laying the groundwork to venture there ourselves. The Mars Atmosphere and Volatile EvolutioN (MAVEN) mission recently went into Mars orbit to study the physical processes active within the Martian atmosphere, and to understand how the atmosphere itself has evolved throughout the planet's history. This thesis is based upon unraveling data from the MAVEN mission, with a focus on the structure and energetics of the Martian ionosphere. Data from many of the instruments carried by MAVEN have been analyzed in this work, in particular, analysis and fitting of current-voltage sweeps measured by the Langmuir Probe and Waves instrument. New insights have been gained about the operation of Langmuir probes in planetary ionospheres, and through first author papers, about the Martian ionosphere itself. The four papers presented in this thesis focus on the structure and energetics of the Martian ionosphere. The first in-situ observations of the Martian nightside electron density and temperature showed that an ionization source is needed to sustain the observed densities. Precipitating electrons were shown as a feasible source, agreeing with suggestions from previous modeling efforts. The transfer of energy from the solar wind to the atmosphere is an important energy source for the Martian atmosphere. An investigation of the electromagnetic environment at Mars shows how the distribution of wave power, and various plasma boundaries within the Martian magnetosphere, respond to upstream solar wind conditions, highlighting regions important for energy dissipation. The combination of magnetic field and ion data allows for the first time at Mars, ion conics to be observed. These show

Insight in bipolar mania: evaluation of its heterogeneity and correlation with clinical symptoms.

PubMed

Silva, Rafael de Assis da; Mograbi, Daniel C; Bifano, Jaqueline; Santana, Cristina M T; Cheniaux, Elie

2016-07-15

Studies on insight in bipolar mania are not numerous and usually consider insight as a unitary construct. Evaluate how different facets of insight are affected in bipolar mania and investigate correlations between insight for each specific object in bipolar disorder and manic symptomatology. A group of 165 bipolar patients were followed during a year, with 51 patients having manic episodes according to DSM-IV-TR criteria. Patients underwent a clinical assessment and insight was evaluated through the Insight Scale for Affective Disorders. The study found that insight regarding symptoms is worse than insight of having bipolar disorder, social relationships and self esteem. Moreover, poor global insight (total ISAD) correlates with more severe changes in mood, speech and thought structure, with worse insight about symptoms correlating with the same alterations and also with more severe symptoms of agitation/energy. Although a large sample of bipolar patients was followed up, the final sample composed of patients with at least one manic episode was relatively smaller. Moreover, the fact that the study was performed in a university hospital may have led to selection biases. Results suggest that patients with BD are reasonably capable of identifying that their condition implies consequences but have more impaired awareness of their energy and activity levels. A lower level of insight specifically about symptoms correlates with more severe symptoms of agitation/energy, which suggests a psychomotor nucleus able to impair insight in mania. Copyright © 2016 Elsevier B.V. All rights reserved.

NMR structural and dynamic characterization of the acid-unfolded state of apomyoglobin provides insights into the early events in protein folding.

PubMed

Yao, J; Chung, J; Eliezer, D; Wright, P E; Dyson, H J

2001-03-27

Apomyoglobin forms a denatured state under low-salt conditions at pH 2.3. The conformational propensities and polypeptide backbone dynamics of this state have been characterized by NMR. Nearly complete backbone and some side chain resonance assignments have been obtained, using a triple-resonance assignment strategy tailored to low protein concentration (0.2 mM) and poor chemical shift dispersion. An estimate of the population and location of residual secondary structure has been made by examining deviations of (13)C(alpha), (13)CO, and (1)H(alpha) chemical shifts from random coil values, scalar (3)J(HN,H)(alpha) coupling constants and (1)H-(1)H NOEs. Chemical shifts constitute a highly reliable indicator of secondary structural preferences, provided the appropriate random coil chemical shift references are used, but in the case of acid-unfolded apomyoglobin, (3)J(HN,H)(alpha) coupling constants are poor diagnostics of secondary structure formation. Substantial populations of helical structure, in dynamic equilibrium with unfolded states, are formed in regions corresponding to the A and H helices of the folded protein. In addition, the deviation of the chemical shifts from random coil values indicates the presence of helical structure encompassing the D helix and extending into the first turn of the E helix. The polypeptide backbone dynamics of acid-unfolded apomyoglobin have been investigated using reduced spectral density function analysis of (15)N relaxation data. The spectral density J(omega(N)) is particularly sensitive to variations in backbone fluctuations on the picosecond to nanosecond time scale. The central region of the polypeptide spanning the C-terminal half of the E helix, the EF turn, and the F helix behaves as a free-flight random coil chain, but there is evidence from J(omega(N)) of restricted motions on the picosecond to nanosecond time scale in the A and H helix regions where there is a propensity to populate helical secondary structure in the

Bench Checkout of InSight's Seismometer Instrument

NASA Image and Video Library

2017-08-28

The Seismic Experiment for Interior Structure (SEIS) instrument for NASA's InSight mission to Mars undergoes a checkout for the spacecraft's assembly, test and launch operations (ATLO) in this photo taken July 20, 2017, in a Lockheed Martin clean room facility in Littleton, Colorado. The SEIS was provided by France's national space agency (CNES) with collaboration from the United States, the United Kingdom, Switzerland and Germany. The InSight mission (for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport) is scheduled to launch in May 2018 and land on Mars Nov. 26, 2018. It will investigate processes that formed and shaped Mars and will help scientists better understand the evolution of our inner solar system's rocky planets, including Earth. https://photojournal.jpl.nasa.gov/catalog/PIA21846

InSight Encapsulation

NASA Image and Video Library

2018-04-16

In the Astrotech facility at Vandenberg Air Force Base in California, NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander is encapsulated in its payload fairing. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

Adsorption and structure of water on kaolinite surfaces: possible insight into ice nucleation from grand canonical monte carlo calculations.

PubMed

Croteau, T; Bertram, A K; Patey, G N

2008-10-30

Grand canonical Monte Carlo calculations are used to determine water adsorption and structure on defect-free kaolinite surfaces as a function of relative humidity at 235 K. This information is then used to gain insight into ice nucleation on kaolinite surfaces. Results for both the SPC/E and TIP5P-E water models are compared and demonstrate that the Al-surface [(001) plane] and both protonated and unprotonated edges [(100) plane] strongly adsorb at atmospherically relevant relative humidities. Adsorption on the Al-surface exhibits properties of a first-order process with evidence of collective behavior, whereas adsorption on the edges is essentially continuous and appears dominated by strong water lattice interactions. For the protonated and unprotonated edges no structure that matches hexagonal ice is observed. For the Al-surface some of the water molecules formed hexagonal rings. However, the a o lattice parameter for these rings is significantly different from the corresponding constant for hexagonal ice ( Ih). A misfit strain of 14.0% is calculated between the hexagonal pattern of water adsorbed on the Al-surface and the basal plane of ice Ih. Hence, the ring structures that form on the Al-surface are not expected to be good building-blocks for ice nucleation due to the large misfit strain.

The structure of psychological life satisfaction: insights from farmers and a general community sample in Australia

PubMed Central

2012-01-01

Background Psychological life satisfaction is a robust predictor of wellbeing. Public health measures to improve wellbeing would benefit from an understanding of how overall life satisfaction varies as a function of satisfaction with multiple life domains, an area that has been little explored. We examine a sample of drought-affected Australian farmers and a general community sample of Australians to investigate how domain satisfaction combines to form psychological satisfaction. In particular, we introduce a way of statistically testing for the presence of “supra-domains” of satisfaction to propose a novel way of examining the composition of psychological life satisfaction to gain insights for health promotion and policy. Methods Covariance between different perceptions of life domain satisfaction was identified by conducting correlation, regression, and exploratory factor analyses on responses to the Personal Wellbeing Index. Structural equations modelling was then used to (a) validate satisfaction supra-domain constructs emerging from different perceptions of life domain satisfaction, and (b) model relationships between supra-domains and an explicit measure of psychological life satisfaction. Results Perceived satisfaction with eight different life domains loaded onto a single unitary satisfaction construct adequately in each sample. However, in both samples, different domains better loaded onto two separate but correlated constructs (‘supra-domains’): “satisfaction with connectedness” and “satisfaction with efficacy”. Modelling reciprocal pathways between these supra-domains and an explicit measure of psychological life satisfaction revealed that efficacy mediated the link between connectedness and psychological satisfaction. Conclusions If satisfaction with connectedness underlies satisfaction with efficacy (and thus psychological satisfaction), a novel insight for health policy emerges: psychological life satisfaction, a vital part of

Insight Is Not in the Problem: Investigating Insight in Problem Solving across Task Types.

PubMed

Webb, Margaret E; Little, Daniel R; Cropper, Simon J

2016-01-01

The feeling of insight in problem solving is typically associated with the sudden realization of a solution that appears obviously correct (Kounios et al., 2006). Salvi et al. (2016) found that a solution accompanied with sudden insight is more likely to be correct than a problem solved through conscious and incremental steps. However, Metcalfe (1986) indicated that participants would often present an inelegant but plausible (wrong) answer as correct with a high feeling of warmth (a subjective measure of closeness to solution). This discrepancy may be due to the use of different tasks or due to different methods in the measurement of insight (i.e., using a binary vs. continuous scale). In three experiments, we investigated both findings, using many different problem tasks (e.g., Compound Remote Associates, so-called classic insight problems, and non-insight problems). Participants rated insight-related affect (feelings of Aha-experience, confidence, surprise, impasse, and pleasure) on continuous scales. As expected we found that, for problems designed to elicit insight, correct solutions elicited higher proportions of reported insight in the solution compared to non-insight solutions; further, correct solutions elicited stronger feelings of insight compared to incorrect solutions.

Insight Is Not in the Problem: Investigating Insight in Problem Solving across Task Types

PubMed Central

Webb, Margaret E.; Little, Daniel R.; Cropper, Simon J.

2016-01-01

The feeling of insight in problem solving is typically associated with the sudden realization of a solution that appears obviously correct (Kounios et al., 2006). Salvi et al. (2016) found that a solution accompanied with sudden insight is more likely to be correct than a problem solved through conscious and incremental steps. However, Metcalfe (1986) indicated that participants would often present an inelegant but plausible (wrong) answer as correct with a high feeling of warmth (a subjective measure of closeness to solution). This discrepancy may be due to the use of different tasks or due to different methods in the measurement of insight (i.e., using a binary vs. continuous scale). In three experiments, we investigated both findings, using many different problem tasks (e.g., Compound Remote Associates, so-called classic insight problems, and non-insight problems). Participants rated insight-related affect (feelings of Aha-experience, confidence, surprise, impasse, and pleasure) on continuous scales. As expected we found that, for problems designed to elicit insight, correct solutions elicited higher proportions of reported insight in the solution compared to non-insight solutions; further, correct solutions elicited stronger feelings of insight compared to incorrect solutions. PMID:27725805

Structures of rat cytosolic PEPCK: insight into the mechanism of phosphorylation and decarboxylation of oxaloacetic acid.

PubMed

Sullivan, Sarah M; Holyoak, Todd

2007-09-04

The structures of the rat cytosolic isoform of phosphoenolpyruvate carboxykinase (PEPCK) reported in the PEPCK-Mn2+, -Mn2+-oxaloacetic acid (OAA), -Mn2+-OAA-Mn2+-guanosine-5'-diphosphate (GDP), and -Mn2+-Mn2+-guanosine-5'-tri-phosphate (GTP) complexes provide insight into the mechanism of phosphoryl transfer and decarboxylation mediated by this enzyme. OAA is observed to bind in a number of different orientations coordinating directly to the active site metal. The Mn2+-OAA and Mn2+-OAA-Mn2+GDP structures illustrate inner-sphere coordination of OAA to the manganese ion through the displacement of two of the three water molecules coordinated to the metal in the holo-enzyme by the C3 and C4 carbonyl oxygens. In the PEPCK-Mn2+-OAA complex, an alternate bound conformation of OAA is present. In this conformation, in addition to the previous interactions, the C1 carboxylate is directly coordinated to the active site Mn2+, displacing all of the waters coordinated to the metal in the holo-enzyme. In the PEPCK-Mn2+-GTP structure, the same water molecule displaced by the C1 carboxylate of OAA is displaced by one of the gamma-phosphate oxygens of the triphosphate nucleotide. The structures are consistent with a mechanism of direct in-line phosphoryl transfer, supported by the observed stereochemistry of the reaction. In the catalytically competent binding mode, the C1 carboxylate of OAA is sandwiched between R87 and R405 in an environment that would serve to facilitate decarboxylation. In the reverse reaction, these two arginines would form the CO2 binding site. Comparison of the Mn2+-OAA-Mn2+GDP and Mn2+-Mn2+GTP structures illustrates a marked difference in the bound conformations of the nucleotide substrates in which the GTP nucleotide is bound in a high-energy state resulting from the eclipsing of all three of the phosphoryl groups along the triphosphate chain. This contrasts a previously determined structure of PEPCK in complex with a triphosphate nucleotide analogue in

Structural insights into the functional role of the Hcn sub-domain of the receptor-binding domain of the botulinum neurotoxin mosaic serotype C/D.

PubMed

Zhang, Yanfeng; Gardberg, Anna S; Edwards, Thomas E; Sankaran, Banumathi; Robinson, Howard; Varnum, Susan M; Buchko, Garry W

2013-07-01

Botulinum neurotoxin (BoNT), the causative agent of the deadly neuroparalytic disease botulism, is the most poisonous protein known for humans. Produced by different strains of the anaerobic bacterium Clostridium botulinum, BoNT effects cellular intoxication via a multistep mechanism executed by the three modules of the activated protein. Endocytosis, the first step of cellular intoxication, is triggered by the ~50 kDa, heavy-chain receptor-binding domain (HCR) that is specific for a ganglioside and a protein receptor on neuronal cell surfaces. This dual receptor recognition mechanism between BoNT and the host cell's membrane is well documented and occurs via specific intermolecular interactions with the C-terminal sub-domain, Hcc, of BoNT-HCR. The N-terminal sub-domain of BoNT-HCR, Hcn, comprises ~50% of BoNT-HCR and adopts a β-sheet jelly roll fold. While suspected in assisting cell surface recognition, no unambiguous function for the Hcn sub-domain in BoNT has been identified. To obtain insights into the potential function of the Hcn sub-domain in BoNT, the first crystal structure of a BoNT with an organic ligand bound to the Hcn sub-domain has been obtained. Here, we describe the crystal structure of BoNT/CD-HCR determined at 1.70 Å resolution with a tetraethylene glycol (PG4) moiety bound in a hydrophobic cleft between β-strands in the β-sheet jelly roll fold of the Hcn sub-domain. The PG4 moiety is completely engulfed in the cleft, making numerous hydrophilic (Y932, S959, W966, and D1042) and hydrophobic (S935, W977, L979, N1013, and I1066) contacts with the protein's side chain and backbone that may mimic in vivo interactions with the phospholipid membranes on neuronal cell surfaces. A sulfate ion was also observed bound to residues T1176, D1177, K1196, and R1243 in the Hcc sub-domain of BoNT/CD-HCR. In the crystal structure of a similar protein, BoNT/D-HCR, a sialic acid molecule was observed bound to the equivalent residues suggesting that residues T

Self-stigma and its relationship with insight, demoralization, and clinical outcome among people with schizophrenia spectrum disorders.

PubMed

Cavelti, Marialuisa; Kvrgic, Sara; Beck, Eva-Marina; Rüsch, Nicolas; Vauth, Roland

2012-07-01

Paradoxically, insight is associated with positive outcomes, such as better treatment adherence and recovery, and negative outcomes, such as depression, hopelessness, low self-esteem, and quality of life. Self-stigma as a moderating variable can be decisive whether more insight leads to better or worse outcome. On the other hand, self-stigma can act as a mediator between insight and outcomes. We therefore examined self-stigma both as a moderator and a mediator. Insight, self-stigma, demoralization, symptoms, and functioning were assessed among 145 outpatients with schizophrenia spectrum disorders using questionnaires and structured interviews. Structural equation modeling was used to analyze the cross-sectional data. Results confirmed self-stigma as a moderator: The association of insight and demoralization was stronger as self-stigma increased. Self-stigma also partially mediated the positive relationship between insight and demoralization. Moreover, demoralization fully mediated the adverse associations of self-stigma with psychotic symptoms and global functioning. Given the decisive role of self-stigma regarding the detrimental consequences of insight, interventions should address self-stigma, particularly if psychoeducational or other interventions have increased insight. Therapeutic implications for changes of dysfunctional beliefs related to illness and self and change of self-concept in the context of recovery at the level of narrative identity are discussed. Copyright © 2012 Elsevier Inc. All rights reserved.

A General Procedure to Assess the Internal Structure of a Noncognitive Measure--The Student360 Insight Program (S360) Time Management Scale. Research Report. ETS RR-11-42

ERIC Educational Resources Information Center

Ling, Guangming; Rijmen, Frank

2011-01-01

The factorial structure of the Time Management (TM) scale of the Student 360: Insight Program (S360) was evaluated based on a national sample. A general procedure with a variety of methods was introduced and implemented, including the computation of descriptive statistics, exploratory factor analysis (EFA), and confirmatory factor analysis (CFA).…

Surprises and insights from long-term aquatic datasets and experiments

Treesearch

Walter K. Dodds; Christopher T. Robinson; Evelyn E. Gaiser; Gretchen J.A. Hansen; Heather Powell; Joseph M. Smith; Nathaniel B. Morse; Sherri L. Johnson; Stanley V. Gregory; Tisza Bell; Timothy K. Kratz; William H. McDowell

2012-01-01

Long-term research on freshwater ecosystems provides insights that can be difficult to obtain from other approaches. Widespread monitoring of ecologically relevant water-quality parameters spanning decades can facilitate important tests of ecological principles. Unique long-term data sets and analytical tools are increasingly available, allowing for powerful and...

Modeling Insight into Battery Electrolyte Electrochemical Stability and Interfacial Structure.

PubMed

Borodin, Oleg; Ren, Xiaoming; Vatamanu, Jenel; von Wald Cresce, Arthur; Knap, Jaroslaw; Xu, Kang

2017-12-19

Electroactive interfaces distinguish electrochemistry from chemistry and enable electrochemical energy devices like batteries, fuel cells, and electric double layer capacitors. In batteries, electrolytes should be either thermodynamically stable at the electrode interfaces or kinetically stable by forming an electronically insulating but ionically conducting interphase. In addition to a traditional optimization of electrolytes by adding cosolvents and sacrificial additives to preferentially reduce or oxidize at the electrode surfaces, knowledge of the local electrolyte composition and structure within the double layer as a function of voltage constitutes the basis of manipulating an interphase and expanding the operating windows of electrochemical devices. In this work, we focus on how the molecular-scale insight into the solvent and ion partitioning in the electrolyte double layer as a function of applied potential could predict changes in electrolyte stability and its initial oxidation and reduction reactions. In molecular dynamics (MD) simulations, highly concentrated lithium aqueous and nonaqueous electrolytes were found to exclude the solvent molecules from directly interacting with the positive electrode surface, which provides an additional mechanism for extending the electrolyte oxidation stability in addition to the well-established simple elimination of "free" solvent at high salt concentrations. We demonstrate that depending on their chemical structures, the anions could be designed to preferentially adsorb or desorb from the positive electrode with increasing electrode potential. This provides additional leverage to dictate the order of anion oxidation and to effectively select a sacrificial anion for decomposition. The opposite electrosorption behaviors of bis(trifluoromethane)sulfonimide (TFSI) and trifluoromethanesulfonate (OTF) as predicted by MD simulation in highly concentrated aqueous electrolytes were confirmed by surface enhanced infrared

Preservation and compensation: The functional neuroanatomy of insight and working memory in schizophrenia☆

PubMed Central

Sapara, Adegboyega; ffytche, Dominic H.; Birchwood, Max; Cooke, Michael A.; Fannon, Dominic; Williams, Steven C.R.; Kuipers, Elizabeth; Kumari, Veena

2014-01-01

Background Poor insight in schizophrenia has been theorised to reflect a cognitive deficit that is secondary to brain abnormalities, localized in the brain regions that are implicated in higher order cognitive functions, including working memory (WM). This study investigated WM-related neural substrates of preserved and poor insight in schizophrenia. Method Forty stable schizophrenia outpatients, 20 with preserved and 20 with poor insight (usable data obtained from 18 preserved and 14 poor insight patients), and 20 healthy participants underwent functional magnetic resonance imaging (fMRI) during a parametric ‘n-back’ task. The three groups were preselected to match on age, education and predicted IQ, and the two patient groups to have distinct insight levels. Performance and fMRI data were analysed to determine how groups of patients with preserved and poor insight differed from each other, and from healthy participants. Results Poor insight patients showed lower performance accuracy, relative to healthy participants (p = 0.01) and preserved insight patients (p = 0.08); the two patient groups were comparable on symptoms and medication. Preserved insight patients, relative to poor insight patients, showed greater activity most consistently in the precuneus and cerebellum (both bilateral) during WM; they also showed greater activity than healthy participants in the inferior–superior frontal gyrus and cerebellum (bilateral). Group differences in brain activity did not co-vary significantly with performance accuracy. Conclusions The precuneus and cerebellum function contribute to preserved insight in schizophrenia. Preserved insight as well as normal-range WM capacity in schizophrenia sub-groups may be achieved via compensatory neural activity in the frontal cortex and cerebellum. PMID:24332795

InSight Encapsulation

NASA Image and Video Library

2018-04-16

In the Astrotech facility at Vandenberg Air Force Base in California, technicians and engineers encapsulate NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander in its payload fairing. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

Biochemical and Structural Insights into the Preference of Nairoviral DeISGylases for Interferon-Stimulated Gene Product 15 Originating from Certain Species

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

Deaton, M. K.; Dzimianski, J. V.; Daczkowski, C. M.

ABSTRACT The regulation of the interferon type I (IFN-I) response has been shown to rely on posttranslational modification by ubiquitin (Ub) and Ub-like interferon-stimulated gene product 15 (ISG15) to stabilize, or activate, a variety of IFN-I signaling and downstream effector proteins. Unlike Ub, which is almost perfectly conserved among eukaryotes, ISG15 is highly divergent, even among mammals. Since zoonotic viruses rely on viral proteins to recognize, or cleave, ISG15 conjugates in order to evade, or suppress, innate immunity, the impact of ISG15 biodiversity on deISGylating proteases of the ovarian tumor family (vOTU) from nairoviruses was evaluated. The enzymatic activities ofmore » vOTUs originating from the Crimean-Congo hemorrhagic fever virus, Erve virus, and Nairobi sheep disease virus were tested against ISG15s from humans, mice, shrews, sheep, bats, and camels, which are mammalian species known to be infected by nairoviruses. This along with investigation of binding by isothermal titration calorimetry illustrated significant differences in the abilities of nairovirus deISGylases to accommodate certain species of ISG15. To investigate the molecular underpinnings of species preferences of these vOTUs, a structure was determined to 2.5 Å for a complex of Erve virus vOTU protease and a mouse ISG15 domain. This structure revealed the molecular basis of Erve virus vOTU's preference for ISG15 over Ub and the first structural insight into a nonhuman ISG15. This structure also revealed key interactions, or lack thereof, surrounding three amino acids that may drive a viral deISgylase to prefer an ISG15 from one species over that of another. IMPORTANCEViral ovarian tumor domain proteases (vOTUs) are one of the two principal classes of viral proteases observed to reverse posttranslational modification of host proteins by ubiquitin and interferon-stimulated gene product 15 (ISG15), subsequently facilitating downregulation of IFN-I signaling pathways. Unlike the

The relationship between theory of mind and insight in obsessive-compulsive disorder.

PubMed

Tulacı, Rıza Gökçer; Cankurtaran, Eylem Şahin; Özdel, Kadir; Öztürk, Nefise; Kuru, Erkan; Özdemir, İlker

2018-02-09

It is known that obsessive-compulsive disorder (OCD) patients with poor insight display more severe neuropsychological impairments than other patients with OCD. There are limited studies of OCD and theory of mind (ToM). To investigate ToM skills in patients with OCD and the relationship between insight and ToM skills by comparing OCD patients with good and poor insight. Eighty patients with OCD and 80 healthy controls completed the structured clinical interview for DSM-IV axis I disorders, the Yale Brown Obsessive-Compulsive Scale, the Beck Anxiety and Beck Depression Inventories, and the Brown Assessment of Beliefs Scale. To assess ToM skills, first- and second-order false-belief tests, a hinting test, a faux pas test, a reading the mind in the eyes test, and a double-bluff test were administered. Patients with OCD had poorer ToM abilities than healthy controls. All ToM scores were significantly lower in the poor insight group than in the good insight group (p < .001). A significant negative correlation was found between the BABS-total scores and all the ToM test mean scores (p < .05). The finding of significantly lower ToM skills in OCD with poor insight than in OCD with good insight may contribute to the idea of OCD with poor insight being a subtype with different clinical and neuropsychological characteristics.

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures.

PubMed

Zhang, S; Nordlund, K; Djurabekova, F; Zhang, Y; Velisa, G; Wang, T S

2016-10-01

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

DOE PAGES

Zhang, S.; Univ. of Helsinki; Nordlund, Kai; ...

2016-10-25

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop in this paper a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms,more » Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Finally, comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.« less

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

NASA Astrophysics Data System (ADS)

Zhang, S.; Nordlund, K.; Djurabekova, F.; Zhang, Y.; Velisa, G.; Wang, T. S.

2016-10-01

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

Structural and functional insight into the carbohydrate receptor binding of F4 fimbriae-producing enterotoxigenic Escherichia coli.

PubMed

Moonens, Kristof; Van den Broeck, Imke; De Kerpel, Maia; Deboeck, Francine; Raymaekers, Hanne; Remaut, Han; De Greve, Henri

2015-03-27

Enterotoxigenic Escherichia coli (ETEC) strains are important causes of intestinal disease in humans and lead to severe production losses in animal farming. A range of fimbrial adhesins in ETEC strains determines host and tissue tropism. ETEC strains expressing F4 fimbriae are associated with neonatal and post-weaning diarrhea in piglets. Three naturally occurring variants of F4 fimbriae (F4ab, F4ac, and F4ad) exist that differ in the primary sequence of their major adhesive subunit FaeG, and each features a related yet distinct receptor binding profile. Here the x-ray structure of FaeGad bound to lactose provides the first structural insight into the receptor specificity and mode of binding by the poly-adhesive F4 fimbriae. A small D'-D″-α1-α2 subdomain grafted on the immunoglobulin-like core of FaeG hosts the carbohydrate binding site. Two short amino acid stretches Phe(150)-Glu(152) and Val(166)-Glu(170) of FaeGad bind the terminal galactose in the lactosyl unit and provide affinity and specificity to the interaction. A hemagglutination-based assay with E. coli expressing mutant F4ad fimbriae confirmed the elucidated co-complex structure. Interestingly, the crucial D'-α1 loop that borders the FaeGad binding site adopts a different conformation in the two other FaeG variants and hints at a heterogeneous binding pocket among the FaeG serotypes. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Insights from molecular dynamics simulations for computational protein design.

PubMed

Childers, Matthew Carter; Daggett, Valerie

2017-02-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

Insights from molecular dynamics simulations for computational protein design

PubMed Central

Childers, Matthew Carter; Daggett, Valerie

2017-01-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures. PMID:28239489

InSight Prelaunch Briefing

NASA Image and Video Library

2018-05-03

Stu Spath, InSight program manager, Lockheed Martin Space, left, and Tom Hoffman, InSight project manager, NASA JPL, discuss NASA's InSight mission during a prelaunch media briefing, Thursday, May 3, 2018, at Vandenberg Air Force Base in California. InSight, short for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, is a Mars lander designed to study the "inner space" of Mars: its crust, mantle, and core. Photo Credit: (NASA/Bill Ingalls)

Combined structures-controls optimization of lattice trusses

NASA Technical Reports Server (NTRS)

Balakrishnan, A. V.

1991-01-01

The role that distributed parameter model can play in CSI is demonstrated, in particular in combined structures controls optimization problems of importance in preliminary design. Closed form solutions can be obtained for performance criteria such as rms attitude error, making possible analytical solutions of the optimization problem. This is in contrast to the need for numerical computer solution involving the inversion of large matrices in traditional finite element model (FEM) use. Another advantage of the analytic solution is that it can provide much needed insight into phenomena that can otherwise be obscured or difficult to discern from numerical computer results. As a compromise in level of complexity between a toy lab model and a real space structure, the lattice truss used in the EPS (Earth Pointing Satellite) was chosen. The optimization problem chosen is a generic one: of minimizing the structure mass subject to a specified stability margin and to a specified upper bond on the rms attitude error, using a co-located controller and sensors. Standard FEM treating each bar as a truss element is used, while the continuum model is anisotropic Timoshenko beam model. Performance criteria are derived for each model, except that for the distributed parameter model, explicit closed form solutions was obtained. Numerical results obtained by the two model show complete agreement.

Structural Insights Into the Recognition of Peroxisomal Targeting Signal 1 By Trypanosoma Brucei Peroxin 5

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

Sampathkumar, P.; Roach, C.; Michels, P.A.M.

2009-05-27

Glycosomes are peroxisome-like organelles essential for trypanosomatid parasites. Glycosome biogenesis is mediated by proteins called 'peroxins,' which are considered to be promising drug targets in pathogenic Trypanosomatidae. The first step during protein translocation across the glycosomal membrane of peroxisomal targeting signal 1 (PTS1)-harboring proteins is signal recognition by the cytosolic receptor peroxin 5 (PEX5). The C-terminal PTS1 motifs interact with the PTS1 binding domain (P1BD) of PEX5, which is made up of seven tetratricopeptide repeats. Obtaining diffraction-quality crystals of the P1BD of Trypanosoma brucei PEX5 (TbPEX5) required surface entropy reduction mutagenesis. Each of the seven tetratricopeptide repeats appears to havemore » a residue in the alpha(L) conformation in the loop connecting helices A and B. Five crystal structures of the P1BD of TbPEX5 were determined, each in complex with a hepta- or decapeptide corresponding to a natural or nonnatural PTS1 sequence. The PTS1 peptides are bound between the two subdomains of the P1BD. These structures indicate precise recognition of the C-terminal Leu of the PTS1 motif and important interactions between the PTS1 peptide main chain and up to five invariant Asn side chains of PEX5. The TbPEX5 structures reported here reveal a unique hydrophobic pocket in the subdomain interface that might be explored to obtain compounds that prevent relative motions of the subdomains and interfere selectively with PTS1 motif binding or release in trypanosomatids, and would therefore disrupt glycosome biogenesis and prevent parasite growth.« less

Structural and Functional Studies of H. seropedicae RecA Protein - Insights into the Polymerization of RecA Protein as Nucleoprotein Filament.

PubMed

Leite, Wellington C; Galvão, Carolina W; Saab, Sérgio C; Iulek, Jorge; Etto, Rafael M; Steffens, Maria B R; Chitteni-Pattu, Sindhu; Stanage, Tyler; Keck, James L; Cox, Michael M

2016-01-01

The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.

Occupational therapists' self-insight into their referral prioritisation policies for clients with mental health needs.

PubMed

Harries, Priscilla Ann; Gilhooly, Kenneth J

2010-12-01

Obtaining valid accounts of professionals' thinking is dependent upon experts' capacity for self-insight. Self-insight has implications for developing professional decision making, facilitating education and promoting agreement among therapists. The aim of this study was to examine occupational therapists' self-insight into their referral prioritisation policies. A total of 40 occupational therapists individually rated the importance that differing types of referral content had on their prioritisation of referrals. These subjective policies were then correlated with their objective referral prioritisation policies that had been previously statistically derived. Self-insight was found to be moderate but with wide variation across individuals and across referral information used. Self-insight on cues that were important to the decision was found to be better than on those cues not so important to the decision.   Occupational therapists have similar levels of self-insight to other professional groups. The 'attention hypothesis' may explain why self-insight varied across referral information used. © 2010 The Authors. Australian Occupational Therapy Journal © 2010 Australian Association of Occupational Therapists.

Gas/vapour separation using ultra-microporous metal-organic frameworks: insights into the structure/separation relationship.

PubMed

Adil, Karim; Belmabkhout, Youssef; Pillai, Renjith S; Cadiau, Amandine; Bhatt, Prashant M; Assen, Ayalew H; Maurin, Guillaume; Eddaoudi, Mohamed

2017-06-06

The separation of related molecules with similar physical/chemical properties is of prime industrial importance and practically entails a substantial energy penalty, typically necessitating the operation of energy-demanding low temperature fractional distillation techniques. Certainly research efforts, in academia and industry alike, are ongoing with the main aim to develop advanced functional porous materials to be adopted as adsorbents for the effective and energy-efficient separation of various important commodities. Of special interest is the subclass of metal-organic frameworks (MOFs) with pore aperture sizes below 5-7 Å, namely ultra-microporous MOFs, which in contrast to conventional zeolites and activated carbons show great prospects for addressing key challenges in separations pertaining to energy and environmental sustainability, specifically materials for carbon capture and separation of olefin/paraffin, acetylene/ethylene, linear/branched alkanes, xenon/krypton, etc. In this tutorial review we discuss the latest developments in ultra-microporous MOF adsorbents and their use as separating agents via thermodynamics and/or kinetics and molecular sieving. Appreciably, we provide insights into the distinct microscopic mechanisms governing the resultant separation performances, and suggest a plausible correlation between the inherent structural features/topology of MOFs and the associated gas/vapour separation performance.

Insights into the structural features and stability of peptide nucleic acid with a D-prolyl-2-aminocyclopentane carboxylic acid backbone that binds to DNA and RNA.

PubMed

Poomsuk, Nattawee; Vilaivan, Tirayut; Siriwong, Khatcharin

2018-06-12

Peptide nucleic acid (PNA) is a powerful biomolecule with a wide variety of important applications. In this work, the molecular structures and binding affinity of PNA with a D-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) that binds to both DNA and RNA were studied using molecular dynamics simulations. The simulated structures of acpcPNA-DNA and acpcPNA-RNA duplexes more closely resembled the typical structures of B-DNA and A-RNA than the corresponding duplexes of aegPNA. The calculated binding free energies are in good agreement with the experimental results that the acpcPNA-DNA duplex is more stable than the acpcPNA-RNA duplex regardless of the base sequences. The results provide further insights in the relationship between structure and stability of this unique PNA system. Copyright © 2018 Elsevier Inc. All rights reserved.

Exploring the structural insights on human laforin mutation K87A in Lafora disease--a molecular dynamics study.

PubMed

Srikumar, P S; Rohini, K

2013-10-01

Lafora disease (LD) is an autosomal recessive, progressive form of myoclonus epilepsy which affects worldwide. LD occurs mainly in countries like southern Europe, northern Africa, South India, and in the Middle East. LD occurs with its onset mainly in teenagers and leads to decline and death within 2 to 10 years. The genes EPM2A and EPM2B are commonly involved in 90 % of LD cases. EPM2A codes for protein laforin which contains an amino terminal carbohydrate binding module (CBM) belonging to the CBM20 family and a carboxy terminal dual specificity phosphatase domain. Mutations in laforin are found to abolish glycogen binding and have been reported in wet lab methods. In order to investigate on structural insights on laforin mutation K81A, we performed molecular dynamics (MD) simulation studies for native and mutant protein. MD simulation results showed loss of stability due to mutation K87A which confirmed the structural reason for conformational changes observed in laforin. The conformational change of mutant laforin was confirmed by analysis using root mean square deviation, root mean square fluctuation, solvent accessibility surface area, radius of gyration, hydrogen bond, and principle component analysis. Our results identified that the flexibility of K87A mutated laforin structure, with replacement of acidic amino acid to aliphatic amino acid in functional CBM domain, have more impact in abolishing glycogen binding that favors LD.

Electronic structures of elements according to ionization energies.

PubMed

Zadeh, Dariush H

2017-11-28

The electronic structures of elements in the periodic table were analyzed using available experimental ionization energies. Two new parameters were defined to carry out the study. The first parameter-apparent nuclear charge (ANC)-quantified the overall charge of the nucleus and inner electrons observed by an outer electron during the ionization process. This parameter was utilized to define a second parameter, which presented the shielding ability of an electron against the nuclear charge. This second parameter-electron shielding effect (ESE)-provided an insight into the electronic structure of atoms. This article avoids any sort of approximation, interpolation or extrapolation. First experimental ionization energies were used to obtain the two aforementioned parameters. The second parameter (ESE) was then graphed against the electron number of each element, and was used to read the corresponding electronic structure. The ESE showed spikes/peaks at the end of each electronic shell, providing insight into when an electronic shell closes and a new one starts. The electronic structures of elements in the periodic table were mapped using this methodology. These graphs did not show complete agreement with the previously known "Aufbau" filling rule. A new filling rule was suggested based on the present observations. Finally, a new way to organize elements in the periodic table is suggested. Two earlier topics of effective nuclear charge, and shielding factor were also briefly discussed and compared numerically to demonstrate the capability of the new approach.

Wood-Polymer composites obtained by gamma irradiation

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

Gago, J.; Lopez, A.; Rodriguez, J.

2007-10-26

In this work we impregnate three Peruvian woods (Calycophy spruceanum Be, Aniba amazonica Meiz and Hura crepitans L) with styrene-polyester resin and methyl methacrylate. The polymerization of the system was promoted by gamma radiation and the experimental optimal condition was obtained with styrene-polyester 1:1 and 15 kGy. The obtained composites show reduced water absorption and better mechanical properties compared to the original wood. The structure of the wood-polymer composites was studied by light microscopy. Water absorption and hardness were also obtained.

Structural insight into catalytic mechanism of PET hydrolase.

PubMed

Han, Xu; Liu, Weidong; Huang, Jian-Wen; Ma, Jiantao; Zheng, Yingying; Ko, Tzu-Ping; Xu, Limin; Cheng, Ya-Shan; Chen, Chun-Chi; Guo, Rey-Ting

2017-12-13

PET hydrolase (PETase), which hydrolyzes polyethylene terephthalate (PET) into soluble building blocks, provides an attractive avenue for the bioconversion of plastics. Here we present the structures of a novel PETase from the PET-consuming microbe Ideonella sakaiensis in complex with substrate and product analogs. Through structural analyses, mutagenesis, and activity measurements, a substrate-binding mode is proposed, and several features critical for catalysis are elucidated.

Insights into the fold organization of TIM barrel from interaction energy based structure networks.

PubMed

Vijayabaskar, M S; Vishveshwara, Saraswathi

2012-01-01

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or "sequence conservation" as the basis for their understanding. Recently "interaction energy" based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the "interaction conservation" viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

Crystal Structures of the Tetratricopeptide Repeat Domains of Kinesin Light Chains: Insight into Cargo Recognition Mechanisms

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

Zhu, Haizhong; Lee, Han Youl; Tong, Yufeng

Kinesin-1 transports various cargos along the axon by interacting with the cargos through its light chain subunit. Kinesin light chains (KLC) utilize its tetratricopeptide repeat (TPR) domain to interact with over 10 different cargos. Despite a high sequence identity between their TPR domains (87%), KLC1 and KLC2 isoforms exhibit differential binding properties towards some cargos. We determined the structures of human KLC1 and KLC2 tetratricopeptide repeat (TPR) domains using X-ray crystallography and investigated the different mechanisms by which KLCs interact with their cargos. Using isothermal titration calorimetry, we attributed the specific interaction between KLC1 and JNK-interacting protein 1 (JIP1) cargomore » to residue N343 in the fourth TRP repeat. Structurally, the N343 residue is adjacent to other asparagines and lysines, creating a positively charged polar patch within the groove of the TPR domain. Whereas, KLC2 with the corresponding residue S328 did not interact with JIP1. Based on these finding, we propose that N343 of KLC1 can form 'a carboxylate clamp' with its neighboring asparagine to interact with JIP1, similar to that of HSP70/HSP90 organizing protein-1's (HOP1) interaction with heat shock proteins. For the binding of cargos shared by KLC1 and KLC2, we propose a different site located within the groove but not involving N343. We further propose a third binding site on KLC1 which involves a stretch of polar residues along the inter-TPR loops that may form a network of hydrogen bonds to JIP3 and JIP4. Together, these results provide structural insights into possible mechanisms of interaction between KLC TPR domains and various cargo proteins.« less

Structural insights of a PI3K/mTOR dual inhibitor with the morpholino-triazine scaffold

NASA Astrophysics Data System (ADS)

Takeda, Takako; Wang, Yanli; Bryant, Stephen H.

2016-04-01

Stimulation of the PI3K/Akt/mTOR pathway, which controls cell proliferation and growth, is often observed in cancer cell. Inhibiting both PI3K and mTOR in this pathway can switch off Akt activation and hence, plays a powerful role for modulating this pathway. PKI-587, a drug containing the structure of morpholino-triazines, shows a dual and nano-molar inhibition activity and is currently in clinical trial. To provide an insight into the mechanism of this dual inhibition, pharmacophore and QSAR models were developed in this work using compounds based on the morpholino-triazines scaffold, followed by a docking study. Pharmacophore model suggested the mechanism of the inhibition of PI3Kα and mTOR by the compounds were mostly the same, which was supported by the docking study showing similar docking modes. The analysis also suggested the importance of the flat plane shape of the ligands, the space surrounding the ligands in the binding pocket, and the slight difference in the shape of the binding sites between PI3Kα and mTOR.

Cyanomethanimine Isomers in Cold Interstellar Clouds: Insights from Electronic Structure and Kinetic Calculations

NASA Astrophysics Data System (ADS)

Vazart, Fanny; Latouche, Camille; Skouteris, Dimitrios; Balucani, Nadia; Barone, Vincenzo

2015-09-01

New insights into the formation of interstellar cyanomethanimine, a species of great relevance in prebiotic chemistry, are provided by electronic structure and kinetic calculations for the reaction CN + CH2 = NH. This reaction is a facile formation route of Z,E-C-cyanomethanimine, even under the extreme conditions of density and temperature typical of cold interstellar clouds. E-C-cyanomethanimine has been recently identified in Sgr B2(N) in the Green Bank Telescope (GBT) PRIMOS survey by P. Zaleski et al. and no efficient formation routes have been envisaged so far. The rate coefficient expression for the reaction channel leading to the observed isomer E-C-cyanomethanimine is 3.15 × 10-10 × (T/300)0.152 × e(-0.0948/T). According to the present study, the more stable Z-C-cyanomethanimine isomer is formed with a slightly larger yield (4.59 × 10-10 × (T/300)0.153 × e(-0.0871/T). As the detection of E-isomer is favored due to its larger dipole moment, the missing detection of the Z-isomer can be due to the sensitivity limit of the GBT PRIMOS survey and the detection of the Z-isomer should be attempted with more sensitive instrumentation. The CN + CH2 = NH reaction can also play a role in the chemistry of the upper atmosphere of Titan where the cyanomethanimine products can contribute to the buildup of the observed nitrogen-rich organic aerosols that cover the moon.

Synthesis, optimization and structural characterization of a chitosan-glucose derivative obtained by the Maillard reaction.

PubMed

Gullón, Beatriz; Montenegro, María I; Ruiz-Matute, Ana I; Cardelle-Cobas, Alejandra; Corzo, Nieves; Pintado, Manuela E

2016-02-10

Chitosan (Chit) was submitted to the Maillard reaction (MR) by co-heating a solution with glucose (Glc). Different reaction conditions as temperature (40, 60 and 80 °C), Glc concentration (0.5%, 1%, and 2%, w/v), and reaction time (72, 52 and 24h) were evaluated. Assessment of the reaction extent was monitored by measuring changes in UV absorbance, browning and fluorescence. Under the best conditions, 2% (w/v) of Chit, 2% (w/v) of Glc at 60°C and 32 h of reaction time, a chitosan-glucose (Chit-Glc) derivative was purified and submitted to structural characterization to confirm its formation. Analysis of its molecular weight (MW) and the degree of substitution (DS) was carried out by HPLC-Size Exclusion Chromatography (SEC) and a colloid titration method, respectively. FT-IR and (1)H NMR were also used to analyze the functional groups and evaluate the introduction of Glc into the Chit molecule. According to our objectives, the results obtained in this work allowed to better understand the key parameters influencing the MR with Chit as well as to confirm the successful introduction of Glc into the Chit molecule obtaining a Chit-Glc derivative with a DS of 64.76 ± 4.40% and a MW of 210.37 kDa. Copyright © 2015 Elsevier Ltd. All rights reserved.

Narrative insight in psychosis: The relationship with spiritual and religious explanatory frameworks.

PubMed

Marriott, Michael R; Thompson, Andrew R; Cockshutt, Graham; Rowse, Georgina

2018-03-25

When considering psychosis, the concept of narrative insight has been offered as an alternative to clinical insight in determining individuals' responses to their difficulties, as it allows for a more holistic and person-centred framework to be embraced within professional practice. This study aims to explore the validity of the narrative insight construct within a group of people who have experienced psychosis. Inductive qualitative methods were used to explore how eight participants utilized spiritual or religious explanatory frameworks for their experiences of psychosis and to consider these in relation to the construct of narrative insight. Semi-structured interviews were undertaken with individuals who identified themselves as interested in spiritual or religious ideas and whose self-reported experiences which were identified as akin to psychosis by experienced academic clinicians. Transcriptions from these interviews were subject to interpretative phenomenological analysis within a broader research question; a selection of themes and data from the resultant phenomenological structure are explored here for their relevance to narrative insight. Participants discussed spiritual and biological explanations for their experiences and were able to hold alternative potential explanations alongside each other. They were reflective regarding the origins of their explanations and would describe a process of testing and proof in relation to them. These findings suggest that the narrative insight construct has the potential to be a valid approach to understanding experiences of psychosis, and challenge the dominance of the clinical insight construct within clinical practice. Clinicians should value the explanatory framework for experiences which are provided by individuals experiencing psychosis, and encourage them to develop a framework which is coherent to their own world view rather than predominantly pursuing a biomedical explanation. Assessments of psychosis should

Expression, Purification, and Structural Insights for the Human Uric Acid Transporter, GLUT9, Using the Xenopus laevis Oocytes System

PubMed Central

Clémençon, Benjamin; Lüscher, Benjamin P.; Fine, Michael; Baumann, Marc U.; Surbek, Daniel V.; Bonny, Olivier; Hediger, Matthias A.

2014-01-01

The urate transporter, GLUT9, is responsible for the basolateral transport of urate in the proximal tubule of human kidneys and in the placenta, playing a central role in uric acid homeostasis. GLUT9 shares the least homology with other members of the glucose transporter family, especially with the glucose transporting members GLUT1-4 and is the only member of the GLUT family to transport urate. The recently published high-resolution structure of XylE, a bacterial D-xylose transporting homologue, yields new insights into the structural foundation of this GLUT family of proteins. While this represents a huge milestone, it is unclear if human GLUT9 can benefit from this advancement through subsequent structural based targeting and mutagenesis. Little progress has been made toward understanding the mechanism of GLUT9 since its discovery in 2000. Before work can begin on resolving the mechanisms of urate transport we must determine methods to express, purify and analyze hGLUT9 using a model system adept in expressing human membrane proteins. Here, we describe the surface expression, purification and isolation of monomeric protein, and functional analysis of recombinant hGLUT9 using the Xenopus laevis oocyte system. In addition, we generated a new homology-based high-resolution model of hGLUT9 from the XylE crystal structure and utilized our purified protein to generate a low-resolution single particle reconstruction. Interestingly, we demonstrate that the functional protein extracted from the Xenopus system fits well with the homology-based model allowing us to generate the predicted urate-binding pocket and pave a path for subsequent mutagenesis and structure-function studies. PMID:25286413

Promoting entrepreneurship among informatics engineering students: insights from a case study

NASA Astrophysics Data System (ADS)

Fernandes, João M.; Afonso, Paulo; Fonte, Victor; Alves, Victor; Ribeiro, António Nestor

2017-01-01

Universities seek to promote entrepreneurship through effective education approaches, which need to be in permanent evolution. Nevertheless, the literature in entrepreneurship education lacks empirical evidence. This article discusses relevant issues related to promoting entrepreneurship in the software field, based on the experience of a 15-European Credit Transfer and Accumulation System course. This course seeks to instil in the students the recognition of the need to reconcile technical and business visions, organisational and commercial aspects, most of which have never been addressed previously. A series of semi-structured interviews made it possible to obtain relevant insights about the teaching-learning process underlying this course and its evolution over a seven-year period. Materials related with this course have been analysed, namely guidelines produced by the teachers and deliverables produced by the students. This article discusses the dimensions that were identified as fundamental for promoting entrepreneurship skills in the field of software, namely teamwork, project engagement, and contact with the market.

Comprehensive insights into the structural and chemical changes in mixed-anion FeOF electrodes by using operando PDF and NMR spectroscopy.

PubMed

Wiaderek, Kamila M; Borkiewicz, Olaf J; Castillo-Martínez, Elizabeth; Robert, Rosa; Pereira, Nathalie; Amatucci, Glenn G; Grey, Clare P; Chupas, Peter J; Chapman, Karena W

2013-03-13

In-depth analysis of operando X-ray pair distribution function (PDF) data is combined with Li NMR spectroscopy to gain comprehensive insights into the electrochemical reaction mechanism of high-performance iron oxyfluoride electrodes. While the full discharge capacity could be recovered upon charge, implying reversibility of the electrochemical reaction, the atomic structure of the electrode formed after cycling (discharge-charge) differs from the pristine uncycled electrode material. Instead, the "active" electrode that forms upon cycling is a nanocomposite of an amorphous rutile phase and a nanoscale rock salt phase. Bond valence sum analysis, based on the precise structural parameters (bond lengths and coordination number) extracted from the in situ PDF data, suggests that anion partitioning occurs during the electrochemical reaction, with the rutile phase being F-rich and the rock salt phase being O-rich. The F- and O-rich phases react sequentially; Fe in a F-rich environment reacts preferentially during both discharge and charge.

Insight into the structure and mechanism of nickel-containing superoxide dismutase derived from peptide-based mimics.

PubMed

Shearer, Jason

2014-08-19

Nickel superoxide dismutase (NiSOD) is a nickel-containing metalloenzyme that catalyzes the disproportionation of superoxide through a ping-pong mechanism that relies on accessing reduced Ni(II) and oxidized Ni(III) oxidation states. NiSOD is the most recently discovered SOD. Unlike the other known SODs (MnSOD, FeSOD, and (CuZn)SOD), which utilize "typical" biological nitrogen and oxygen donors, NiSOD utilizes a rather unexpected ligand set. In the reduced Ni(II) oxidation state, NiSOD utilizes nitrogen ligands derived from the N-terminal amine and an amidate along with two cysteinates sulfur donors. These are unusual biological ligands, especially for an SOD: amine and amidate donors are underrepresented as biological ligands, whereas cysteinates are highly susceptible to oxidative damage. An axial histidine imidazole binds to nickel upon oxidation to Ni(III). This bond is long (2.3-2.6 Å) owing to a tight hydrogen-bonding network. All of the ligating residues to Ni(II) and Ni(III) are found within the first 6 residues from the NiSOD N-terminus. Thus, small nickel-containing metallopeptides derived from the first 6-12 residues of the NiSOD sequence can reproduce many of the properties of NiSOD itself. Using these nickel-containing metallopeptide-based NiSOD mimics, we have shown that the minimal sequence needed for nickel binding and reproduction of the structural, spectroscopic, and functional properties of NiSOD is H2N-HCXXPC. Insight into how NiSOD avoids oxidative damage has also been gained. Using small NiN2S2 complexes and metallopeptide-based mimics, it was shown that the unusual nitrogen donor atoms protect the cysteinates from oxidative damage (both one-electron oxidation and oxygen atom insertion reactions) by fine-tuning the electronic structure of the nickel center. Changing the nitrogen donor set to a bis-amidate or bis-amine nitrogen donor led to catalytically nonviable species owing to nickel-cysteinate bond oxidative damage. Only the amine

Insight into Amyloid Structure Using Chemical Probes

PubMed Central

Reinke, Ashley A.; Gestwicki, Jason E.

2011-01-01

Alzheimer’s disease (AD) is a common neurodegenerative disorder characterized by the deposition of amyloids in the brain. One prominent form of amyloid is composed of repeating units of the amyloid-β (Aβ) peptide. Over the past decade, it has become clear that these Aβ amyloids are not homogeneous; rather, they are composed of a series of structures varying in their overall size and shape and the number of Aβ peptides they contain. Recent theories suggest that these different amyloid conformations may play distinct roles in disease, although their relative contributions are still being discovered. Here, we review how chemical probes, such as congo red, thioflavin T and their derivatives, have been powerful tools for better understanding amyloid structure and function. Moreover, we discuss how design and deployment of conformationally selective probes might be used to test emerging models of AD. PMID:21457473

Influence of annealing temperature on optical properties of the photonic-crystal structures obtained by self-organization of colloidal microspheres of polystyrene and silica

NASA Astrophysics Data System (ADS)

Mikhnev, L. V.; Bondarenko, E. A.; Chapura, O. M.; Skomorokhov, A. A.; Kravtsov, A. A.

2018-01-01

The influence of annealing temperature on the transmission spectra of photonic crystals composed of polystyrene and silicon dioxide microspheres was studied. It was found that annealing of photonic crystals based on polystyrene and silica leads to a shift in the photonic band gap to the short-wavelength region. Based on the results of optical studies, the dependences of the structural parameters of the obtained opal-like crystals on annealing temperature were obtained. In the case of polystyrene photonic crystals, the displacement of the photonic band gap is observed in a narrow temperature range above the glass transition temperature. For SiO2 photonic crystals, it was found that the process of microspheres sintering is complex and involves three stages of structural modification.

Structure and mechanical properties of parts obtained by selective laser melting of metal powder based on intermetallic compounds Ni3Al

NASA Astrophysics Data System (ADS)

Smelov, V. G.; Sotov, A. V.; Agapovichev, A. V.; Nosova, E. A.

2018-03-01

The structure and mechanical properties of samples are obtained from metal powder based on intermetallic compound by selective laser melting. The chemical analysis of the raw material and static tensile test of specimens were made. Change in the samples’ structure and mechanical properties after homogenization during four and twenty-four hours were investigated. A small-sized combustion chamber of a gas turbine engine was performed by the selective laser melting method. The print combustion chamber was subjected to the gas-dynamic test in a certain temperature and time range.

Impaired insight into illness and cognitive insight in schizophrenia spectrum disorders: Resting state functional connectivity

PubMed Central

Gerretsen, Philip; Menon, Mahesh; Mamo, David C.; Fervaha, Gagan; Remington, Gary; Pollock, Bruce G.; Graff-Guerrero, Ariel

2015-01-01

Background Impaired insight into illness (clinical insight) in schizophrenia has negative effects on treatment adherence and clinical outcomes. Schizophrenia is described as a disorder of disrupted brain connectivity. In line with this concept, resting state networks (RSNs) appear differentially affected in persons with schizophrenia. Therefore, impaired clinical, or the related construct of cognitive insight (which posits that impaired clinical insight is a function of metacognitive deficits), may reflect alterations in RSN functional connectivity (fc). Based on our previous research, which showed that impaired insight into illness was associated with increased left hemisphere volume relative to right, we hypothesized that impaired clinical insight would be associated with increased connectivity in the DMN with specific left hemisphere brain regions. Methods Resting state MRI scans were acquired for participants with schizophrenia or schizoaffective disorder (n = 20). Seed-to-voxel and ROI-to-ROI fc analyses were performed using the CONN-fMRI fc toolbox v13 for established RSNs. Clinical and cognitive insight were measured with the Schedule for the Assessment of Insight—Expanded Version and Beck Cognitive Insight Scale, respectively, and included as the regressors in fc analyses. Results As hypothesized, impaired clinical insight was associated with increased connectivity in the default mode network (DMN) with the left angular gyrus, and also in the self-referential network (SRN) with the left insula. Cognitive insight was associated with increased connectivity in the dorsal attention network (DAN) with the right inferior frontal cortex (IFC) and left anterior cingulate cortex (ACC). Conclusion Increased connectivity in DMN and SRN with the left angular gyrus and insula, respectively, may represent neural correlates of impaired clinical insight in schizophrenia spectrum disorders, and is consistent with the literature attributing impaired insight to left

Lanthanide complexes with aromatic o-phosphorylated ligands: synthesis, structure elucidation and photophysical properties.

PubMed

Shuvaev, Sergey; Utochnikova, Valentina; Marciniak, Łukasz; Freidzon, Alexandra; Sinev, Ilya; Van Deun, Rik; Freire, Ricardo O; Zubavichus, Yan; Grünert, Wolfgang; Kuzmina, Natalia

2014-02-28

Lanthanide complexes LnL3 (Ln = Sm, Eu, Tb, Dy, Tm, Yb, Lu) with aromatic o-phosphorylated ligands (HL(1) and HL(2)) have been synthesized and identified. Their molecular structure was proposed on the basis of a new complex approach, including DFT calculations, Sparkle/PM3 modelling, EXAFS spectroscopy and luminescent probing. The photophysical properties of all of the complexes were investigated in detail to obtain a deeper insight into the energy transfer processes.

The yeast Golgi apparatus: insights and mysteries

PubMed Central

Papanikou, Effrosyni; Glick, Benjamin S.

2009-01-01

The Golgi apparatus is known to modify and sort newly synthesized secretory proteins. However, fundamental mysteries remain about the structure, operation, and dynamics of this organelle. Important insights have emerged from studying the Golgi in yeasts. For example, yeasts have provided direct evidence for Golgi cisternal maturation, a mechanism that is likely to be broadly conserved. Here, we highlight features of the yeast Golgi as well as challenges that lie ahead. PMID:19879270

A mechanistic insight into the amyloidogenic structure of hIAPP peptide revealed from sequence analysis and molecular dynamics simulation.

PubMed

Chakraborty, Sandipan; Chatterjee, Barnali; Basu, Soumalee

2012-07-01

A collective approach of sequence analysis, phylogenetic tree and in silico prediction of amyloidogenecity using bioinformatics tools have been used to correlate the observed species-specific variations in IAPP sequences with the amyloid forming propensity. Observed substitution patterns indicate that probable changes in local hydrophobicity are instrumental in altering the aggregation propensity of the peptide. In particular, residues at 17th, 22nd and 23rd positions of the IAPP peptide are found to be crucial for amyloid formation. Proline25 primarily dictates the observed non-amyloidogenecity in rodents. Furthermore, extensive molecular dynamics simulation of 0.24 μs have been carried out with human IAPP (hIAPP) fragment 19-27, the portion showing maximum sequence variation across different species, to understand the native folding characteristic of this region. Principal component analysis in combination with free energy landscape analysis illustrates a four residue turn spanning from residue 22 to 25. The results provide a structural insight into the intramolecular β-sheet structure of amylin which probably is the template for nucleation of fibril formation and growth, a pathogenic feature of type II diabetes. Copyright © 2012 Elsevier B.V. All rights reserved.

Mars Lander Deck of NASA's InSight Mission

NASA Image and Video Library

2017-08-28

This view looks upward toward the InSight Mars lander suspended upside down. It shows the top of the lander's science deck with the mission's two main science instruments -- the Seismic Experiment for Interior Structure (SEIS) and the Heat Flow and Physical Properties Probe (HP3) -- plus the robotic arm and other subsystems installed. The photo was taken Aug. 9, 2017, in a Lockheed Martin clean room facility in Littleton, Colorado. The InSight mission (for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport) is scheduled to launch in May 2018 and land on Mars Nov. 26, 2018. It will investigate processes that formed and shaped Mars and will help scientists better understand the evolution of our inner solar system's rocky planets, including Earth. https://photojournal.jpl.nasa.gov/catalog/PIA21847

Stellar Rotation: New Insight from CoRoT

NASA Astrophysics Data System (ADS)

Catala, C.; Goupil, M. J.; Michel, E.; Baglin, A.; de Medeiros, J. Renan; Gondoin, Ph.

2009-02-01

We present an overview of the new insight provided by the CoRoT satellite on stellar rotation. Thanks to its ultra-high precision, high duty cycle, long photometric monitoring of thousands of stars, CoRoT gives us a powerful tool to study stellar rotational modulation, and therefore to measure stellar rotational periods and to study active structures at the surface of stars. This paper presents preliminary results concerning this type of study. CoRoT will also provide us with an insight of internal stellar rotation via the measurement and exploitation of rotational splittings of oscillation modes. This approach to stellar rotation with CoRoT will require a careful analysis of the oscillation power spectra, which is in progress, but prospects for such measurements are presented.

Challenges of Obtaining Informed Consent in Emergency Ward: A Qualitative Study in One Iranian Hospital

PubMed Central

Davoudi, Nayyereh; Nayeri, Nahid Dehghan; Zokaei, Mohammad Saeed; Fazeli, Nematallah

2017-01-01

Background and Objective: Regarding the fact that emergency ward has unique characteristics, whose uniqueness affects informed consent processes by creating specific challenges. Hence, it seems necessary to identify the process and challenges of informed consent in the emergency ward through a qualitative study to understand actual patients’ and health care providers’ experiences, beliefs, values, and feelings about the informed consent in the emergency ward. Through such studies, new insight can be gained on the process of informed consent and its challenges with the hope that the resulting knowledge will enable the promotion of ethical, legal as well as effective health services to the patients in the emergency ward. Method: In this qualitative study, research field was one of the emergency wards of educational and public hospitals in Iran. Field work and participant observation were carried out for 515 hours from June 2014 to March 2016. Also, conversations and semi-structured interviews based on the observations were conducted. The participants of the study were nurses and physicians working in the emergency ward, as well as patients and their attendants who were involved in the process of obtaining informed consent. Results: Three main categories were extracted from the data: a sense of frustration; reverse protection; and culture of paternalism in consent process. Conclusion: Findings of this study can be utilized in correcting the structures and processes of obtaining informed consent together with promotion of patients' ethical and legal care in emergency ward. In this way, the approaches in consent process will be changed from paternalistic approach to patient-centered care which concomitantly protects patient’s autonomy. PMID:29399235

Insightful problem solving in an Asian elephant.

PubMed

Foerder, Preston; Galloway, Marie; Barthel, Tony; Moore, Donald E; Reiss, Diana

2011-01-01

The "aha" moment or the sudden arrival of the solution to a problem is a common human experience. Spontaneous problem solving without evident trial and error behavior in humans and other animals has been referred to as insight. Surprisingly, elephants, thought to be highly intelligent, have failed to exhibit insightful problem solving in previous cognitive studies. We tested whether three Asian elephants (Elephas maximus) would use sticks or other objects to obtain food items placed out-of-reach and overhead. Without prior trial and error behavior, a 7-year-old male Asian elephant showed spontaneous problem solving by moving a large plastic cube, on which he then stood, to acquire the food. In further testing he showed behavioral flexibility, using this technique to reach other items and retrieving the cube from various locations to use as a tool to acquire food. In the cube's absence, he generalized this tool utilization technique to other objects and, when given smaller objects, stacked them in an attempt to reach the food. The elephant's overall behavior was consistent with the definition of insightful problem solving. Previous failures to demonstrate this ability in elephants may have resulted not from a lack of cognitive ability but from the presentation of tasks requiring trunk-held sticks as potential tools, thereby interfering with the trunk's use as a sensory organ to locate the targeted food.

Combining NMR and Molecular Dynamics Studies for Insights into the Allostery of Small GTPase–Protein Interactions

PubMed Central

Zhang, Liqun; Bouguet-Bonnet, Sabine; Buck, Matthias

2014-01-01

Combinations of experimentally derived data from nuclear magnetic resonance spectroscopy and analyses of molecular dynamics trajectories increasingly allow us to obtain a detailed description of the molecular mechanisms by which proteins function in signal transduction. This chapter provides an introduction into these two methodologies, illustrated by example of a small GTPase–effector interaction. It is increasingly becoming clear that new insights are provided by the combination of experimental and computational methods. Understanding the structural and protein dynamical contributions to allostery will be useful for the engineering of new binding interfaces and protein functions, as well as for the design/in silico screening of chemical agents that can manipulate the function of small GTPase–protein interactions in diseases such as cancer. PMID:22052494

PV Calibration Insights | NREL

Science.gov Websites

PV Calibration Insights PV Calibration Insights The Photovoltaic (PV) Calibration Insights blog will provide updates on the testing done by the NREL PV Device Performance group. This NREL research group measures the performance of any and all technologies and sizes of PV devices from around the world

Diverse 2D structures obtained by adsorption of charged ABA triblock copolymer on different surfaces

NASA Astrophysics Data System (ADS)

Kontturi, Katri S.; Vesterinen, Arja-Helena; Seppälä, Jukka; Laine, Janne

2012-11-01

In the larger context of 2D polymeric structures, the morphologies obtained by adsorption and subsequent drying of charged, ABA type amphiphilic triblock copolymer of poly[2-(dimethylamino)ethyl metacrylate] (PDMAEMA) and poly(propylene oxide) (PPO) were investigated with atomic force microscopy and X-ray photoelectron spectroscopy as well as in situ adsorption analysis with quartz crystal microbalance with dissipation monitoring. Hydrophilic silica and hydrophobic polystyrene (PS) were used as substrates for adsorption. The structures emerging from the self-assembly of adsorbing polymer were profoundly influenced by composition of the aqueous solution and the choice of substrate. When adsorbed from dilute polymer solution where the concentration is so low that the polymer does not yet show surface-active behavior, the triblock copolymer unimers associated on hydrophilic silica surface forming large, irregular clustered aggregates, with sizes increasing with electrolyte concentration of the solution. On a hydrophobic PS substrate, on the other hand, unimers spread much more evenly, forming clear surface patterns. The roughness of these patterned structures was tuned with the electrolyte concentration of the solution. Adsorption from a more concentrated polymer solution, where the surface-activity of the polymer is perceptible, resulted in the formation of a smooth film with complete coverage over the hydrophilic silica substrate when the electrolyte concentration was high. On PS, on the other hand, nucleation of evenly scattered globular, disk-like micelles was induced. Besides the dry film morphology, the even distribution of the irreversibly adsorbed polymer over the PS surface was likely to serve as an optimal platform for the build-up of reversible hydrophobically bound multilayers at high electrolyte concentration. The multilayer formation was reversible because a decrease in the electrolyte concentration of the solution re-introduces strong electrostatic

Shallow structure of the InSight 2018 landing site in Elysium Planitia, Mars, from ambient vibration Rayleigh wave ellipticity: A modeling study

NASA Astrophysics Data System (ADS)

Knapmeyer-Endrun, B.; Golombek, M.; Ohrnberger, M. M.

2016-12-01

The SEIS (Seismic Experiment for Interior Structure) instrument onboard NASA's InSight mission, scheduled to land in November 2018, will be the first seismometer directly deployed on the surface of Mars. From studies on both the Earth and the Moon, it is well known that site amplification in low-velocity sediments, e.g. regolith, on top of more competent rocks has a strong influence on seismic signals, but can also be used to constrain the subsurface structure. Based on orbital data, lab measurements and terrestrial analogues, we construct a model of the shallow sub-surface at the landing site in western Elysium Planitia and simulate the ambient vibration wavefield. We show how Rayleigh wave ellipticity can be extracted from these data and inverted for shallow structure. Using reasonable variations in regolith properties, we do not expect any influence of site resonances on teleseismic quakes recorded by InSight, but recordings of local events will likely be affected. We find that higher mode ellipticity information might be extracted from the data, significantly reducing uncertainties in the inversion. Though the data are most sensitive to properties of the upper-most layer and show a strong trade-off between layer depth and velocity, it is possible to estimate the velocity and thickness of the sub-regolith layer and distinguish between different models by using reasonable constraints on regolith properties. Model parameters are best constrained if either higher mode data can be used or additional constraints on regolith properties, e.g. from analysis of hammer strokes of the HP3 heat flow probe or orbital mapping of regolith thickness from the onset diameter of rocky ejecta craters, are available. In addition, Rayleigh wave ellipticity can differentiate between models with a constant regolith velocity and models with increasing velocity with depth. We also discuss the influence of lander and leveling system mechanical noise on the identification of site

Structural and Functional Studies of H. seropedicae RecA Protein – Insights into the Polymerization of RecA Protein as Nucleoprotein Filament

PubMed Central

Galvão, Carolina W.; Saab, Sérgio C.; Iulek, Jorge; Etto, Rafael M.; Steffens, Maria B. R.; Chitteni-Pattu, Sindhu; Stanage, Tyler; Keck, James L.; Cox, Michael M.

2016-01-01

The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament. PMID:27447485

Structure of Arabidopsis thaliana FUT1 Reveals a Variant of the GT-B Class Fold and Provides Insight into Xyloglucan Fucosylation

PubMed Central

Chazalet, Valérie

2016-01-01

The plant cell wall is a complex and dynamic network made mostly of cellulose, hemicelluloses, and pectins. Xyloglucan, the major hemicellulosic component in Arabidopsis thaliana, is biosynthesized in the Golgi apparatus by a series of glycan synthases and glycosyltransferases before export to the wall. A better understanding of the xyloglucan biosynthetic machinery will give clues toward engineering plants with improved wall properties or designing novel xyloglucan-based biomaterials. The xyloglucan-specific α2-fucosyltransferase FUT1 catalyzes the transfer of fucose from GDP-fucose to terminal galactosyl residues on xyloglucan side chains. Here, we present crystal structures of Arabidopsis FUT1 in its apoform and in a ternary complex with GDP and a xylo-oligosaccharide acceptor (named XLLG). Although FUT1 is clearly a member of the large GT-B fold family, like other fucosyltransferases of known structures, it contains a variant of the GT-B fold. In particular, it includes an extra C-terminal region that is part of the acceptor binding site. Our crystal structures support previous findings that FUT1 behaves as a functional dimer. Mutational studies and structure comparison with other fucosyltransferases suggest that FUT1 uses a SN2-like reaction mechanism similar to that of protein-O-fucosyltransferase 2. Thus, our results provide new insights into the mechanism of xyloglucan fucosylation in the Golgi. PMID:27637560

Velocity Structure of the Subducted Yakutat Terrane, Alaska: Insights from Guided Waves

NASA Astrophysics Data System (ADS)

Coulson, S.; Garth, T.; Rietbrock, A.

2017-12-01

Subduction zone guided wave arrivals from intermediate depth earthquakes provide insight into the fine scale velocity structure of the subducting oceanic crust as it dehydrates. These observations can be used to determine the average velocity and thickness of the crustal low velocity layer (LVL) at depth, allowing inferences to be drawn about composition and degree of hydration. We constrain guided wave dispersion by comparing waveforms recorded in the subduction forearc with simulated waveforms, produced using a 2D finite difference waveform propagation model. The structure of the Aleutian arc is complex due to the accretion of the Yakutat Terrane (YT) to the east, which is partially coupled with the subducting Pacific plate. An unusually thick LVL associated with the YT has been inferred down to 140 km depth by receiver function studies and travel time tomography. Focussing on a profile running NNW-SSE close to Anchorage, we constrain slab geometry using global and local catalogues, as well as the curvature inferred from receiver functions (Kim et al., 2014). P-wave arrivals from 41 earthquakes (2012-2015) show significant guided wave dispersion on at least one station; high frequency (>1-3 Hz) energy is delayed by up to 2-3 seconds. Choosing the clearest dispersion observations, we systematically vary both LVL width and P-wave velocity, to find the lowest misfit between the observed and synthetic waveforms. Multiple modelled events show the thickness of the LVL associated with subducted YT to be 6-10 km, significantly thinner than inferred by receiver function studies. Most events are accounted for by an LVL velocity contrast of 12.5-15% with overriding mantle material, however, observations of the deepest event in the northern corner of the YT require a velocity contrast of 6%. Lower velocities in the shallower slab (70-120 km) cannot be accounted for by reacted or unreacted MORB or gabbro compositions. We postulate the presence of interbedded sediments within

Structural analysis of enzymes used for bioindustry and bioremediation.

PubMed

Tanokura, Masaru; Miyakawa, Takuya; Guan, Lijun; Hou, Feng

2015-01-01

Microbial enzymes have been widely applied in the large-scale, bioindustrial manufacture of food products and pharmaceuticals due to their high substrate specificity and stereoselectivity, and their effectiveness under mild conditions with low environmental burden. At the same time, bioremedial techniques using microbial enzymes have been developed to solve the problem of industrial waste, particularly with respect to persistent chemicals and toxic substances. And finally, structural studies of these enzymes have revealed the mechanistic basis of enzymatic reactions, including the stereoselectivity and binding specificity of substrates and cofactors. The obtained structural insights are useful not only to deepen our understanding of enzymes with potential bioindustrial and/or bioremedial application, but also for the functional improvement of enzymes through rational protein engineering. This review shows the structural bases for various types of enzymatic reactions, including the substrate specificity accompanying cofactor-controlled and kinetic mechanisms.

New method for obtaining position and time structure of source in HDR remote afterloading brachytherapy unit utilizing light emission from scintillator

PubMed Central

Hanada, Takashi; Katsuta, Shoichi; Yorozu, Atsunori; Maruyama, Koichi

2009-01-01

When using a HDR remote afterloading brachytherapy unit, results of treatment can be greatly influenced by both source position and treatment time. The purpose of this study is to obtain information on the source of the HDR remote afterloading unit, such as its position and time structure, with the use of a simple system consisting of a plastic scintillator block and a charge‐coupled device (CCD) camera. The CCD camera was used for recording images of scintillation luminescence at a fixed rate of 30 frames per second in real time. The source position and time structure were obtained by analyzing the recorded images. For a preset source‐step‐interval of 5 mm, the measured value of the source position was 5.0±1.0mm, with a pixel resolution of 0.07 mm in the recorded images. For a preset transit time of 30 s, the measured value was 30.0±0.6 s, when the time resolution of the CCD camera was 1/30 s. This system enabled us to obtain the source dwell time and movement time. Therefore, parameters such as I192r source position, transit time, dwell time, and movement time at each dwell position can be determined quantitatively using this plastic scintillator‐CCD camera system. PACS number: 87.53.Jw

Anesthetics mechanism on a DMPC lipid membrane model: Insights from molecular dynamics simulations.

PubMed

Saeedi, Marzieh; Lyubartsev, Alexander P; Jalili, Seifollah

2017-07-01

To provide insight into the molecular mechanisms of local anesthetic action, we have carried out an extensive investigation of two amide type local anesthetics, lidocaine and articaine in both charged and uncharged forms, interacting with DMPC lipid membrane. We have applied both standard molecular dynamics simulations and metadynamics simulations to provide a detailed description of the free energy landscape of anesthetics embedded in the lipid bilayer. The global minimum of the free energy surface (equilibrium position of anesthetics in the lipid membrane) occurred around 1nm of the bilayer center. The uncharged anesthetics show more affinity to bind to this region compared to the charged drugs. The binding free energy of uncharged lidocaine in the membrane (-30.3kJ/mol) is higher than uncharged articaine (-24.0kJ/mol), which is in good agreement with higher lipid solubility of lidocaine relative to the articaine. The octanol/water partition coefficient of uncharged drugs was also investigated using expanded ensemble simulations. In addition, complementary standard MD simulations were carried out to study the partitioning behavior of multiple anesthetics inside the lipid bilayer. The results obtained here are in line with previously reported simulations and suggest that the different forms of anesthetics induce different structural modifications in the lipid bilayer, which can provide new insights into their complex membrane translocation phenomena. Copyright © 2017 Elsevier B.V. All rights reserved.

Distributed collaborative probabilistic design of multi-failure structure with fluid-structure interaction using fuzzy neural network of regression

NASA Astrophysics Data System (ADS)

Song, Lu-Kai; Wen, Jie; Fei, Cheng-Wei; Bai, Guang-Chen

2018-05-01

To improve the computing efficiency and precision of probabilistic design for multi-failure structure, a distributed collaborative probabilistic design method-based fuzzy neural network of regression (FR) (called as DCFRM) is proposed with the integration of distributed collaborative response surface method and fuzzy neural network regression model. The mathematical model of DCFRM is established and the probabilistic design idea with DCFRM is introduced. The probabilistic analysis of turbine blisk involving multi-failure modes (deformation failure, stress failure and strain failure) was investigated by considering fluid-structure interaction with the proposed method. The distribution characteristics, reliability degree, and sensitivity degree of each failure mode and overall failure mode on turbine blisk are obtained, which provides a useful reference for improving the performance and reliability of aeroengine. Through the comparison of methods shows that the DCFRM reshapes the probability of probabilistic analysis for multi-failure structure and improves the computing efficiency while keeping acceptable computational precision. Moreover, the proposed method offers a useful insight for reliability-based design optimization of multi-failure structure and thereby also enriches the theory and method of mechanical reliability design.

Structural and biochemical insights into the substrate-binding mechanism of a novel glycoside hydrolase family 134 β-mannanase.

PubMed

You, Xin; Qin, Zhen; Li, Yan-Xiao; Yan, Qiao-Juan; Li, Bin; Jiang, Zheng-Qiang

2018-06-01

Mannan is one of the major constituent groups of hemicellulose, which is a renewable resource from higher plants. β-Mannanases are enzymes capable of degrading lignocellulosic biomass. Here, an endo-β-mannanase from Rhizopus microsporus (RmMan134A) was cloned and expressed. The recombinant RmMan134A showed maximal activity at pH 5.0 and 50 °C, and exhibited high specific activity towards locust bean gum (2337 U/mg). To gain insight into the substrate-binding mechanism of RmMan134A, four complex structures (RmMan134A-M3, RmMan134A-M4, RmMan134A-M5 and RmMan134A-M6) were further solved. These structures showed that there were at least seven subsites (-3 to +4) in the catalytic groove of RmMan134A. Mannose in the -1 subsite hydrogen bonded with His113 and Tyr131, revealing a unique conformation. Lys48 and Val159 formed steric hindrance, which impedes to bond with galactose branches. In addition, the various binding modes of RmMan134A-M5 indicated that subsites -2 to +2 are indispensable during the hydrolytic process. The structure of RmMan134A-M4 showed that mannotetrose only binds at subsites +1 to +4, and RmMan134A could therefore not hydrolyze mannan oligosaccharides with degree of polymerization ≤4. Through rational design, the specific activity and optimal conditions of RmMan134A were significantly improved. The purpose of this paper is to investigate the structure and function of fungal GH family 134 β-1,4-mannanases, and substrate-binding mechanism of GH family 134 members. Copyright © 2018 Elsevier B.V. All rights reserved.

Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking

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

Rumpf, Tobias; Gerhardt, Stefan; Einsle, Oliver, E-mail: einsle@biochemie.uni-freiburg.de

2015-11-18

In the present study, microseed matrix seeding was successfully applied to obtain a large number of crystals of the human sirtuin isotypes Sirt2 and Sirt3. These crystals appeared predictably in diverse crystallization conditions, diffracted to a higher resolution than reported in the literature and were subsequently used to study the protein–ligand interactions of two indole inhibitors. Sirtuins constitute a family of NAD{sup +}-dependent enzymes that catalyse the cleavage of various acyl groups from the ∊-amino group of lysines. They regulate a series of cellular processes and their misregulation has been implicated in various diseases, making sirtuins attractive drug targets. Tomore » date, only a few sirtuin modulators have been reported that are suitable for cellular research and their development has been hampered by a lack of structural information. In this work, microseed matrix seeding (MMS) was used to obtain crystals of human Sirt3 in its apo form and of human Sirt2 in complex with ADP ribose (ADPR). Crystal formation using MMS was predictable, less error-prone and yielded a higher number of crystals per drop than using conventional crystallization screening methods. The crystals were used to solve the crystal structures of apo Sirt3 and of Sirt2 in complex with ADPR at an improved resolution, as well as the crystal structures of Sirt2 in complex with ADPR and the indoles EX527 and CHIC35. These Sirt2–ADPR–indole complexes unexpectedly contain two indole molecules and provide novel insights into selective Sirt2 inhibition. The MMS approach for Sirt2 and Sirt3 may be used as the basis for structure-based optimization of Sirt2/3 inhibitors in the future.« less

Cognitive insight: A systematic review.

PubMed

Van Camp, L S C; Sabbe, B G C; Oldenburg, J F E

2017-07-01

Cognitive insight is the ability to re-evaluate thoughts and beliefs in order to make thoughtful conclusions. It differs from clinical insight, as it focuses on more general metacognitive processes. Therefore, it could be relevant to diverse disorders and non-clinical subjects. There is a growing body of research on cognitive insight in individuals with and without psychosis. This review has summarised the current state of the art regarding this topic. We conclude that while cognitive insight in its current form seems valid for use in individuals with psychosis, it is less so for individuals without psychosis. Additionally, higher cognitive insight not always leads to better psychological functioning. For instance, higher levels of self-reflection are often associated with depressive mood. We therefore recommend the sub-components of cognitive insight to be studied separately. Also, it is unclear what position cognitive insight takes within the spectrum of metacognitive processes and how it relates to other self-related concepts that have been defined previously in literature. Combining future and past research on cognitive insight and its analogue concepts will help in the formation of a uniform definition that fits all subjects discussed here. Copyright © 2017. Published by Elsevier Ltd.

The proteome: structure, function and evolution

PubMed Central

Fleming, Keiran; Kelley, Lawrence A; Islam, Suhail A; MacCallum, Robert M; Muller, Arne; Pazos, Florencio; Sternberg, Michael J.E

2006-01-01

This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family. PMID:16524832

CYANOMETHANIMINE ISOMERS IN COLD INTERSTELLAR CLOUDS: INSIGHTS FROM ELECTRONIC STRUCTURE AND KINETIC CALCULATIONS

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

Vazart, Fanny; Latouche, Camille; Skouteris, Dimitrios

2015-09-10

New insights into the formation of interstellar cyanomethanimine, a species of great relevance in prebiotic chemistry, are provided by electronic structure and kinetic calculations for the reaction CN + CH{sub 2} = NH. This reaction is a facile formation route of Z,E-C-cyanomethanimine, even under the extreme conditions of density and temperature typical of cold interstellar clouds. E-C-cyanomethanimine has been recently identified in Sgr B2(N) in the Green Bank Telescope (GBT) PRIMOS survey by P. Zaleski et al. and no efficient formation routes have been envisaged so far. The rate coefficient expression for the reaction channel leading to the observed isomermore » E-C-cyanomethanimine is 3.15 × 10-10 × (T/300){sup 0.152} × e{sup (−0.0948/T)}. According to the present study, the more stable Z-C-cyanomethanimine isomer is formed with a slightly larger yield (4.59 × 10{sup −10} × (T/300){sup 0.153} × e{sup (−0.0871/T)}. As the detection of E-isomer is favored due to its larger dipole moment, the missing detection of the Z-isomer can be due to the sensitivity limit of the GBT PRIMOS survey and the detection of the Z-isomer should be attempted with more sensitive instrumentation. The CN + CH{sub 2} = NH reaction can also play a role in the chemistry of the upper atmosphere of Titan where the cyanomethanimine products can contribute to the buildup of the observed nitrogen-rich organic aerosols that cover the moon.« less

InSight Prelaunch Briefing

NASA Image and Video Library

2018-05-03

Stu Spath, InSight program manager, Lockheed Martin Space, discusses NASA's InSight mission during a prelaunch media briefing, Thursday, May 3, 2018, at Vandenberg Air Force Base in California. InSight, short for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, is a Mars lander designed to study the "inner space" of Mars: its crust, mantle, and core. Photo Credit: (NASA/Bill Ingalls)

InSight Prelaunch Briefing

NASA Image and Video Library

2018-05-03

Tom Hoffman, InSight project manager, NASA JPL, right, discusses NASA's InSight mission during a prelaunch media briefing, Thursday, May 3, 2018, at Vandenberg Air Force Base in California. InSight, short for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, is a Mars lander designed to study the "inner space" of Mars: its crust, mantle, and core. Photo Credit: (NASA/Bill Ingalls)

InSight Prelaunch Briefing

NASA Image and Video Library

2018-05-03

Bruce Banerdt, InSight principal investigator, NASA JPL, discusses NASA's InSight mission during a prelaunch media briefing, Thursday, May 3, 2018, at Vandenberg Air Force Base in California. InSight, short for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, is a Mars lander designed to study the "inner space" of Mars: its crust, mantle, and core. Photo Credit: (NASA/Bill Ingalls)

Three-dimensional structural analysis of eukaryotic flagella/cilia by electron cryo-tomography

PubMed Central

Bui, Khanh Huy; Pigino, Gaia; Ishikawa, Takashi

2011-01-01

Electron cryo-tomography is a potential approach to analyzing the three-dimensional conformation of frozen hydrated biological macromolecules using electron microscopy. Since projections of each individual object illuminated from different orientations are merged, electron tomography is capable of structural analysis of such heterogeneous environments as in vivo or with polymorphism, although radiation damage and the missing wedge are severe problems. Here, recent results on the structure of eukaryotic flagella, which is an ATP-driven bending organelle, from green algae Chlamydomonas are presented. Tomographic analysis reveals asymmetric molecular arrangements, especially that of the dynein motor proteins, in flagella, giving insight into the mechanism of planar asymmetric bending motion. Methodological challenges to obtaining higher-resolution structures from this technique are also discussed. PMID:21169680

Aquarius main structure configuration

NASA Astrophysics Data System (ADS)

Eremenko, A.

The Aquarius/SAC-D Observatory is a joint US-Argentine mission to map the salinity at the ocean surface. This information is critical to improving our understanding of two major components of Earth's climate system - the water cycle and ocean circulation. By measuring ocean salinity from space, the Aquarius/SAC-D Mission will provide new insights into how the massive natural exchange of freshwater between the ocean, atmosphere and sea ice influences ocean circulation, weather and climate. Aquarius is the primary instrument on the SAC-D spacecraft. It consists of a Passive Microwave Radiometer to detect the surface emission that is used to obtain salinity and an Active Scatterometer to measure the ocean waves that affect the precision of the salinity measurement. The Aquarius Primary Structure houses instrument electronics, feed assemblies, and supports a deployable boom with a 2.5 m Reflector, and provides the structural interface to the SAC-D Spacecraft. The key challenge for the Aquarius main structure configuration is to satisfy the needs of component accommodations, ensuring that the instrument can meet all operational, pointing, environmental, and launch vehicle requirements. This paper describes the evolution of the Aquarius main structure configuration, the challenges of balancing the conflicting requirements, and the major configuration driving decisions and compromises.

Aquarius Main Structure Configuration

NASA Technical Reports Server (NTRS)

Eremenko, Alexander

2012-01-01

The Aquarius/SAC-D Observatory is a joint US-Argentine mission to map the salinity at the ocean surface. This information is critical to improving our understanding of two major components of Earth's climate system - the water cycle and ocean circulation. By measuring ocean salinity from space, the Aquarius/SAC-D Mission will provide new insights into how the massive natural exchange of freshwater between the ocean, atmosphere and sea ice influences ocean circulation, weather and climate. Aquarius is the primary instrument on the SAC-D spacecraft. It consists of a Passive Microwave Radiometer to detect the surface emission that is used to obtain salinity and an Active Scatterometer to measure the ocean waves that affect the precision of the salinity measurement. The Aquarius Primary Structure houses instrument electronics, feed assemblies, and supports a deployable boom with a 2.5 m Reflector, and provides the structural interface to the SAC-D Spacecraft. The key challenge for the Aquarius main structure configuration is to satisfy the needs of component accommodations, ensuring that the instrument can meet all operational, pointing, environmental, and launch vehicle requirements. This paper describes the evolution of the Aquarius main structure configuration, the challenges of balancing the conflicting requirements, and the major configuration driving decisions and compromises.

Insights into Learning Profiles and Learning Outcomes within Introductory Accounting

ERIC Educational Resources Information Center

Teixeira, Cláudia; Gomes, Delfina

2017-01-01

This paper reports an empirical study aiming to explore aspects of learning and studying introductory accounting in Portuguese higher education. It specifically provides insight into patterns of learning and learning outcomes. To do so, it draws on qualitative data collected from students' answers to a semi-structured interview about their…

Dreaming and insight

PubMed Central

Edwards, Christopher L.; Ruby, Perrine M.; Malinowski, Josie E.; Bennett, Paul D.; Blagrove, Mark T.

2013-01-01

This paper addresses claims that dreams can be a source of personal insight. Whereas there has been anecdotal backing for such claims, there is now tangential support from findings of the facilitative effect of sleep on cognitive insight, and of REM sleep in particular on emotional memory consolidation. Furthermore, the presence in dreams of metaphorical representations of waking life indicates the possibility of novel insight as an emergent feature of such metaphorical mappings. In order to assess whether personal insight can occur as a result of the consideration of dream content, 11 dream group discussion sessions were conducted which followed the Ullman Dream Appreciation technique, one session for each of 11 participants (10 females, 1 male; mean age = 19.2 years). Self-ratings of deepened self-perception and personal gains from participation in the group sessions showed that the Ullman technique is an effective procedure for establishing connections between dream content and recent waking life experiences, although wake life sources were found for only 14% of dream report text. The mean Exploration-Insight score on the Gains from Dream Interpretation questionnaire was very high and comparable to outcomes from the well-established Hill (1996) therapist-led dream interpretation method. This score was associated between-subjects with pre-group positive Attitude Toward Dreams (ATD). The need to distinguish “aha” experiences as a result of discovering a waking life source for part of a dream, from “aha” experiences of personal insight as a result of considering dream content, is discussed. Difficulties are described in designing a control condition to which the dream report condition can be compared. PMID:24550849

Syntheses, crystal structures and properties of novel copper(II) complexes obtained by reactions of copper(II) sulfate pentahydrate with tripodal ligands.

PubMed

Zhao, Wei; Fan, Jian; Song, You; Kawaguchi, Hiroyuki; Okamura, Taka-aki; Sun, Wei-Yin; Ueyama, Norikazu

2005-04-21

Three novel metal-organic frameworks (MOFs), [Cu(1)SO4].H2O (4), [Cu2(2)2(SO4)2].4H2O (5) and [Cu(3)(H2O)]SO4.5.5H2O (6), were obtained by hydrothermal reactions of CuSO4.5H2O with the corresponding ligands, which have different flexibility. The structures of the synthesized complexes were determined by single-crystal X-ray diffraction analyses. Complex 4 has a 2D network structure with two types of metallacycles. Complex 5 also has a 2D network structure in which each independent 2D sheet contains two sub-layers bridged by oxygen atoms of the sulfate anions. Complex 6 has a 2D puckered structure in which the sulfate anions serve as counter anions, which are different from those in complexes 4 (terminators) and 5 (bridges). The different structures of complexes 4, 5 and 6 indicate that the nature of organic ligands affected the structures of the assemblies greatly. The magnetic behavior of complex 5 and anion-exchange properties of complex 6 were investigated.

The Structures of Life

ERIC Educational Resources Information Center

National Institute of General Medical Sciences (NIGMS), 2007

2007-01-01

This booklet reveals how structural biology provides insight into health and disease and is useful in developing new medications. It contains a general introduction to proteins, coverage of the techniques used to determine protein structures, and a chapter on structure-based drug design. The booklet features "Student Snapshots," designed to…

Crystal structure of the dopamine N-acetyltransferase–acetyl-CoA complex provides insights into the catalytic mechanism

PubMed Central

Cheng, Kuo-Chang; Liao, Jhen-Ni; Lyu, Ping-Chiang

2012-01-01

The daily cycle of melatonin biosynthesis in mammals is regulated by AANAT (arylalkylamine N-acetyltransferase; EC 2.3.1.87), making it an attractive target for therapeutic control of abnormal melatonin production in mood and sleep disorders. Drosophila melanogaster Dat (dopamine N-acetyltransferase) is an AANAT. Until the present study, no insect Dat structure had been solved, and, consequently, the structural basis for its acetyl-transfer activity was not well understood. We report in the present paper the high-resolution crystal structure for a D. melanogaster Dat–AcCoA (acetyl-CoA) complex obtained using one-edge (selenium) single-wavelength anomalous diffraction. A binding study using isothermal titration calorimetry suggested that the cofactor bound to Dat first before substrate. Examination of the complex structure and a substrate-docked model indicated that Dat contains a novel AANAT catalytic triad. Site-directed mutagenesis, kinetic studies and pH-rate profiles confirmed that Glu47, Ser182 and Ser186 were critical for catalysis. Collectively, the results of the present study suggest that Dat possesses a specialized active site structure dedicated to a catalytic mechanism. PMID:22716280

Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations

NASA Astrophysics Data System (ADS)

Khosravian, N.; Kamaraj, B.; Neyts, E. C.; Bogaerts, A.

2016-02-01

This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment.

Animal NLRs provide structural insights into plant NLR function.

PubMed

Bentham, Adam; Burdett, Hayden; Anderson, Peter A; Williams, Simon J; Kobe, Bostjan

2017-03-01

The plant immune system employs intracellular NLRs (nucleotide binding [NB], leucine-rich repeat [LRR]/nucleotide-binding oligomerization domain [NOD]-like receptors) to detect effector proteins secreted into the plant cell by potential pathogens. Activated plant NLRs trigger a range of immune responses, collectively known as the hypersensitive response (HR), which culminates in death of the infected cell. Plant NLRs show structural and functional resemblance to animal NLRs involved in inflammatory and innate immune responses. Therefore, knowledge of the activation and regulation of animal NLRs can help us understand the mechanism of action of plant NLRs, and vice versa. This review provides an overview of the innate immune pathways in plants and animals, focusing on the available structural and biochemical information available for both plant and animal NLRs. We highlight the gap in knowledge between the animal and plant systems, in particular the lack of structural information for plant NLRs, with crystal structures only available for the N-terminal domains of plant NLRs and an integrated decoy domain, in contrast to the more complete structures available for animal NLRs. We assess the similarities and differences between plant and animal NLRs, and use the structural information on the animal NLR pair NAIP/NLRC4 to derive a plausible model for plant NLR activation. Signalling by cooperative assembly formation (SCAF) appears to operate in most innate immunity pathways, including plant and animal NLRs. Our proposed model of plant NLR activation includes three key steps: (1) initially, the NLR exists in an inactive auto-inhibited state; (2) a combination of binding by activating elicitor and ATP leads to a structural rearrangement of the NLR; and (3) signalling occurs through cooperative assembly of the resistosome. Further studies, structural and biochemical in particular, will be required to provide additional evidence for the different features of this model and

Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi

PubMed Central

2011-01-01

Background Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans. Results 97% of the 22.5 megabase genome sequences of A. benhamiae and T. verrucosum are unambiguously alignable and collinear. To unravel dermatophyte-specific virulence-associated traits, we compared sets of potentially pathogenicity-associated proteins, such as secreted proteases and enzymes involved in secondary metabolite production, with those of closely related onygenales (Coccidioides species) and the mould Aspergillus fumigatus. The comparisons revealed expansion of several gene families in dermatophytes and disclosed the peculiarities of the dermatophyte secondary metabolite gene sets. Secretion of proteases and other hydrolytic enzymes by A. benhamiae was proven experimentally by a global secretome analysis during keratin degradation. Molecular insights into the interaction of A. benhamiae with human keratinocytes were obtained for the first time by global transcriptome profiling. Given that A. benhamiae is able to undergo mating, a detailed comparison of the genomes further unraveled the genetic basis of sexual reproduction in this species. Conclusions Our results enlighten the genetic basis of fundamental and putatively virulence-related traits of dermatophytes, advancing future research on these medically important pathogens. PMID:21247460

InSight Prelaunch Briefing

NASA Image and Video Library

2018-05-03

Social media guest listen as Bruce Banerdt, InSight principal investigator, NASA JPL, discusses NASA's InSight mission during a prelaunch media briefing, Thursday, May 3, 2018, at Vandenberg Air Force Base in California. InSight, short for Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, is a Mars lander designed to study the "inner space" of Mars: its crust, mantle, and core. Photo Credit: (NASA/Bill Ingalls)

Structural insight into GRIP1-PDZ6 in Alzheimer's disease: study from protein expression data to molecular dynamics simulations.

PubMed

Chatterjee, Paulami; Roy, Debjani

2017-08-01

Protein-protein interaction domain, PDZ, plays a critical role in efficient synaptic transmission in brain. Dysfunction of synaptic transmission is thought to be the underlying basis of many neuropsychiatric and neurodegenerative disorders including Alzheimer's disease (AD). In this study, Glutamate Receptor Interacting Protein1 (GRIP1) was identified as one of the most important differentially expressed, topologically significant proteins in the protein-protein interaction network. To date, very few studies have analyzed the detailed structural basis of PDZ-mediated protein interaction of GRIP1. In order to gain better understanding of structural and dynamic basis of these interactions, we employed molecular dynamics (MD) simulations of GRIP1-PDZ6 dimer bound with Liprin-alpha and GRIP1-PDZ6 dimer alone each with 100 ns simulations. The analyses of MD simulations of Liprin-alpha bound GRIP1-PDZ6 dimer show considerable conformational differences than that of peptide-free dimer in terms of SASA, hydrogen bonding patterns, and along principal component 1 (PC1). Our study also furnishes insight into the structural attunement of the PDZ6 domains of Liprin-alpha bound GRIP1 that is attributed by significant shift of the Liprin-alpha recognition helix in the simulated peptide-bound dimer compared to the crystal structure and simulated peptide-free dimer. It is evident that PDZ6 domains of peptide-bound dimer show differential movements along PC1 than that of peptide-free dimers. Thus, Liprin-alpha also serves an important role in conferring conformational changes along the dimeric interface of the peptide-bound dimer. Results reported here provide information that may lead to novel therapeutic approaches in AD.

Importance of intrinsic properties of dense caseinate dispersions for structure formation.

PubMed

Manski, Julita M; van Riemsdijk, Lieke E; van der Goot, Atze J; Boom, Remko M

2007-11-01

Rheological measurements of dense calcium caseinate and sodium caseinate dispersions (> or =15%) provided insight into the factors determining shear-induced structure formation in caseinates. Calcium caseinate at a sufficiently high concentration (30%) was shown to form highly anisotropic structures during shearing and concurrent enzymatic cross-linking. In contrast, sodium caseinate formed isotropic structures using similar processing conditions. The main difference between the two types of caseinates is the counterion present, and as a consequence, the size of structural elements and their interactions. The rheological behavior of calcium caseinate and sodium caseinate reflected these differences, yielding non-monotonic and shear thinning flow behavior for calcium caseinate whereas sodium caseinate behaved only slightly shear thinning. It appears that the intrinsic properties of the dense caseinate dispersions, which are reflected in their rheological behavior, affect the structure formation that was found after applying shear. Therefore, rheological measurements are useful to obtain an indication of the structure formation potential of caseinate dispersions.

InSight Lift & Mate

NASA Image and Video Library

2018-04-23

At Space Launch Complex 3 at Vandenberg Air Force Base in California, technicians and engineers position NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander atop a United Launch Alliance Atlas V rocket. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Lift & Mate

NASA Image and Video Library

2018-04-23

Encapsulated in its payload fairing NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander is prepared for transport to Space Launch Complex 3 at Vandenberg Air Force Base in California. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Battery Installation

NASA Image and Video Library

2018-04-20

In the gantry at Space Launch Complex 3 at Vandenberg Air Force Base in California, a technician prepares batteries for installation in NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

InSight Battery Installation

NASA Image and Video Library

2018-04-20

In the gantry at Space Launch Complex 3 at Vandenberg Air Force Base in California, technicians and engineers prepare batteries for installation in NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

Obtaining an equivalent beam

NASA Technical Reports Server (NTRS)

Butler, Thomas G.

1990-01-01

In modeling a complex structure the researcher was faced with a component that would have logical appeal if it were modeled as a beam. The structure was a mast of a robot controlled gantry crane. The structure up to this point already had a large number of degrees of freedom, so the idea of conserving grid points by modeling the mast as a beam was attractive. The researcher decided to make a separate problem of of the mast and model it in three dimensions with plates, then extract the equivalent beam properties by setting up the loading to simulate beam-like deformation and constraints. The results could then be used to represent the mast as a beam in the full model. A comparison was made of properties derived from models of different constraints versus manual calculations. The researcher shows that the three-dimensional model is ineffective in trying to conform to the requirements of an equivalent beam representation. If a full 3-D plate model were used in the complete representation of the crane structure, good results would be obtained. Since the attempt is to economize on the size of the model, a better way to achieve the same results is to use substructuring and condense the mast to equivalent end boundary and intermediate mass points.

Measuring Adaptive Coping of Hospitalized Patients With a Severe Medical Condition: The Sickness Insight in Coping Questionnaire.

PubMed

Boezeman, Edwin J; Hofhuis, José G M; Hovingh, Aly; Cox, Christopher E; de Vries, Reinout E; Spronk, Peter E

2016-09-01

Adaptive coping strategies are associated with less psychological distress. However, there is no brief, specific, and validated instrument for assessing adaptive coping among seriously ill patients. Our objective was to examine the validity and patient-proxy agreement of a novel instrument, the Sickness Insight in Coping Questionnaire. A cross-sectional design which included two related studies. A single university-affiliated Dutch hospital. Hospitalized patients (study 1) and ICU-patients and proxies (study 2). None. Study 1 (n = 103 hospitalized patients) addressed the Sickness Insight in Coping Questionnaire's performance relative to questionnaires addressing similar content areas. Coping subscales of the BRIEF COPE, Illness Cognition Questionnaire, and Utrecht Coping List were used as comparator measures in testing the construct validity of the Sickness Insight in Coping Questionnaire-subscales (fighting spirit, toughness, redefinition, positivism, and non-acceptance). The Sickness Insight in Coping Questionnaire had good internal consistency (0.64 ≤ α ≤ 0.79), a clear initial factor structure, and fair convergent (0.24 ≤ r ≤ 0.50) and divergent (r, ≤ 0.12) construct validity. Study 2 examined the performance of the Sickness Insight in Coping Questionnaire among 100 ICU patients and their close family members. This study showed that the Sickness Insight in Coping Questionnaire has good structural validity (confirmatory factor analyses with Comparative Fit Index > 0.90 and Root Mean Square Error of Approximation < 0.08) and moderate (r, 0.37; non-acceptance) to strong (r, > 0.50; fighting spirit, toughness, redefinition, and positivism) patient-close proxy agreement. Overall, the Sickness Insight in Coping Questionnaire has good psychometric properties. ICU clinicians can use the Sickness Insight in Coping Questionnaire to gain insight in adaptive coping style of patients through ratings of patients or their close family members.

Structural and functional insights into the role of the N-terminal Mps1 TPR domain in the SAC (spindle assembly checkpoint).

PubMed

Thebault, Philippe; Chirgadze, Dimitri Y; Dou, Zhen; Blundell, Tom L; Elowe, Sabine; Bolanos-Garcia, Victor M

2012-12-15

The SAC (spindle assembly checkpoint) is a surveillance system that ensures the timely and accurate transmission of the genetic material to offspring. The process implies kinetochore targeting of the mitotic kinases Bub1 (budding uninhibited by benzamidine 1), BubR1 (Bub1 related) and Mps1 (monopolar spindle 1), which is mediated by the N-terminus of each kinase. In the present study we report the 1.8 Å (1 Å=0.1 nm) crystal structure of the TPR (tetratricopeptide repeat) domain in the N-terminal region of human Mps1. The structure reveals an overall high similarity to the TPR motif of the mitotic checkpoint kinases Bub1 and BubR1, and a number of unique features that include the absence of the binding site for the kinetochore structural component KNL1 (kinetochore-null 1; blinkin), and determinants of dimerization. Moreover, we show that a stretch of amino acids at the very N-terminus of Mps1 is required for dimer formation, and that interfering with dimerization results in mislocalization and misregulation of kinase activity. The results of the present study provide an important insight into the molecular details of the mitotic functions of Mps1 including features that dictate substrate selectivity and kinetochore docking.

Magnetotelluric 2D Modelling Provides Insight on the Structural Characteristics of the Guadalajara (Mexico) Triple Junction Domains

NASA Astrophysics Data System (ADS)

Arboleda Zapata, M. D. J., Sr.; Arzate-Flores, J.; Guevara Betancourt, R. E., Sr.

2017-12-01

The Jalisco Block is a continental microplate produced by the extension along three large structures: the Tepic-Zacoalco rift (TZR), the Colima rift (CR) and the Chapala rift that converge in a triple junction 50 km southwest of Guadalajara, Mexico, with orientation NW-SE, N-S, and E-W respectively. The present study focuses on investigating the deep structure of the north Colima and eastern Zacoalco grabens close to the Guadalajara triple junction (GTJ). This is a first study of its type that provide insight on the grabens structures and crustal characteristics underneath. We measured along two magnetotellurics (MT) profiles that cut perpendicularly the TZR (profile ZAC), and the northern CR (profile SAY) comprising a total of 24 broad band MT soundings. The ZAC profile has 11 stations and has a NE orientation, and the SAY profile has 14 station aligned E-W. Standard processing and editing procedures were completed, and distortion analysis was applied to the data set in order to define the dimensionality and electric strike of the separated profiles. Static shift was corrected using geology information to distinguish the different types of soundings and later averaging for those soundings located over the same lithology. The Bahr dimensionality parameters showed that the medium is mainly 3D for the SAY profile and 2D for the ZAC profile; furthermore, the regional geoelectric strike azimuth calculated with Bahr methodology were -4° and -48° respectively, with good concordance with the main surface structures. The tipper analysis permitted validated these results, as the real induction vectors were nearly perpendicular to main fault structures. All soundings were rotated to the respective regional strike and a 2D simultaneous inversion of the transverse electric (TE) mode, the transvers magnetic (TM) mode and the Tipper was completed. The RMS fitting error yield 3.2% for ZAC profile and 3.7% for SAY profile. Both profiles show a shallow conductive zone at north of

Structural Insights into l-Tryptophan Dehydrogenase from a Photoautotrophic Cyanobacterium, Nostoc punctiforme.

PubMed

Wakamatsu, Taisuke; Sakuraba, Haruhiko; Kitamura, Megumi; Hakumai, Yuichi; Fukui, Kenji; Ohnishi, Kouhei; Ashiuchi, Makoto; Ohshima, Toshihisa

2017-01-15

l-Tryptophan dehydrogenase from Nostoc punctiforme NIES-2108 (NpTrpDH), despite exhibiting high amino acid sequence identity (>30%)/homology (>50%) with NAD(P) + -dependent l-Glu/l-Leu/l-Phe/l-Val dehydrogenases, exclusively catalyzes reversible oxidative deamination of l-Trp to 3-indolepyruvate in the presence of NAD + Here, we determined the crystal structure of the apo form of NpTrpDH. The structure of the NpTrpDH monomer, which exhibited high similarity to that of l-Glu/l-Leu/l-Phe dehydrogenases, consisted of a substrate-binding domain (domain I, residues 3 to 133 and 328 to 343) and an NAD + /NADH-binding domain (domain II, residues 142 to 327) separated by a deep cleft. The apo-NpTrpDH existed in an open conformation, where domains I and II were apart from each other. The subunits dimerized themselves mainly through interactions between amino acid residues around the β-1 strand of each subunit, as was observed in the case of l-Phe dehydrogenase. The binding site for the substrate l-Trp was predicted by a molecular docking simulation and validated by site-directed mutagenesis. Several hydrophobic residues, which were located in the active site of NpTrpDH and possibly interacted with the side chain of the substrate l-Trp, were arranged similarly to that found in l-Leu/l-Phe dehydrogenases but fairly different from that of an l-Glu dehydrogenase. Our crystal structure revealed that Met-40, Ala-69, Ile-74, Ile-110, Leu-288, Ile-289, and Tyr-292 formed a hydrophobic cluster around the active site. The results of the site-directed mutagenesis experiments suggested that the hydrophobic cluster plays critical roles in protein folding, l-Trp recognition, and catalysis. Our results provide critical information for further characterization and engineering of this enzyme. In this study, we determined the three-dimensional structure of l-Trp dehydrogenase, analyzed its various site-directed substitution mutants at residues located in the active site, and obtained the

Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach.

PubMed

Kumar, Anuj; Kumar, Sanjay; Kumar, Upendra; Suravajhala, Prashanth; Gajula, M N V Prasad

2016-10-01

Triticum aestivum L. known as common wheat is one of the most important cereal crops feeding a large and growing population. Various environmental stress factors including drought, high salinity and heat etc. adversely affect wheat production in a significant manner. Dehydration-responsive element-binding (DREB1A) factors, a class of transcription factors (TF) play an important role in combating drought stress. It is known that DREB1A specifically interacts with the dehydration responsive elements (DRE/CRT) inducing expression of genes involved in environmental stress tolerance in plants. Despite its critical interplay in plants, the structural and functional aspects of DREB1A TF in wheat remain unresolved. Previous studies showed that wheat DREBs (DREB1 and DREB2) were isolated using various methods including yeast two-hybrid screens but no extensive structural models were reported. In this study, we made an extensive in silico study to gain insight into DREB1A TF and reported the location of novel DREB1A in wheat chromosomes. We inferred the three-dimensional structural model of DREB1A using homology modelling and further evaluated them using molecular dynamics(MD) simulations yielding refined modelled structures. Our biochemical function predictions suggested that the wheat DREB1A orthologs have similar biochemical functions and pathways to that of AtDREB1A. In conclusion, the current study presents a structural perspective of wheat DREB1A and helps in understanding the molecular basis for the mechanism of DREB1A in response to environmental stress. Copyright © 2016 Elsevier Ltd. All rights reserved.

Magnetic resonance imaging in patients with obsessive-compulsive disorder with good versus poor insight.

PubMed

Aigner, Martin; Zitterl, Werner; Prayer, Daniela; Demal, Ulrike; Bach, Michael; Prayer, Lucas; Stompe, Thomas; Lenz, Gerhard

2005-11-30

The DSM-IV provides two subtypes of obsessive-compulsive disorder (OCD), labelled as OCD with insight and OCD with poor insight. For the latter, patients generally fail to recognize that the obsessions or compulsions are excessive or unreasonable. Several studies have shown significant brain abnormalities in OCD patients. However, at present, it remains unclear whether a specific pattern of structural brain abnormalities is related to poor insight in OCD. In the present study, magnetic resonance imaging (MRI) findings were compared in OCD patients with insight versus those with poor insight. Outpatients with diagnoses of OCD according to DSM-IV (300.30) and ICD-10 (F42) (n = 84; mean age 38+/-13; 35 females, 49 males) were dichotomized into the two subtypes. All subjects underwent an MRI examination. MRI findings were rated as "MRI abnormality" and "normal MRI." In our sample, 48% of the patients had MRI abnormalities. There was a highly significant difference between the two groups according to frequencies of MRI abnormalities, with 83% of the patients with poor insight showing MRI abnormalities compared with only 21% of the patients with insight. The specifier "poor insight" helps to identify a subgroup of OCD with a higher frequency of brain abnormalities of various types. This distinction should be taken into account in future studies concerning the course and therapeutic outcome of OCD.

Drug-eluting stents. Insights from invasive imaging technologies.

PubMed

Honda, Yasuhiro

2009-08-01

Drug-eluting stents (DES) represent a revolutionary technology in their unique ability to provide both mechanical and biological solutions simultaneously to the target lesion. As a result of biological effects from the pharmacological agents and interaction of DES components with the arterial wall, considerable differences exist between DES and conventional bare metal stents (BMS), yet some of the old lessons learned in the BMS era remain clinically significant. In this context, contrast angiography provides very little information about in vivo device properties and their biomechanical effects on the arterial wall. In contrast, current catheter-based imaging tools, such as intravascular ultrasound, optical coherence tomography, and intracoronary angioscopy can offer unique insights into DES through direct assessment of the device and treated vessel in the clinical setting. This article reviews these insights from current DES with particular focus on performance and safety characteristics as well as discussing an optimal deployment technique, based upon findings obtained through the use of the invasive imaging technologies.

Fractal bimetallic plasmonic structures obtained by laser deposition of colloidal nanoparticles

NASA Astrophysics Data System (ADS)

Bukharov, D. N.; Arakelyan, S. M.; Kutrovskaya, S. V.; Kucherik, A. O.; Osipov, A. V.; Istratov, A. V.; Vartanyan, T. A.; Itina, T. E.; Kavokin, A. V.

2017-09-01

We produce bimetallic Au:Ag thin films by laser irradiation of the mixed solutions. After several laser scans, granular nanometric films are found to grow with a well-controlled composition, thickness and morphology. By changing laser scanning parameters, the film morphology can be varied from island structures to quasi-periodic arrays. The optical properties of the deposited structures are found to depend on the film composition, thickness and spacing between the particles. The transmittance spectra of the deposited films are shown to be governed by their morphology.

Neuroimaging Insights into the Pathophysiology of Sleep Disorders

PubMed Central

Desseilles, Martin; Dang-Vu, Thanh; Schabus, Manuel; Sterpenich, Virginie; Maquet, Pierre; Schwartz, Sophie

2008-01-01

Neuroimaging methods can be used to investigate whether sleep disorders are associated with specific changes in brain structure or regional activity. However, it is still unclear how these new data might improve our understanding of the pathophysiology underlying adult sleep disorders. Here we review functional brain imaging findings in major intrinsic sleep disorders (i.e., idiopathic insomnia, narcolepsy, and obstructive sleep apnea) and in abnormal motor behavior during sleep (i.e., periodic limb movement disorder and REM sleep behavior disorder). The studies reviewed include neuroanatomical assessments (voxel-based morphometry, magnetic resonance spectroscopy), metabolic/functional investigations (positron emission tomography, single photon emission computed tomography, functional magnetic resonance imaging), and ligand marker measurements. Based on the current state of the research, we suggest that brain imaging is a useful approach to assess the structural and functional correlates of sleep impairments as well as better understand the cerebral consequences of various therapeutic approaches. Modern neuroimaging techniques therefore provide a valuable tool to gain insight into possible pathophysiological mechanisms of sleep disorders in adult humans. Citation: Desseilles M; Dang-Vu TD; Schabus M; Sterpenich V; Maquet P; Schwartz S. Neuroimaging insights into the pathophysiology of sleep disorders. SLEEP 2008;31(6):777–794. PMID:18548822

InSight Liftoff

NASA Image and Video Library

2018-05-05

A United Launch Alliance Atlas V rocket lifts off from Space Launch Complex 3 at Vandenberg Air Force Base, California, carrying NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander. Liftoff was at 4:05 a.m. PDT (7:05 a.m. EDT). The spacecraft will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. InSight will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created.

Insights into ionic transport and structural changes in magnetite during multiple-electron transfer reactions

DOE PAGES

Zhang, Wei; Bock, David C.; Pelliccione, Christopher J.; ...

2016-03-08

Metal oxides, such as Fe 3O 4, hold promise for future battery applications due to their abundance, low cost, and opportunity for high lithium storage capacity. In order to better understand the mechanisms of multiple-electron transfer reactions leading to high capacity in Fe 3O 4, a comprehensive investigation on local ionic transport and ordering is made by probing site occupancies of anions (O 2–) and cations (Li +, Fe 3+/Fe 2+) using multiple synchrotron X-ray and electron-beam techniques, in combination with ab-initio calculations. Results from this study provide the first experimental evidence that the cubic-close-packed (ccp) O-anion array in Femore » 3O 4 is sustained throughout the lithiation and delithiation processes, thereby enabling multiple lithium intercalation and conversion reactions. Cation displacement/reordering occurs within the ccp O-anion framework, which leads to a series of phase transformations, starting from the inverse spinel phase and turning into intermediate rock-salt-like phases (Li xFe 3O 4; 0 < x < 2), then into a cation-segregated phase (Li 2O•FeO), and finally converting into metallic Fe and Li 2O. Subsequent delithiation and lithiation processes involve interconversion between metallic Fe and FeO-like phases. Lastly, these results may offer new insights into the structure-determined ionic transport and electrochemical reactions in metal oxides, and those of other compounds sharing a ccp anion framework, reminiscent of magnetite.« less

Longitudinal trajectory of clinical insight and covariation with cortical thickness in first-episode psychosis.

PubMed

Buchy, Lisa; Makowski, Carolina; Malla, Ashok; Joober, Ridha; Lepage, Martin

2017-03-01

Among people with a first-episode of psychosis, those with poorer clinical insight show neuroanatomical abnormalities in frontal, temporal and parietal cortices compared to those with better clinical insight. Whether changes in clinical insight are associated with progressive structural brain changes is unknown. We aimed to evaluate 1) associations between clinical insight and cortical thickness at a baseline assessment, 2) covariation between clinical insight and cortical thickness across baseline, one-year and two-year follow-up assessments, and 3) the predictive value of clinical insight for cortical thickness at one-year and two-year follow-ups. Scale for the assessment of Unawareness of Mental Disorder ratings and magnetic resonance imaging scans were acquired at baseline, one-year, and two-year follow-ups in 128, 74, and 44 individuals with a first-episode psychosis, respectively. Cortical thickness metrics were then computed at baseline, one-year and two-year follow-ups and analyzed with linear mixed models. At baseline, clinical insight was not significantly associated with cortical thickness in any region. Longitudinal mixed effects models showed that a worsening in clinical insight between the one-year and two-year assessments was significantly associated with cortical thinning in dorsal pre-central and post-central gyri. Cortical thinning in left fusiform gyrus at two-years was predicted by poorer clinical insight at baseline. Results suggest that poor clinical insight soon after the onset of a first-episode psychosis may lead to progressive cortical changes in temporal lobe, while changes in clinical insight during the second year covary with cortical thinning in circumscribed dorsal frontal and parietal cortices. Copyright © 2016 Elsevier Ltd. All rights reserved.

Failures of metacognition and lack of insight in neuropsychiatric disorders

PubMed Central

David, Anthony S.; Bedford, Nicholas; Wiffen, Ben; Gilleen, James

2012-01-01

Lack of insight or unawareness of illness are the hallmarks of many psychiatric disorders, especially schizophrenia (SCZ) and other psychoses and could be conceived of as a failure in metacognition. Research in this area in the mental health field h as burgeoned with the development and widespread use of standard assessment instruments and the mapping out of the clinical and neuropsychological correlates of insight and its loss. There has been a growing appreciation of the multi-faceted nature of the concept and of the different ‘objects’ of insight, such as the general awareness that one is ill, to more specific metacognitive awareness of individual symptoms, impairments and performance. This in turn has led to the notion that insight may show modularity and may fractionate across different domains and disorders, supported by work that directly compares metacognition of memory deficits and illness awareness in patients with SCZ, Alzheimer's disease and brain injury. The focus of this paper will be on the varieties of metacognitive failure in psychiatry, particularly the psychoses. We explore cognitive models based on self-reflectiveness and their possible social and neurological bases, including data from structural and functional MRI. The medial frontal cortex appears to play an important role in self-appraisal in health and disease. PMID:22492754

InSight Lift & Mate

NASA Image and Video Library

2018-04-23

At Space Launch Complex 3 at Vandenberg Air Force Base in California, a crane is used to lift NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, Mars lander for mating atop a United Launch Alliance Atlas V rocket. InSight will be the first mission to look deep beneath the Martian surface. It will study the planet's interior by measuring its heat output and listen for marsquakes. The spacecraft will use the seismic waves generated by marsquakes to develop a map of the planet’s deep interior. The resulting insight into Mars’ formation will provide a better understanding of how other rocky planets, including Earth, were created. InSight is scheduled for liftoff May 5, 2018.

Structural and Functional Studies of H. seropedicae RecA Protein – Insights into the Polymerization of RecA Protein as Nucleoprotein Filament

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

Leite, Wellington C.; Galvão, Carolina W.; Saab, Sérgio C.

The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminalmore » polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. In conclusion, our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.« less

First Insights into the Genetic Diversity of the Pinewood Nematode in Its Native Area Using New Polymorphic Microsatellite Loci

PubMed Central

Mallez, Sophie; Castagnone, Chantal; Espada, Margarida; Vieira, Paulo; Eisenback, Jonathan D.; Mota, Manuel; Guillemaud, Thomas; Castagnone-Sereno, Philippe

2013-01-01

The pinewood nematode, Bursaphelenchus xylophilus, native to North America, is the causative agent of pine wilt disease and among the most important invasive forest pests in the East-Asian countries, such as Japan and China. Since 1999, it has been found in Europe in the Iberian Peninsula, where it also causes significant damage. In a previous study, 94 pairs of microsatellite primers have been identified in silico in the pinewood nematode genome. In the present study, specific PCR amplifications and polymorphism tests to validate these loci were performed and 17 microsatellite loci that were suitable for routine analysis of B. xylophilus genetic diversity were selected. The polymorphism of these markers was evaluated on nematodes from four field origins and one laboratory collection strain, all originate from the native area. The number of alleles and the expected heterozygosity varied between 2 and 11 and between 0.039 and 0.777, respectively. First insights into the population genetic structure of B. xylophilus were obtained using clustering and multivariate methods on the genotypes obtained from the field samples. The results showed that the pinewood nematode genetic diversity is spatially structured at the scale of the pine tree and probably at larger scales. The role of dispersal by the insect vector versus human activities in shaping this structure is discussed. PMID:23554990

Crystal structure and function of an unusual dimeric Hsp20.1 provide insight into the thermal protection mechanism of small heat shock proteins.

PubMed

Liu, Liang; Chen, Jiyun; Yang, Bo; Wang, Yonghua

2015-03-06

Small heat shock proteins (sHSPs) are ubiquitous chaperones that play a vital role in protein homeostasis. sHSPs are characterized by oligomeric architectures and dynamic exchange of subunits. The flexible oligomeric assembling associating with function remains poorly understood. Based on the structural data, it is certainly agreed that two dimerization models depend on the presence or absence of a β6 strand to differentiate nonmetazoan sHSPs from metazoan sHSPs. Here, we report the Sulfolobus solfataricus Hsp20.1 ACD dimer structure, which shows a distinct dimeric interface. We observed that, in the absence of β6, Hsp20.1 dimer does not depend on β7 strand for forming dimer interface as metazoan sHSPs, nor dissociates to monomers. This is in contrast to other published sHSPs. Our structure reveals a variable, highly polar dimer interface that has advantages for rapid subunits exchange and substrate binding. Remarkably, we find that the C-terminal truncation variant has chaperone activity comparable to that of wild-type despite lack of the oligomer structure. Our further study indicates that the N-terminal region is essential for the oligomer and dimer binding to the target protein. Together, the structure and function of Hsp20.1 give more insight into the thermal protection mechanism of sHSPs. Copyright © 2015 Elsevier Inc. All rights reserved.

Analysis shear wave velocity structure obtained from surface wave methods in Bornova, Izmir

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

Pamuk, Eren, E-mail: eren.pamuk@deu.edu.tr; Akgün, Mustafa, E-mail: mustafa.akgun@deu.edu.tr; Özdağ, Özkan Cevdet, E-mail: cevdet.ozdag@deu.edu.tr

2016-04-18

Properties of the soil from the bedrock is necessary to describe accurately and reliably for the reduction of earthquake damage. Because seismic waves change their amplitude and frequency content owing to acoustic impedance difference between soil and bedrock. Firstly, shear wave velocity and depth information of layers on bedrock is needed to detect this changing. Shear wave velocity can be obtained using inversion of Rayleigh wave dispersion curves obtained from surface wave methods (MASW- the Multichannel Analysis of Surface Waves, ReMi-Refraction Microtremor, SPAC-Spatial Autocorrelation). While research depth is limeted in active source study, a passive source methods are utilized formore » deep depth which is not reached using active source methods. ReMi method is used to determine layer thickness and velocity up to 100 m using seismic refraction measurement systems.The research carried out up to desired depth depending on radius using SPAC which is utilized easily in conditions that district using of seismic studies in the city. Vs profiles which are required to calculate deformations in under static and dynamic loads can be obtained with high resolution using combining rayleigh wave dispersion curve obtained from active and passive source methods. In the this study, Surface waves data were collected using the measurements of MASW, ReMi and SPAC at the İzmir Bornova region. Dispersion curves obtained from surface wave methods were combined in wide frequency band and Vs-depth profiles were obtained using inversion. Reliability of the resulting soil profiles were provided by comparison with theoretical transfer function obtained from soil paremeters and observed soil transfer function from Nakamura technique and by examination of fitting between these functions. Vs values are changed between 200-830 m/s and engineering bedrock (Vs>760 m/s) depth is approximately 150 m.« less

Structure influence on mechanical and acoustic properties of freeze-dried gels obtained with the use of hydrocolloids.

PubMed

Ciurzyńska, Agnieszka; Marzec, Agata; Mieszkowska, Arleta; Lenart, Andrzej

2017-04-01

The influence of the structure formed by the type of hydrocolloids (low-methoxyl pectin, the mixture of xanthan gum, and locust bean gum, and mixture of xanthan gum, and guar gum) and the aeration time (3, 5, 7, and 9 min) on textural properties of freeze-dried gels were investigated. The hardest texture generating the strongest acoustic emission was obtained by freeze-dried pectin gel, characterised by the lowest porosity and the largest pore diameter. Aeration time significantly affected mechanical and acoustic properties of the pectin gel lyophilisate. No effect of gel aeration time on tested characteristics of samples with mixture of hydrocolloids was observed. Strong positive correlations between acoustic energy as well as the maximum force and work and negative ones between porosity and pore diameter indicate that greater resilience and stronger acoustic emission of freeze-dried gels was caused by the reduction of porosity and the increase in the pore size of the material. The research is expected to show the phenomenon of structure formation when preparing and freeze-drying gels and explain the influence of the process parameters (time of aeration, the type of hydrocolloids) on the formation of the internal structure and physical properties of a dried product, especially mechanical and acoustic properties. This achievement will contribute to the development of the science of food and human nutrition, especially within the context of the popular research on aerated diet products. The expected result will be the ability to develop a new technology for producing food with a delicate texture, using the phenomenon of sublimation. As a result, designing changes in the structure of freeze-dried fruit gels with a delicate structure will be possible due to the choice of ingredients and aeration parameters in order to develop innovative food characterised by favorable nutritional, health and functional properties, which will be attractive for the consumers. © 2016

Carbon nanofibers obtained from electrospinning process

NASA Astrophysics Data System (ADS)

Bovi de Oliveira, Juliana; Müller Guerrini, Lília; Sizuka Oishi, Silvia; Rogerio de Oliveira Hein, Luis; dos Santos Conejo, Luíza; Cerqueira Rezende, Mirabel; Cocchieri Botelho, Edson

2018-02-01

In recent years, reinforcements consisting of carbon nanostructures, such as carbon nanotubes, fullerenes, graphenes, and carbon nanofibers have received significant attention due mainly to their chemical inertness and good mechanical, electrical and thermal properties. Since carbon nanofibers comprise a continuous reinforcing with high specific surface area, associated with the fact that they can be obtained at a low cost and in a large amount, they have shown to be advantageous compared to traditional carbon nanotubes. The main objective of this work is the processing of carbon nanofibers, using polyacrylonitrile (PAN) as a precursor, obtained by the electrospinning process via polymer solution, with subsequent use for airspace applications as reinforcement in polymer composites. In this work, firstly PAN nanofibers were produced by electrospinning with diameters in the range of (375 ± 85) nm, using a dimethylformamide solution. Using a furnace, the PAN nanofiber was converted into carbon nanofiber. Morphologies and structures of PAN and carbon nanofibers were investigated by scanning electron microscopy, Raman Spectroscopy, thermogravimetric analyses and differential scanning calorimeter. The resulting residual weight after carbonization was approximately 38% in weight, with a diameters reduction of 50%, and the same showed a carbon yield of 25%. From the analysis of the crystalline structure of the carbonized material, it was found that the material presented a disordered structure.

Structure and transformation of tactoids in cellulose nanocrystal suspensions

NASA Astrophysics Data System (ADS)

Wang, Pei-Xi; Hamad, Wadood Y.; MacLachlan, Mark J.

2016-05-01

Cellulose nanocrystals obtained from natural sources are of great interest for many applications. In water, cellulose nanocrystals form a liquid crystalline phase whose hierarchical structure is retained in solid films after drying. Although tactoids, one of the most primitive components of liquid crystals, are thought to have a significant role in the evolution of this phase, they have evaded structural study of their internal organization. Here we report the capture of cellulose nanocrystal tactoids in a polymer matrix. This method allows us to visualize, for the first time, the arrangement of cellulose nanocrystals within individual tactoids by electron microscopy. Furthermore, we can follow the structural evolution of the liquid crystalline phase from tactoids to iridescent-layered films. Our insights into the early nucleation events of cellulose nanocrystals give important information about the growth of cholesteric liquid crystalline phases, especially for cellulose nanocrystals, and are crucial for preparing photonics-quality films.

Recent Neurobiological Insights into the Concept of Insight in Psychosis

PubMed Central

Mythri, Starlin Vijay; Sanjay, Y

2016-01-01

The concept of insight in psychosis has been an interesting area in clinical psychiatry for well over a century with a surge in research interest over the past 25 years. Moreover, the past 5 years have been particularly fruitful in deciphering its neurobiological underpinnings. This article presents the development of the concept of insight in psychosis and reviews the current neurobiological research findings in this area. PMID:27335512

Flow Structure along the 1303 UCAV

NASA Astrophysics Data System (ADS)

Kosoglu, Mehmet A.; Rockwell, Donald

2007-11-01

The 1303 Unmanned Combat Air Vehicle is representative of a variety of UCAVs with blended wing-body configurations. Flow structure along a scale model of this configuration was investigated using dye visualization and particle image velocimetry for variations of Reynolds number and angle-of-attack. Both of these parameters substantially influence onset and structure of the leading-edge vortex (LEV) and a separation bubble/stall region along the tip. The onset of formation of the LEV initially occurs at a location well downstream of the apex and moves upstream for increasing values of either Reynolds number or angle-of-attack. In cases where a separation bubble or stall region exists, quantitative information on its structure was obtained via PIV imaging on a plane nearly parallel to the surface of the wing. By acquiring images on planes at successively larger elevations from the surface, it was possible to gain insight into the space-time features of the three-dimensional and highly time-dependent structure of the bubble or stall region. Time-averaged images indicate that maximum velocity defect decreases in magnitude and moves downstream with increasing elevation from the surface.

Intrabasement structures as structural templates for rifts: Insights from the Taranaki Basin, offshore New Zealand

NASA Astrophysics Data System (ADS)

Collanega, L.; Jackson, C. A. L.; Bell, R. E.; Lenhart, A.; Coleman, A. J.; Breda, A.; Massironi, M.

2017-12-01

Intrabasement structures are often envisaged to have acted as structural templates for normal fault growth in the overlying sedimentary cover during rifting (e.g. East African Rift; NE Brazilian Margin; Norwegian North Sea). However, in some settings, the geometry of rift-related faults is apparently unaffected by pre-existing basement fabric (Måløy Slope and Lofoten Ridge, offshore Norway). Understanding the nucleation and propagation of normal faults in the presence of basement structures may elucidate how and under what conditions basement fabric can exert an influence on rifting. Here, we investigate the 3D geometry of a series of normal faults and intrabasement structures from the Taranaki Basin, offshore New Zealand to understand how normal faults grow in the presence of basement heterogeneities. The Taranaki Basin is an ideal setting because the basement structures, related to the Mesozoic compressional tectonics, are shallow and well-imaged on 3D seismic reflection data, and the relatively thin and stratigraphically simple sedimentary cover is only affected by mild Pliocene extension. Our kinematic analysis highlights two classes of normal faults affecting different vertical intervals of the sedimentary cover. Deep faults, just above the basement, strike NW-SE to NE-SW, reflecting the trend of underlying intrabasement structures. In contrast, shallow faults strike according to the NE-SW to NNE-SSW Pliocene trend and are not generally affected by intrabasement structures at distances >500 m above the basement. Deep and shallow faults are only linked when they strike similarly, and are located above strong intrabasement reflections. We infer that cover deformation is significantly influenced by intrabasement structures within the 500 m interval above the crystalline basement, whereas shallower faults are optimally aligned to the Pliocene regional stress field. Since we do not observe an extensional reactivation of intrabasement structures during Pliocene