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Sample records for facilitates beta-sheet recognition

Natural polypeptide scaffolds: beta-sheets, beta-turns, and beta-hairpins.

PubMed

Rotondi, Kenneth S; Gierasch, Lila M

2006-01-01

This paper provides an introduction to fundamental conformational states of polypeptides in the beta-region of phi,psi space, in which the backbone is extended near to its maximal length, and to more complex architectures in which extended segments are linked by turns and loops. There are several variants on these conformations, and they comprise versatile scaffolds for presentation of side chains and backbone amides for molecular recognition and designed catalysts. In addition, the geometry of these fundamental folds can be readily mimicked in peptidomimetics. Copyright 2005 Wiley Periodicals, Inc.
Coupling ligand recognition to protein folding in an engineered variant of rabbit ileal lipid binding protein.

PubMed

Kouvatsos, Nikolaos; Meldrum, Jill K; Searle, Mark S; Thomas, Neil R

2006-11-28

We have engineered a variant of the beta-clam shell protein ILBP which lacks the alpha-helical motif that caps the central binding cavity; the mutant protein is sufficiently destabilised that it is unfolded under physiological conditions, however, it unexpectedly binds its natural bile acid substrates with high affinity forming a native-like beta-sheet rich structure and demonstrating strong thermodynamic coupling between ligand binding and protein folding.
Origin of higher affinity to RNA of the N-terminal RNA-binding domain than that of the C-terminal one of a mouse neural protein, musashi1, as revealed by comparison of their structures, modes of interaction, surface electrostatic potentials, and backbone dynamics.

PubMed

Miyanoiri, Youhei; Kobayashi, Hisanori; Imai, Takao; Watanabe, Michinao; Nagata, Takashi; Uesugi, Seiichi; Okano, Hideyuki; Katahira, Masato

2003-10-17

Musashi1 is an RNA-binding protein abundantly expressed in the developing mouse central nervous system. Its restricted expression in neural precursor cells suggests that it is involved in maintenance of the character of progenitor cells. Musashi1 contains two ribonucleoprotein-type RNA-binding domains (RBDs), RBD1 and RBD2, the affinity to RNA of RBD1 being much higher than that of RBD2. We previously reported the structure and mode of interaction with RNA of RBD2. Here, we have determined the structure and mode of interaction with RNA of RBD1. We have also analyzed the surface electrostatic potential and backbone dynamics of both RBDs. The two RBDs exhibit the same ribo-nucleoprotein-type fold and commonly make contact with RNA on the beta-sheet side. On the other hand, there is a remarkable difference in surface electrostatic potential, the beta-sheet of RBD1 being positively charged, which is favorable for binding negatively charged RNA, but that of RBD2 being almost neutral. There is also a difference in backbone dynamics, the central portion of the beta-sheet of RBD1 being flexible, but that of RBD2 not being flexible. The flexibility of RBD1 may be utilized in the recognition process to facilitate an induced fit. Thus, comparative studies have revealed the origin of the higher affinity of RBD1 than that of RBD2 and indicated that the affinity of an RBD to RNA is not governed by its fold alone but is also determined by its surface electrostatic potential and/or backbone dynamics. The biological role of RBD2 with lower affinity is also discussed.
Students' understanding of primary and secondary protein structure: drawing secondary protein structure reveals student understanding better than simple recognition of structures.

PubMed

Harle, Marissa; Towns, Marcy H

2013-01-01

The interdisciplinary nature of biochemistry courses requires students to use both chemistry and biology knowledge to understand biochemical concepts. Research that has focused on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations in addition to a fragmented understanding of fundamental biochemistry concepts. This project focuses on students' understanding of primary and secondary protein structure and drawings (representations) of hydrogen-bonding in alpha helices and beta sheets. Analysis demonstrated that students can recognize and identify primary protein structure concepts when given a polypeptide. However, when asked to draw alpha helices and beta sheets and explain the role of hydrogen bonding their drawings students exhibited a fragmented understanding that lacked coherence. Faculty are encouraged to have students draw molecular level representations to make their mental models more explicit, complete, and coherent. This is in contrast to recognition and identification tasks, which do not adequately probe mental models and molecular level understanding. © 2013 by The International Union of Biochemistry and Molecular Biology.
The Promiscuity of [beta]-Strand Pairing Allows for Rational Design of [beta]-Sheet Face Inversion

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

Makabe, Koki; Koide, Shohei

2009-06-17

Recent studies suggest the dominant role of main-chain H-bond formation in specifying {beta}-sheet topology. Its essentially sequence-independent nature implies a large degree of freedom in designing {beta}-sheet-based nanomaterials. Here we show rational design of {beta}-sheet face inversions by incremental deletions of {beta}-strands from the single-layer {beta}-sheet of Borrelia outer surface protein A. We show that a {beta}-sheet structure can be maintained when a large number of native contacts are removed and that one can design large-scale conformational transitions of a {beta}-sheet such as face inversion by exploiting the promiscuity of strand-strand interactions. High-resolution X-ray crystal structures confirmed the success ofmore » the design and supported the importance of main-chain H-bonds in determining {beta}-sheet topology. This work suggests a simple but effective strategy for designing and controlling nanomaterials based on {beta}-rich peptide self-assemblies.« less
Determining Beta Sheet Crystallinity in Fibrous Proteins by Thermal Analysis and Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Hu, Xiao; Kaplan, David; Cebe, Peggy

2007-03-01

We report a study of self-assembled beta pleated sheets in Bombyx mori silk fibroin films using thermal analysis and infrared spectroscopy. Crystallization of beta pleated sheets was effected either by heating the films above the glass transition temperature (Tg) and holding isothermally, or by exposure to methanol. The fractions of secondary structural components including random coils, alpha helices, beta pleated sheets, turns, and side chains, were evaluated using Fourier self-deconvolution (FSD) of the infrared absorbance spectra. As crystalline beta sheets form, the heat capacity increment from the TMDSC trace at Tg is systematically decreased and is linearly well correlated with beta sheet content determined from FSD. This analysis of beta sheet content can serve as an alternative to X-ray methods and may have wide applicability to other crystalline beta sheet forming proteins.
Precursor-product discrimination by La protein during tRNA metabolism.

PubMed

Bayfield, Mark A; Maraia, Richard J

2009-04-01

La proteins bind pre-tRNAs at their UUU-3'OH ends, facilitating their maturation. Although the mechanism by which La binds pre-tRNA 3' trailers is known, the function of the RNA binding beta-sheet surface of the RNA-recognition motif (RRM1) is unknown. How La dissociates from UUU-3'OH-containing trailers after 3' processing is also unknown. Here we show that La preferentially binds pre-tRNAs over processed tRNAs or 3' trailer products through coupled use of two sites: one on the La motif and another on the RRM1 beta-surface that binds elsewhere on tRNA. Two sites provide stable pre-tRNA binding, whereas the processed tRNA and 3' trailer are released from their single sites relatively fast. RRM1 loop-3 mutations decrease affinity for pre-tRNA and tRNA, but not for the UUU-3'OH trailer, and impair tRNA maturation in vivo. We propose that RRM1 functions in activities that are more complex than UUU-3'OH binding. Accordingly, the RRM1 mutations also impair an RNA chaperone activity of La. The results suggest how La distinguishes precursor from product RNAs, allowing it to recycle onto a new pre-tRNA.
A recipe for designing water-soluble, beta-sheet-forming peptides.

PubMed Central

Mayo, K. H.; Ilyina, E.; Park, H.

1996-01-01

Based on observations of solubility and folding properties of peptide 33-mers derived from the beta-sheet domains of platelet factor-4 (PF4), interleukin-8 (IL-8), and growth related protein (Gro-alpha), as well as other beta-sheet-forming peptides, general guidelines have been developed to aid in the design of water soluble, self-association-induced beta-sheet-forming peptides. CD, 1H-NMR, and pulsed field gradient NMR self-diffusion measurements have been used to assess the degree of folding and state of aggregation. PF4 peptide forms native-like beta-sheet tetramers and is sparingly soluble above pH 6. IL-8 peptide is insoluble between pH 4.5 and pH 7.5, yet forms stable, native-like beta-sheet dimers at higher pH. Gro-alpha peptide is soluble at all pH values, yet displays no discernable beta-sheet structure even when diffusion data indicate dimer-tetramer aggregation. A recipe used in the de novo design of water-soluble beta-sheet-forming peptides calls for the peptide to contain 40-50% hydrophobic residues, usually aliphatic ones (I, L, V, A, M) (appropriately paired and mostly but not always alternating with polar residues in the sheet sequence), a positively charged (K, R) to negatively charged (E, D) residue ratio between 4/2 and 6/2, and a noncharged polar residue (N, Q, T, S) composition of about 20% or less. Results on four de novo designed, 33-residue peptides are presented supporting this approach. Under near physiologic conditions, all four peptides are soluble, form beta-sheet structures to varying degrees, and self-associate. One peptide folds as a stable, compact beta-sheet tetramer, whereas the others are transient beta-sheet-containing aggregates. PMID:8819163
Mechanistic insights into phosphoprotein-binding FHA domains.

PubMed

Liang, Xiangyang; Van Doren, Steven R

2008-08-01

[Structure: see text]. FHA domains are protein modules that switch signals in diverse biological pathways by monitoring the phosphorylation of threonine residues of target proteins. As part of the effort to gain insight into cellular avoidance of cancer, FHA domains involved in the cellular response to DNA damage have been especially well-characterized. The complete protein where the FHA domain resides and the interaction partners determine the nature of the signaling. Thus, a key biochemical question is how do FHA domains pick out their partners from among thousands of alternatives in the cell? This Account discusses the structure, affinity, and specificity of FHA domains and the formation of their functional structure. Although FHA domains share sequence identity at only five loop residues, they all fold into a beta-sandwich of two beta-sheets. The conserved arginine and serine of the recognition loops recognize the phosphorylation of the threonine targeted. Side chains emanating from loops that join beta-strand 4 with 5, 6 with 7, or 10 with 11 make specific contacts with amino acids of the ligand that tailor sequence preferences. Many FHA domains choose a partner in extended conformation, somewhat according to the residue three after the phosphothreonine in sequence (pT + 3 position). One group of FHA domains chooses a short carboxylate-containing side chain at pT + 3. Another group chooses a long, branched aliphatic side chain. A third group prefers other hydrophobic or uncharged polar side chains at pT + 3. However, another FHA domain instead chooses on the basis of pT - 2, pT - 3, and pT + 1 positions. An FHA domain from a marker of human cancer instead chooses a much longer protein fragment that adds a beta-strand to its beta-sheet and that presents hydrophobic residues from a novel helix to the usual recognition surface. This novel recognition site and more remote sites for the binding of other types of protein partners were predicted for the entire family of FHA domains by a bioinformatics approach. The phosphopeptide-dependent dynamics of an FHA domain, SH2 domain, and PTB domain suggest a common theme: rigid, preformed binding surfaces support van der Waals contacts that provide favorable binding enthalpy. Despite the lack of pronounced conformational changes in FHA domains linked to binding events, more subtle adjustments may be possible. In the one FHA domain tested, phosphothreonine peptide binding is accompanied by increased flexibility just outside the binding site and increased rigidity across the beta-sandwich. The folding of the same FHA domain progresses through near-native intermediates that stabilize the recognition loops in the center of the phosphoprotein-binding surface; this may promote rigidity in the interface and affinity for targets phosphorylated on threonine.
Beating the Heat - Fast Scanning Melts Silk Beta Sheet Crystals

NASA Astrophysics Data System (ADS)

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

2013-01-01

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

PubMed

Wang, Chang-Sheng; Sun, Chang-Liang

2010-04-15

In this article, the binding energies of 16 antiparallel and parallel beta-sheet models are estimated using the analytic potential energy function we proposed recently and the results are compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparisons indicate that the analytic potential energy function can produce reasonable binding energies for beta-sheet models. Further comparisons suggest that the binding energy of the beta-sheet models might come mainly from dipole-dipole attractive and repulsive interactions and VDW interactions between the two strands. The dipole-dipole attractive and repulsive interactions are further obtained in this article. The total of N-H...H-N and C=O...O=C dipole-dipole repulsive interaction (the secondary electrostatic repulsive interaction) in the small ring of the antiparallel beta-sheet models is estimated to be about 6.0 kcal/mol. The individual N-H...O=C dipole-dipole attractive interaction is predicted to be -6.2 +/- 0.2 kcal/mol in the antiparallel beta-sheet models and -5.2 +/- 0.6 kcal/mol in the parallel beta-sheet models. The individual C(alpha)-H...O=C attractive interaction is -1.2 +/- 0.2 kcal/mol in the antiparallel beta-sheet models and -1.5 +/- 0.2 kcal/mol in the parallel beta-sheet models. These values are important in understanding the interactions at protein-protein interfaces and developing a more accurate force field for peptides and proteins. 2009 Wiley Periodicals, Inc.
Structural Basis for the Histone Chaperone Activity of Asf1

PubMed Central

English, Christine M.; Adkins, Melissa W.; Carson, Joshua J.; Churchill, Mair E.A.; Tyler, Jessica K.

2010-01-01

SUMMARY Asf1 is a highly conserved chaperone of histones H3/H4 that assembles or disassembles chromatin during transcription, replication, and repair. The structure of the globular domain of Asf1 bound to H3/H4 determined by X-ray crystallography to a resolution of 1.7 Å shows how Asf1 binds the H3/H4 heterodimer, enveloping the C-terminus of histone H3 and physically blocking formation of the H3/H4 heterotetramer. Unexpectedly, the C-terminus of histone H4 that forms a mini-beta sheet with histone H2A in the nucleosome, undergoes a major conformational change upon binding to Asf1 and adds a beta strand to the Asf1 beta-sheet sandwich. Interactions with both H3 and H4 were required for Asf1 histone chaperone function in vivo and in vitro. The Asf1-H3/H4 structure suggests a “strand-capture” mechanism whereby the H4 tail acts as a lever to facilitate chromatin disassembly / assembly that may be used ubiquitously by histone chaperones. PMID:17081973
Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins.

PubMed Central

Zhu, H.; Braun, W.

1999-01-01

A statistical analysis of a representative data set of 169 known protein structures was used to analyze the specificity of residue interactions between spatial neighboring strands in beta-sheets. Pairwise potentials were derived from the frequency of residue pairs in nearest contact, second nearest and third nearest contacts across neighboring beta-strands compared to the expected frequency of residue pairs in a random model. A pseudo-energy function based on these statistical pairwise potentials recognized native beta-sheets among possible alternative pairings. The native pairing was found within the three lowest energies in 73% of the cases in the training data set and in 63% of beta-sheets in a test data set of 67 proteins, which were not part of the training set. The energy function was also used to detect tripeptides, which occur frequently in beta-sheets of native proteins. The majority of native partners of tripeptides were distributed in a low energy range. Self-correcting distance geometry (SECODG) calculations using distance constraints sets derived from possible low energy pairing of beta-strands uniquely identified the native pairing of the beta-sheet in pancreatic trypsin inhibitor (BPTI). These results will be useful for predicting the structure of proteins from their amino acid sequence as well as for the design of proteins containing beta-sheets. PMID:10048326
Rapid model building of beta-sheets in electron-density maps.

PubMed

Terwilliger, Thomas C

2010-03-01

A method for rapidly building beta-sheets into electron-density maps is presented. beta-Strands are identified as tubes of high density adjacent to and nearly parallel to other tubes of density. The alignment and direction of each strand are identified from the pattern of high density corresponding to carbonyl and C(beta) atoms along the strand averaged over all repeats present in the strand. The beta-strands obtained are then assembled into a single atomic model of the beta-sheet regions. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 A. The beta-sheet regions were nearly completely built in all but two cases, the exceptions being one structure at 2.5 A resolution in which a third of the residues in beta-sheets were built and a structure at 3.8 A in which under 10% were built. The overall average r.m.s.d. of main-chain atoms in the residues built using this method compared with refined models of the structures was 1.5 A.
Beating the Heat: Fast Scanning Melts Beta Sheet Crystals

NASA Astrophysics Data System (ADS)

Cebe, Peggy; Hu, Xiao; Kaplan, David; Zhuravlev, Evgeny; Wurm, Andreas; Arbeiter, Daniella; Schick, Christoph

2014-03-01

Beta-pleated-sheet crystals are among the most stable of protein secondary structures, and are responsible for the remarkable physical properties of many fibrous proteins, such as silk. Previous thinking was that beta-pleated-sheet crystals in the dry solid state would not melt upon input of heat energy alone. Indeed, at conventional heating rates (~1-50 °C/min), silk exhibits its glass transition (~175 °C), followed by cold crystallization, and then by immediate thermal degradation beginning at about 225 °C. Here we demonstrate that beta-pleated-sheet crystals can melt directly from the solid state to become random coils, helices, and turns. We use fast scanning chip calorimetry at 2,000 K/s to avoid thermal degradation, and report the first reversible thermal melting of protein beta-pleated-sheet crystals, exemplified by silk fibroin. The similarity between thermal melting behavior of lamellar crystals of synthetic polymers and beta-pleated-sheet crystals is confirmed. The authors acknowledge support from the National Science Foundation and German Academic Exchange Service DAAD; EZ acknowledges a European Union funded Marie Curie EST fellowship (ADVATEC); XH and DK acknowledge NIH P41 Tissue Engineering Resource Center.
Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices.

PubMed

Zanuy, David; Gunasekaran, Kannan; Lesk, Arthur M; Nussinov, Ruth

2006-04-21

The formation of fibril aggregates by long polyglutamine sequences is assumed to play a major role in neurodegenerative diseases such as Huntington. Here, we model peptides rich in glutamine, through a series of molecular dynamics simulations. Starting from a rigid nanotube-like conformation, we have obtained a new conformational template that shares structural features of a tubular helix and of a beta-helix conformational organization. Our new model can be described as a super-helical arrangement of flat beta-sheet segments linked by planar turns or bends. Interestingly, our comprehensive analysis of the Protein Data Bank reveals that this is a common motif in beta-helices (termed beta-bend), although it has not been identified so far. The motif is based on the alternation of beta-sheet and helical conformation as the protein sequence is followed from the N to the C termini (beta-alpha(R)-beta-polyPro-beta). We further identify this motif in the ssNMR structure of the protofibril of the amyloidogenic peptide Abeta(1-40). The recurrence of the beta-bend suggests a general mode of connecting long parallel beta-sheet segments that would allow the growth of partially ordered fibril structures. The design allows the peptide backbone to change direction with a minimal loss of main chain hydrogen bonds. The identification of a coherent organization beyond that of the beta-sheet segments in different folds rich in parallel beta-sheets suggests a higher degree of ordered structure in protein fibrils, in agreement with their low solubility and dense molecular packing.
Characterization of two distinct beta2-microglobulin unfolding intermediates that may lead to amyloid fibrils of different morphology.

PubMed

Armen, Roger S; Daggett, Valerie

2005-12-13

The self-assembly of beta(2)-microglobulin into fibrils leads to dialysis-related amyloidosis. pH-mediated partial unfolding is required for the formation of the amyloidogenic intermediate that then self-assembles into amyloid fibrils. Two partially folded intermediates of beta(2)-microglobulin have been identified experimentally and linked to the formation of fibrils of distinct morphology, yet it remains difficult to characterize these partially unfolded states at high resolution using experimental approaches. Consequently, we have performed molecular dynamics simulations at neutral and low pH to determine the structures of these partially unfolded amyloidogenic intermediates. In the low-pH simulations, we observed the formation of alpha-sheet structure, which was first proposed by Pauling and Corey. Multiple simulations were performed, and two distinct intermediate state ensembles were identified that may account for the different fibril morphologies. The predominant early unfolding intermediate was nativelike in structure, in agreement with previous NMR studies. The late unfolding intermediate was significantly disordered, but it maintained an extended elongated structure, with hydrophobic clusters and residual alpha-extended chain strands in specific regions of the sequence that map to amyloidogenic peptides. We propose that the formation of alpha-sheet facilitates self-assembly into partially unfolded prefibrillar amyloidogenic intermediates.
Orientation determination of interfacial beta-sheet structures in situ.

PubMed

Nguyen, Khoi Tan; King, John Thomas; Chen, Zhan

2010-07-01

Structural information such as orientations of interfacial proteins and peptides is important for understanding properties and functions of such biological molecules, which play crucial roles in biological applications and processes such as antimicrobial selectivity, membrane protein activity, biocompatibility, and biosensing performance. The alpha-helical and beta-sheet structures are the most widely encountered secondary structures in peptides and proteins. In this paper, for the first time, a method to quantify the orientation of the interfacial beta-sheet structure using a combined attenuated total reflectance Fourier transformation infrared spectroscopic (ATR-FTIR) and sum frequency generation (SFG) vibrational spectroscopic study was developed. As an illustration of the methodology, the orientation of tachyplesin I, a 17 amino acid peptide with an antiparallel beta-sheet, adsorbed to polymer surfaces as well as associated with a lipid bilayer was determined using the regular and chiral SFG spectra, together with polarized ATR-FTIR amide I signals. Both the tilt angle (theta) and the twist angle (psi) of the beta-sheet at interfaces are determined. The developed method in this paper can be used to obtain in situ structural information of beta-sheet components in complex molecules. The combination of this method and the existing methodology that is currently used to investigate alpha-helical structures will greatly broaden the application of optical spectroscopy in physical chemistry, biochemistry, biophysics, and structural biology.
Structural Determinants of DNA Binding by a P. falciparum ApiAP2 Transcriptional Regulator

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

Lindner, Scott E.; De Silva, Erandi K.; Keck, James L.

2010-11-05

Putative transcription factors have only recently been identified in the Plasmodium spp., with the major family of regulators comprising the Apicomplexan Apetala2 (AP2) proteins. To better understand the DNA-binding mechanisms of these transcriptional regulators, we characterized the structure and in vitro function of an AP2 DNA-binding domain from a prototypical Apicomplexan AP2 protein, PF14{_}0633 from Plasmodium falciparum. The X-ray crystal structure of the PF14{_}0633 AP2 domain bound to DNA reveals a {beta}-sheet fold that binds the DNA major groove through base-specific and backbone contacts; a prominent {alpha}-helix supports the {beta}-sheet structure. Substitution of predicted DNA-binding residues with alanine weakened ormore » eliminated DNA binding in solution. In contrast to plant AP2 domains, the PF14{_}0633 AP2 domain dimerizes upon binding to DNA through a domain-swapping mechanism in which the {alpha}-helices of the AP2 domains pack against the {beta}-sheets of the dimer mates. DNA-induced dimerization of PF14{_}0633 may be important for tethering two distal DNA loci together in the nucleus and/or for inducing functional rearrangements of its domains to facilitate transcriptional regulation. Consistent with a multisite binding mode, at least two copies of the consensus sequence recognized by PF14{_}0633 are present upstream of a previously identified group of sporozoite-stage genes. Taken together, these findings illustrate how Plasmodium has adapted the AP2 DNA-binding domain for genome-wide transcriptional regulation.« less
Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities.

PubMed

Zheng, Jie; Jang, Hyunbum; Ma, Buyong; Tsai, Chung-Jun; Nussinov, Ruth

2007-11-01

We investigate Abeta(17-42) protofibril structures in solution using molecular dynamics simulations. Recently, NMR and computations modeled the Abeta protofibril as a longitudinal stack of U-shaped molecules, creating an in-parallel beta-sheet and loop spine. Here we study the molecular architecture of the fibril formed by spine-spine association. We model in-register intermolecular beta-sheet-beta-sheet associations and study the consequences of Alzheimer's mutations (E22G, E22Q, E22K, and M35A) on the organization. We assess the structural stability and association force of Abeta oligomers with different sheet-sheet interfaces. Double-layered oligomers associating through the C-terminal-C-terminal interface are energetically more favorable than those with the N-terminal-N-terminal interface, although both interfaces exhibit high structural stability. The C-terminal-C-terminal interface is essentially stabilized by hydrophobic and van der Waals (shape complementarity via M35-M35 contacts) intermolecular interactions, whereas the N-terminal-N-terminal interface is stabilized by hydrophobic and electrostatic interactions. Hence, shape complementarity, or the "steric zipper" motif plays an important role in amyloid formation. On the other hand, the intramolecular Abeta beta-strand-loop-beta-strand U-shaped motif creates a hydrophobic cavity with a diameter of 6-7 A, allowing water molecules and ions to conduct through. The hydrated hydrophobic cavities may allow optimization of the sheet association and constitute a typical feature of fibrils, in addition to the tight sheet-sheet association. Thus, we propose that Abeta fiber architecture consists of alternating layers of tight packing and hydrated cavities running along the fibrillar axis, which might be possibly detected by high-resolution imaging.

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

Vitiello, Giuseppe; CSGI; Grimaldi, Manuela

Highlights: Black-Right-Pointing-Pointer iA{beta}5p shows a significant tendency to deeply penetrates the hydrophobic core of lipid membrane. Black-Right-Pointing-Pointer A{beta}(25-35) locates in the external region of the membrane causing a re-positioning of CHOL. Black-Right-Pointing-Pointer iA{beta}5p withholds cholesterol in the inner hydrophobic core of the lipid membrane. Black-Right-Pointing-Pointer iA{beta}5p prevents the A{beta}(25-35) release from the lipid membrane. -- Abstract: Alzheimer's disease is characterized by the deposition of aggregates of the {beta}-amyloid peptide (A{beta}) in the brain. A potential therapeutic strategy for Alzheimer's disease is the use of synthetic {beta}-sheet breaker peptides, which are capable of binding A{beta} but unable to become part ofmore » a {beta}-sheet structure, thus inhibiting the peptide aggregation. Many studies suggest that membranes play a key role in the A{beta} aggregation; consequently, it is strategic to investigate the interplay between {beta}-sheet breaker peptides and A{beta} in the presence of lipid bilayers. In this work, we focused on the effect of the {beta}-sheet breaker peptide acetyl-LPFFD-amide, iA{beta}5p, on the interaction of the A{beta}(25-35) fragment with lipid membranes, studied by Electron Spin Resonance spectroscopy, using spin-labeled membrane components (either phospholipids or cholesterol). The ESR results show that iA{beta}5p influences the A{beta}(25-35) interaction with the bilayer through a cholesterol-mediated mechanism: iA{beta}5p withholds cholesterol in the inner hydrophobic core of the bilayer, making the interfacial region more fluid and capable to accommodate A{beta}(25-35). As a consequence, iA{beta}5p prevents the A{beta}(25-35) release from the lipid membrane, which is the first step of the {beta}-amyloid aggregation process.« less
In silico study of full-length amyloid beta 1-42 tri- and penta-oligomers in solution.

PubMed

Masman, Marcelo F; Eisel, Ulrich L M; Csizmadia, Imre G; Penke, Botond; Enriz, Ricardo D; Marrink, Siewert Jan; Luiten, Paul G M

2009-08-27

Amyloid oligomers are considered to play causal roles in the pathogenesis of amyloid-related degenerative diseases including Alzheimer's disease. Using MD simulation techniques, we explored the contributions of the different structural elements of trimeric and pentameric full-length Abeta1-42 aggregates in solution to their stability and conformational dynamics. We found that our models are stable at a temperature of 310 K, and converge toward an interdigitated side-chain packing for intermolecular contacts within the two beta-sheet regions of the aggregates: beta1 (residues 18-26) and beta2 (residues 31-42). MD simulations reveal that the beta-strand twist is a characteristic element of Abeta-aggregates, permitting a compact, interdigitated packing of side chains from neighboring beta-sheets. The beta2 portion formed a tightly organized beta-helix, whereas the beta1 portion did not show such a firm structural organization, although it maintained its beta-sheet conformation. Our simulations indicate that the hydrophobic core comprising the beta2 portion of the aggregate is a crucial stabilizing element in the Abeta aggregation process. On the basis of these structure-stability findings, the beta2 portion emerges as an optimal target for further antiamyloid drug design.
Circular dichroism studies of the mitochondrial channel, VDAC, from Neurospora crassa.

PubMed Central

Shao, L; Kinnally, K W; Mannella, C A

1996-01-01

The protein that forms the voltage-gated channel VDAC (or mitochondrial porin) has been purified from Neurospora crassa. At room temperature and pH 7, the circular dichoism (CD) spectrum of VDAC suspended in octyl beta-glucoside is similar to those of bacterial porins, consistent with a high beta-sheet content. When VDAC is reconstituted into phospholipid liposomes at pH 7, a similar CD spectrum is obtained and the liposomes are rendered permeable to sucrose. Heating VDAC in octyl beta-glucoside or in liposomes results in thermal denaturation. The CD spectrum irreversibly changes to one consistent with total loss of beta-sheet content, and VDAC-containing liposomes irreversibly lose sucrose permeability. When VDAC is suspended at room temperature in octyl beta-glucoside at pH < 5 or in sodium dodecyl sulfate at pH 7, its CD spectrum is consistent with partial loss of beta-sheet content. The sucrose permeability of VDAC-containing liposomes is decreased at low pH and restored at pH 7. Similarly, the pH-dependent changes in the CD spectrum of VDAC suspended in octyl beta-glucoside also are reversible. These results suggest that VDAC undergoes a reversible conformational change at low pH involving reduced beta-sheet content and loss of pore-forming activity. Images FIGURE 1 PMID:8842216
Design and preparation of beta-sheet forming repetitive and block-copolymerized polypeptides.

PubMed

Higashiya, Seiichiro; Topilina, Natalya I; Ngo, Silvana C; Zagorevskii, Dmitri; Welch, John T

2007-05-01

The design and rapid construction of libraries of genes coding beta-sheet forming repetitive and block-copolymerized polypeptides bearing various C- and N-terminal sequences are described. The design was based on the assembly of DNA cassettes coding for the (GA)3GX amino acid sequence where the (GAGAGA) sequences would constitute the beta-strand units of a larger beta-sheet assembly. The edges of this beta-sheet would be functionalized by the turn-inducing amino acids (GX). The polypeptides were expressed in Escherichia coli using conventional vectors and were purified by Ni-nitriloacetic acid (NTA) chromatography. The correlation of polymer structure with molecular weight was investigated by gel electrophoresis and mass spectrometry. The monomer sequences and post-translational chemical modifications were found to influence the mobility of the polypeptides over the full range of polypeptide molecular weights while the electrophoretic mobility of lower molecular weight polypeptides was more susceptible to C- and N-termini polypeptide modifications.
Anatomy of an amyloidogenic intermediate: conversion of beta-sheet to alpha-sheet structure in transthyretin at acidic pH.

PubMed

Armen, Roger S; Alonso, Darwin O V; Daggett, Valerie

2004-10-01

The homotetramer of transthyretin (TTR) dissociates into a monomeric amyloidogenic intermediate that self-assembles into amyloid fibrils at low pH. We have performed molecular dynamics simulations of monomeric TTR at neutral and low pH at physiological (310 K) and very elevated temperature (498 K). In the low-pH simulations at both temperatures, one of the two beta-sheets (strands CBEF) becomes disrupted, and alpha-sheet structure forms in the other sheet (strands DAGH). alpha-sheet is formed by alternating alphaL and alphaR residues, and it was first proposed by Pauling and Corey. Overall, the simulations are in agreement with the available experimental observations, including solid-state NMR results for a TTR-peptide amyloid. In addition, they provide a unique explanation for the results of hydrogen exchange experiments of the amyloidogenic intermediate-results that are difficult to explain with beta-structure. We propose that alpha-sheet may represent a key pathological conformation during amyloidogenesis. Copyright 2004 Elsevier Ltd.
Minimalist design of water-soluble cross-[beta] architecture

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

Biancalana, Matthew; Makabe, Koki; Koide, Shohei

Demonstrated successes of protein design and engineering suggest significant potential to produce diverse protein architectures and assemblies beyond those found in nature. Here, we describe a new class of synthetic protein architecture through the successful design and atomic structures of water-soluble cross-{beta} proteins. The cross-{beta} motif is formed from the lamination of successive {beta}-sheet layers, and it is abundantly observed in the core of insoluble amyloid fibrils associated with protein-misfolding diseases. Despite its prominence, cross-{beta} has been designed only in the context of insoluble aggregates of peptides or proteins. Cross-{beta}'s recalcitrance to protein engineering and conspicuous absence among the knownmore » atomic structures of natural proteins thus makes it a challenging target for design in a water-soluble form. Through comparative analysis of the cross-{beta} structures of fibril-forming peptides, we identified rows of hydrophobic residues ('ladders') running across {beta}-strands of each {beta}-sheet layer as a minimal component of the cross-{beta} motif. Grafting a single ladder of hydrophobic residues designed from the Alzheimer's amyloid-{beta} peptide onto a large {beta}-sheet protein formed a dimeric protein with a cross-{beta} architecture that remained water-soluble, as revealed by solution analysis and x-ray crystal structures. These results demonstrate that the cross-{beta} motif is a stable architecture in water-soluble polypeptides and can be readily designed. Our results provide a new route for accessing the cross-{beta} structure and expanding the scope of protein design.« less
Minimalist design of water-soluble cross-beta architecture.

PubMed

Biancalana, Matthew; Makabe, Koki; Koide, Shohei

2010-02-23

Demonstrated successes of protein design and engineering suggest significant potential to produce diverse protein architectures and assemblies beyond those found in nature. Here, we describe a new class of synthetic protein architecture through the successful design and atomic structures of water-soluble cross-beta proteins. The cross-beta motif is formed from the lamination of successive beta-sheet layers, and it is abundantly observed in the core of insoluble amyloid fibrils associated with protein-misfolding diseases. Despite its prominence, cross-beta has been designed only in the context of insoluble aggregates of peptides or proteins. Cross-beta's recalcitrance to protein engineering and conspicuous absence among the known atomic structures of natural proteins thus makes it a challenging target for design in a water-soluble form. Through comparative analysis of the cross-beta structures of fibril-forming peptides, we identified rows of hydrophobic residues ("ladders") running across beta-strands of each beta-sheet layer as a minimal component of the cross-beta motif. Grafting a single ladder of hydrophobic residues designed from the Alzheimer's amyloid-beta peptide onto a large beta-sheet protein formed a dimeric protein with a cross-beta architecture that remained water-soluble, as revealed by solution analysis and x-ray crystal structures. These results demonstrate that the cross-beta motif is a stable architecture in water-soluble polypeptides and can be readily designed. Our results provide a new route for accessing the cross-beta structure and expanding the scope of protein design.
Destruction of {alpha}-synuclein based amyloid fibrils by a low temperature plasma jet

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

Karakas, Erdinc; Laroussi, Mounir; Munyanyi, Agatha

2010-10-04

Amyloid fibrils are ordered beta-sheet aggregates that are associated with a number of neurodegenerative diseases such as Alzheimer and Parkinson. At present, there is no cure for these progressive and debilitating diseases. Here we report initial studies that indicate that low temperature atmospheric pressure plasma can break amyloid fibrils into smaller units in vitro. The plasma was generated by the 'plasma pencil', a device capable of emitting a long, low temperature plasma plume/jet. This avenue of research may facilitate the development of a plasma-based medical treatment.
Microphase Separation Controlled Beta Sheet Crystallization Kinetics in Silk Fibroin Protein.

NASA Astrophysics Data System (ADS)

Hu, Xiao; Lu, Qiang; Kaplan, David; Cebe, Peggy

2009-03-01

We investigate the mechanism of isothermal crystallization kinetics of beta-sheet crystals in silk multiblock fibrous proteins. The Avrami analysis kinetic theory, for studies of synthetic polymer crystal growth, is for the first time extended to investigate protein self-assembly in beta-sheet rich Bombyx mori silk fibroin samples, using time-resolved Fourier transform infrared spectroscopy, differential scanning calorimetry and synchrotron real-time wide-angle X-ray scattering. Results indicate formation of beta sheet crystals in silk proteins is different from the 3-D spherulitic crystal growth found in synthetic homopolymers. Observations by scanning electron microscopy support the view that the protein structures vary during the different stages of crystal growth, and show a microphase separation pattern after chymotrypsin enzyme biodegradation. We present a model to explain the crystallization of the multiblock silk fibroin protein, by analogy to synthetic block copolymers. This model could be widely applicable in other proteins with multiblock (i.e., crystallizable and non-crystallizable) domains.
Amyloid-beta-sheet formation at the air-water interface.

PubMed Central

Schladitz, C; Vieira, E P; Hermel, H; Möhwald, H

1999-01-01

An amyloid(1-40) solution rich in coil, turn, and alpha-helix, but poor in beta-sheet, develops monolayers with a high beta-sheet content when spread at the air-water interface. These monolayers are resistant to repeated compression-dilatation cycles and interaction with trifluoroethanol. The secondary structure motifs were detected by circular dichroism (CD) in solution and with infrared reflection-absorption spectroscopy (IRRAS) at the interface. Hydrophobic influences are discussed for the structure conversion in an effort to understand the completely unknown reason for the natural change of the normal prion protein cellular (PrP(C)) into the abnormal prion protein scrapie (PrP(Sc)). PMID:10585952
Higher-order molecular packing in amyloid-like fibrils constructed with linear arrangements of hydrophobic and hydrogen-bonding side-chains.

PubMed

Saiki, Masatoshi; Honda, Shinya; Kawasaki, Kazunori; Zhou, Deshan; Kaito, Akira; Konakahara, Takeo; Morii, Hisayuki

2005-05-13

Various mutants of the protein fragment, barnase module-1 (1-24) were investigated in order to reveal the structural principle of amyloid-like fibrils. By means of circular dichroism spectroscopy, X-ray diffraction, electron microscopy, and thioflavin T binding assay, we found that the molecules containing two beta-strands and an intervening turn structure are assembled to form a cross-beta structure. Stabilization by both the hydrophobic interactions and hydrogen bonding between the respective paired side-chains on the coupled beta-strands was essential for fibril formation. These two types of interaction can also arrange the corresponding residues in lines on both sheet surfaces of protofilaments with a cross-beta structure. This leads to the most probable fibril structure constructed with the line-matching interactions between protofilaments. Consideration of the geometrical symmetry resulted in our finding that a limited number of essential models for molecular packing in fibril structure are stable, which would rationally explain the occurrence of two or three morphologies from an identical molecular species. The ribbon-like fibrils exhibited striped texture along the axis, which was assigned to a stacked two-sheet repeat as a structural unit. The comprehensively proposed structural model, that is, the sheet-sheet interaction between left-handed cross-beta structures, results in a slightly right-handed twist of beta-sheet stacking, which reasonably elucidates the intrinsic sizes of the fibril width and its helical period along the fibril axis, as the bias in the orientation of the hydrogen-bonded beta-strand pair at the lateral edge is larger than that at the central protofilament.
Tuning peptide amphiphile supramolecular structure for biomedical applications

NASA Astrophysics Data System (ADS)

Pashuck, Eugene Thomas, III

The use of biomaterials in regenerative medicine has been an active area of research for more than a decade. Peptide amphiphiles, which are short peptide sequences coupled to alkyl tails, have been studied in the Stupp group since the beginning of the decade and been used for a variety of biomedical applications. Most of the work has focused on the bioactive epitopes places on the periphery of the PA molecules, but the interior amino acids, known as the beta-sheet region, give the PA nanofiber gel much of its mechanical strength. To study the important parameters in the beta-sheet region, six PA molecules were constructed to determine the influence of beta-sheet length and order of the amino acids in the beta-sheet. It was found that having beta-sheet forming amino acids near the center of the fiber improves PA gel stiffness, and that having extra amino acids that have preferences for other secondary structures, like alpha-helix decreased the gels stiffness. Using FTIR and circular dichroism it was found that the mechanical properties are influenced by the amount of twist in the beta-sheet, and PAs that have more twisted beta-sheets form weaker gels. The effect amino acid properties have on peptide amphiphile self-assembly where studied by synthesizining molecules with varying side group size and hydrophobicity. It was found that smaller amino acids lead to stiffer gels and when two amino acids had the same size the amino acid with the larger beta-sheet propensity lead to a stiffer gel. Furthermore, small changes in peptide structure were found to lead to big changes in nanostructure, as leucine and isoleucine, which have the same size but slightly different structures, form flat ribbons and cylindrical nanofibers, respectively. Phenylalanine and alanine were studied more indepth because they represent the effects of adding an aromatic group to amino acids in the beta-sheet regon. These phenylalanine PAs formed short, twisted ribbons when freshly dissolved in water that rapdily elongate to form long twisted ribbons. After being aged for two weeks half of these twisted ribbons turn into helical ribbons and by one month all of them have formed this new nanostructure. As a target in regenerative medicine, spinal cord injury repair presents a daunting challenge that has so far eluded successful pharmaceutical treatment. Previous work showing that PAs bearing the IKVAV epitope were found to increase functional recovery in mice paved the way for the more complex systems studied here. By making a PA that bound growth factors like neurotrophin-3 (NT-3) and glial cell line derived neurotrophic factor (GDNF) in with the PA matrix, it was found that the release of NT-3 could be significantly slowed from an IKVAV with the presence of a novel binding epitope, and that including GDNF into the gel significantly increased neurite outgrowth compared to the standard IKVAV PA.
Engineering Vascularized Bone Grafts by Integrating a Biomimetic Periosteum and β-TCP Scaffold

PubMed Central

2015-01-01

Treatment of large bone defects using synthetic scaffolds remain a challenge mainly due to insufficient vascularization. This study is to engineer a vascularized bone graft by integrating a vascularized biomimetic cell-sheet-engineered periosteum (CSEP) and a biodegradable macroporous beta-tricalcium phosphate (β-TCP) scaffold. We first cultured human mesenchymal stem cells (hMSCs) to form cell sheet and human umbilical vascular endothelial cells (HUVECs) were then seeded on the undifferentiated hMSCs sheet to form vascularized cell sheet for mimicking the fibrous layer of native periosteum. A mineralized hMSCs sheet was cultured to mimic the cambium layer of native periosteum. This mineralized hMSCs sheet was first wrapped onto a cylindrical β-TCP scaffold followed by wrapping the vascularized HUVEC/hMSC sheet, thus generating a biomimetic CSEP on the β-TCP scaffold. A nonperiosteum structural cell sheets-covered β-TCP and plain β-TCP were used as controls. In vitro studies indicate that the undifferentiated hMSCs sheet facilitated HUVECs to form rich capillary-like networks. In vivo studies indicate that the biomimetic CSEP enhanced angiogenesis and functional anastomosis between the in vitro preformed human capillary networks and the mouse host vasculature. MicroCT analysis and osteocalcin staining show that the biomimetic CSEP/β-TCP graft formed more bone matrix compared to the other groups. These results suggest that the CSEP that mimics the cellular components and spatial configuration of periosteum plays a critical role in vascularization and osteogenesis. Our studies suggest that a biomimetic periosteum-covered β-TCP graft is a promising approach for bone regeneration. PMID:24858072
SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone.

PubMed

Daniels, Noah M; Hosur, Raghavendra; Berger, Bonnie; Cowen, Lenore J

2012-05-01

One of the most successful methods to date for recognizing protein sequences that are evolutionarily related has been profile hidden Markov models (HMMs). However, these models do not capture pairwise statistical preferences of residues that are hydrogen bonded in beta sheets. These dependencies have been partially captured in the HMM setting by simulated evolution in the training phase and can be fully captured by Markov random fields (MRFs). However, the MRFs can be computationally prohibitive when beta strands are interleaved in complex topologies. We introduce SMURFLite, a method that combines both simplified MRFs and simulated evolution to substantially improve remote homology detection for beta structures. Unlike previous MRF-based methods, SMURFLite is computationally feasible on any beta-structural motif. We test SMURFLite on all propeller and barrel folds in the mainly-beta class of the SCOP hierarchy in stringent cross-validation experiments. We show a mean 26% (median 16%) improvement in area under curve (AUC) for beta-structural motif recognition as compared with HMMER (a well-known HMM method) and a mean 33% (median 19%) improvement as compared with RAPTOR (a well-known threading method) and even a mean 18% (median 10%) improvement in AUC over HHPred (a profile-profile HMM method), despite HHpred's use of extensive additional training data. We demonstrate SMURFLite's ability to scale to whole genomes by running a SMURFLite library of 207 beta-structural SCOP superfamilies against the entire genome of Thermotoga maritima, and make over a 100 new fold predictions. Availability and implementaion: A webserver that runs SMURFLite is available at: http://smurf.cs.tufts.edu/smurflite/
Probing alpha-helical and beta-sheet structures of peptides at solid/liquid interfaces with SFG.

PubMed

Chen, Xiaoyun; Wang, Jie; Sniadecki, Jason J; Even, Mark A; Chen, Zhan

2005-03-29

We demonstrated that sum frequency generation (SFG) vibrational spectroscopy can distinguish different secondary structures of proteins or peptides adsorbed at solid/liquid interfaces. The SFG spectrum for tachyplesin I at the polystyrene (PS)/solution interface has a fingerprint peak corresponding to the B1/B3 mode of the antiparallel beta-sheet. This peak disappeared upon the addition of dithiothreitol, which can disrupt the beta-sheet structure. The SFG spectrum indicative of the MSI594 alpha-helical structure was observed at the PS/MSI594 solution interface. This research validates SFG as a powerful technique for revealing detailed secondary structures of interfacial proteins and peptides.
BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra.

PubMed

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

2018-06-11

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

PubMed

Huang, Ying; Bayfield, Mark A; Intine, Robert V; Maraia, Richard J

2006-07-01

By sequence-specific binding to 3' UUU-OH, the La protein shields precursor (pre)-RNAs from 3' end digestion and is required to protect defective pre-transfer RNAs from decay. Although La is comprised of a La motif and an RNA-recognition motif (RRM), a recent structure indicates that the RRM beta-sheet surface is not involved in UUU-OH recognition, raising questions as to its function. Progressively defective suppressor tRNAs in Schizosaccharomyces pombe reveal differential sensitivities to La and Rrp6p, a 3' exonuclease component of pre-tRNA decay. 3' end protection is compromised by mutations to the La motif but not the RRM surface. The most defective pre-tRNAs require a second activity of La, in addition to 3' protection, that requires an intact RRM surface. The two activities of La in tRNA maturation map to its two conserved RNA-binding surfaces and suggest a modular model that has implications for its other ligands.
Colour Based Image Processing Method for Recognizing Ribbed Smoked Sheet Grade

NASA Astrophysics Data System (ADS)

Fibriani, Ike; Sumardi; Bayu Satriya, Alfredo; Budi Utomo, Satryo

2017-03-01

This research proposes a colour based image processing technique to recognize the Ribbed Smoked Sheet (RSS) grade so that the RSS sorting process can be faster and more accurate than the traditional one. The RSS sheet image captured by the camera is transformed into grayscale image to simplify the recognition of rust and mould on the RSS sheet. Then the grayscale image is transformed into binary image using threshold value which is obtained from the RSS 1 reference colour. The grade recognition is determined by counting the white pixel percentage. The result shows that the system has 88% of accuracy. Most faults exist on RSS 2 recognition. This is due to the illumination distribution which is not equal over the RSS image.
Reversible thermal denaturation of a 60-kDa genetically engineered beta-sheet polypeptide.

PubMed

Lednev, Igor K; Ermolenkov, Vladimir V; Higashiya, Seiichiro; Popova, Ludmila A; Topilina, Natalya I; Welch, John T

2006-11-15

A de novo 687-amino-acid residue polypeptide with a regular 32-amino-acid repeat sequence, (GA)(3)GY(GA)(3)GE(GA)(3)GH(GA)(3)GK, forms large beta-sheet assemblages that exhibit remarkable folding properties and, as well, form fibrillar structures. This construct is an excellent tool to explore the details of beta-sheet formation yielding intimate folding information that is otherwise difficult to obtain and may inform folding studies of naturally occurring materials. The polypeptide assumes a fully folded antiparallel beta-sheet/turn structure at room temperature, and yet is completely and reversibly denatured at 125 degrees C, adopting a predominant polyproline II conformation. Deep ultraviolet Raman spectroscopy indicated that melting/refolding occurred without any spectroscopically distinct intermediates, yet the relaxation kinetics depend on the initial polypeptide state, as would be indicative of a non-two-state process. Thermal denaturation and refolding on cooling appeared to be monoexponential with characteristic times of approximately 1 and approximately 60 min, respectively, indicating no detectable formation of hairpin-type nuclei in the millisecond timescale that could be attributed to nonlocal "nonnative" interactions. The polypeptide folding dynamics agree with a general property of beta-sheet proteins, i.e., initial collapse precedes secondary structure formation. The observed folding is much faster than expected for a protein of this size and could be attributed to a less frustrated free-energy landscape funnel for folding. The polypeptide sequence suggests an important balance between the absence of strong nonnative contacts (salt bridges or hydrophobic collapse) and limited repulsion of charged side chains.
A single-residue mutation, G203E, causes 3-hydroxy-3-methylglutaric aciduria by occluding the substrate channel in the 3D structural model of HMG-CoA lyase.

PubMed

Mir, C; Lopez-Viñas, E; Aledo, R; Puisac, B; Rizzo, C; Dionisi-Vici, C; Deodato, F; Pié, J; Gomez-Puertas, P; Hegardt, F G; Casals, N

2006-02-01

3-Hydroxy-3-methylglutaric aciduria is a rare autosomal recessive genetic disorder that affects ketogenesis and leucine metabolism. The disease is caused by mutations in the gene coding for 3-hydroxy-3-methylglutaryl-coenzyme A lyase (HL). To date 26 different mutations have been described. A (betaalpha)(8) TIM barrel structure has been proposed for the protein, and almost all missense mutations identified so far localize in the beta sheets that define the inside cavity. We report an Italian patient who bears homozygously a novel HL mutation, c.608G > A (p. G203E) in beta sheet six. A structural model of the mutated protein suggests that glutamic acid 203 impedes catalysis by blocking the entrance to the inner cavity of the enzyme. Loss of functionality has been confirmed in expression studies in E. coli, which demonstrate that the G203E mutation completely abolishes enzyme activity. Beta sheet six and beta sheet two are the two protein regions that accumulate most missense mutations, indicating their importance in enzyme functionality. A model for the mechanism of enzyme function is proposed.

I. The design, synthesis, and structure of antiparallel beta-sheet and beta-strand mimics. II. The design of a scripted chemistry outreach program to high schools

NASA Astrophysics Data System (ADS)

Waldman, Amy Sue

I. Protein structure is not easily predicted from the linear sequence of amino acids. An increased ability to create protein structures would allow researchers to develop new peptide-based therapeutics and materials, and would provide insights into the mechanisms of protein folding. Toward this end, we have designed and synthesized two-stranded antiparallel beta-sheet mimics containing conformationally biased scaffolds and semicarbazide, urea, and hydrazide linker groups that attach peptide chains to the scaffold. The mimics exhibited populations of intramolecularly hydrogen-bonded beta-sheet-like conformers as determined by spectroscopic techniques such as FTIR, sp1H NMR, and ROESY studies. During our studies, we determined that a urea-hydrazide beta-strand mimic was able to tightly hydrogen bond to peptides in an antiparallel beta-sheet-like configuration. Several derivatives of the urea-hydrazide beta-strand mimic were synthesized. Preliminary data by electron microscopy indicate that the beta-strand mimics have an effect on the folding of Alzheimer's Abeta peptide. These data suggest that the urea-hydrazide beta-strand mimics and related compounds may be developed into therapeutics which effect the folding of the Abeta peptide into neurotoxic aggregates. II. In recent years, there has been concern about the low level of science literacy and science interest among Americans. A declining interest in science impacts the abilities of people to make informed decisions about technology. To increase the interest in science among secondary students, we have developed the UCI Chemistry Outreach Program to High Schools. The Program features demonstration shows and discussions about chemistry in everyday life. The development and use of show scripts has enabled large numbers of graduate and undergraduate student volunteers to demonstrate chemistry to more than 12,000 local high school students. Teachers, students, and volunteers have expressed their enjoyment of The UCI Chemistry Outreach Program to High Schools.
Contact Prediction for Beta and Alpha-Beta Proteins Using Integer Linear Optimization and its Impact on the First Principles 3D Structure Prediction Method ASTRO-FOLD

PubMed Central

Rajgaria, R.; Wei, Y.; Floudas, C. A.

2010-01-01

An integer linear optimization model is presented to predict residue contacts in β, α + β, and α/β proteins. The total energy of a protein is expressed as sum of a Cα – Cα distance dependent contact energy contribution and a hydrophobic contribution. The model selects contacts that assign lowest energy to the protein structure while satisfying a set of constraints that are included to enforce certain physically observed topological information. A new method based on hydrophobicity is proposed to find the β-sheet alignments. These β-sheet alignments are used as constraints for contacts between residues of β-sheets. This model was tested on three independent protein test sets and CASP8 test proteins consisting of β, α + β, α/β proteins and was found to perform very well. The average accuracy of the predictions (separated by at least six residues) was approximately 61%. The average true positive and false positive distances were also calculated for each of the test sets and they are 7.58 Å and 15.88 Å, respectively. Residue contact prediction can be directly used to facilitate the protein tertiary structure prediction. This proposed residue contact prediction model is incorporated into the first principles protein tertiary structure prediction approach, ASTRO-FOLD. The effectiveness of the contact prediction model was further demonstrated by the improvement in the quality of the protein structure ensemble generated using the predicted residue contacts for a test set of 10 proteins. PMID:20225257
Kinetic Studies of Inhibition of the Aβ(1–42) Aggregation Using a Ferrocene-tagged β-Sheet Breaker Peptide

PubMed Central

Zhang, Lin; Yagnik, Gargey; Peng, Yong; Wang, Jianxiu; Xu, H. Howard; Hao, Yuanqiang; Liu, You-Nian; Zhou, Feimeng

2013-01-01

The aggregation of amyloidogenic proteins/peptides has been closely linked to the neuropathology of several important neurological disorders. In Alzheimer's disease (AD), amyloid beta (Aβ) peptides and their aggregation are believed to be at least partially responsible for the etiology of AD. The aggregate-inflicted cellular toxicity can be inhibited by short peptides whose sequence are homologous to segments of the Aβ(1–42) peptide responsible for β-sheet stacking (referred to as the β-sheet breaker peptides). Herein a water-soluble ferrocene (Fc)-tagged β-sheet breaker peptide (Fc-KLVFFK6) is used as an electrochemical probe for kinetic studies of the inhibition of the Aβ(1–42) fibrillation process and for determination of the optimal concentration of β-sheet breaker peptide for efficient inhibition. Our results demonstrated that Fc-KLVFFK6 interacts with the Aβ aggregates instantaneously in solution, and sub-stoichiometric amount of Fc-KLVFFK6 is sufficient to inhibit the formation of the Aβ oligomers and fibrils and to reduce the toxicity of Aβ(1–42). The interaction between Fc-KLVFFK6 and Aβ(1–42) follows a pseudo-first-order reaction, with a rate constant of 1.89 ± 0.05 × 10−4 s−1. Tagging β-sheet breaker peptides with a redox label facilitates design, screening, and rational use of peptidic inhibitors for impeding/altering Aβ aggregation. PMID:23232068
Causes of 30-day bariatric surgery mortality: with emphasis on bypass obstruction.

PubMed

Mason, Edward E; Renquist, Kathleen E; Huang, Yu-Hui; Jamal, Mohammad; Samuel, Isaac

2007-01-01

This is a study of the causes of 30-day postoperative death following surgical treatment for obesity and a search for ways to decrease an already low mortality rate. Data were contributed from 1986-2004 to the International Bariatric Surgery Registry by 85 sites, representing 137 surgeons. A spread-sheet was prepared with rows for causes and columns for patients. The 251 causes contributing to 93 deaths were then marked in cells wherever a patient was noted to have one of the causes. Rows and columns were then moved into positions that provided patterns of best fit. 11 patterns were found. 10 had well known initiating causes of death. Overall operative 30-day mortality was 0.24% (93 / 38,501). The most common cause of death was pulmonary embolism (32%, 30/93). 14 deaths were caused by leaks (15%, 14/93), and were equally prevalent after simple (15%, 2/14) or complex (15%, 12/79) operations. Small bowel obstruction caused 8 deaths, exclusively after complex operations. 5 of these involved the bypassed biliopancreatic limb and were defined as "bypass obstruction". A spread-sheet study of cause of 30-day postoperative death revealed a rapidly lethal initiating complication of Roux-en-Y gastric bypass obstruction that requires the earliest possible recognition and treatment. Bypass obstruction needs a name and code to facilitate recognition, study, prevention and early treatment. Spread-sheet pattern analysis of all available data helped identify the initiating cause of death for individual patients when multiple data elements were present.
Role of Polyalanine Domains in -Sheet Formation in Spider Silk Block Copolymers

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

Rabotyagova, O.; Cebe, P; Kaplan, D

2010-01-01

Genetically engineered spider silk-like block copolymers were studied to determine the influence of polyalanine domain size on secondary structure. The role of polyalanine block distribution on {beta}-sheet formation was explored using FT-IR and WAXS. The number of polyalanine blocks had a direct effect on the formation of crystalline {beta}-sheets, reflected in the change in crystallinity index as the blocks of polyalanines increased. WAXS analysis confirmed the crystalline nature of the sample with the largest number of polyalanine blocks. This approach provides a platform for further exploration of the role of specific amino acid chemistries in regulating the assembly of {beta}-sheetmore » secondary structures, leading to options to regulate material properties through manipulation of this key component in spider silks.« less
Pauling and Corey's alpha-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease.

PubMed

Armen, Roger S; DeMarco, Mari L; Alonso, Darwin O V; Daggett, Valerie

2004-08-10

Transthyretin, beta(2)-microglobulin, lysozyme, and the prion protein are four of the best-characterized proteins implicated in amyloid disease. Upon partial acid denaturation, these proteins undergo conformational change into an amyloidogenic intermediate that can self-assemble into amyloid fibrils. Many experiments have shown that pH-mediated changes in structure are required for the formation of the amyloidogeneic intermediate, but it has proved impossible to characterize these conformational changes at high resolution using experimental means. To probe these conformational changes at atomic resolution, we have performed molecular dynamics simulations of these proteins at neutral and low pH. In low-pH simulations of all four proteins, we observe the formation of alpha-pleated sheet secondary structure, which was first proposed by L. Pauling and R. B. Corey [(1951) Proc. Natl. Acad. Sci. USA 37, 251-256]. In all beta-sheet proteins, transthyretin and beta(2)-microglobulin, alpha-pleated sheet structure formed over the strands that are highly protected in hydrogen-exchange experiments probing amyloidogenic conditions. In lysozyme and the prion protein, alpha-sheets formed in the specific regions of the protein implicated in the amyloidogenic conversion. We propose that the formation of alpha-pleated sheet structure may be a common conformational transition in amyloidosis.
Statistical physics approaches to Alzheimer's disease

NASA Astrophysics Data System (ADS)

Peng, Shouyong

Alzheimer's disease (AD) is the most common cause of late life dementia. In the brain of an AD patient, neurons are lost and spatial neuronal organizations (microcolumns) are disrupted. An adequate quantitative analysis of microcolumns requires that we automate the neuron recognition stage in the analysis of microscopic images of human brain tissue. We propose a recognition method based on statistical physics. Specifically, Monte Carlo simulations of an inhomogeneous Potts model are applied for image segmentation. Unlike most traditional methods, this method improves the recognition of overlapped neurons, and thus improves the overall recognition percentage. Although the exact causes of AD are unknown, as experimental advances have revealed the molecular origin of AD, they have continued to support the amyloid cascade hypothesis, which states that early stages of aggregation of amyloid beta (Abeta) peptides lead to neurodegeneration and death. X-ray diffraction studies reveal the common cross-beta structural features of the final stable aggregates-amyloid fibrils. Solid-state NMR studies also reveal structural features for some well-ordered fibrils. But currently there is no feasible experimental technique that can reveal the exact structure or the precise dynamics of assembly and thus help us understand the aggregation mechanism. Computer simulation offers a way to understand the aggregation mechanism on the molecular level. Because traditional all-atom continuous molecular dynamics simulations are not fast enough to investigate the whole aggregation process, we apply coarse-grained models and discrete molecular dynamics methods to increase the simulation speed. First we use a coarse-grained two-bead (two beads per amino acid) model. Simulations show that peptides can aggregate into multilayer beta-sheet structures, which agree with X-ray diffraction experiments. To better represent the secondary structure transition happening during aggregation, we refine the model to four beads per amino acid. Typical essential interactions, such as backbone hydrogen bond, hydrophobic and electrostatic interactions, are incorporated into our model. We study the aggregation of Abeta16-22, a peptide that can aggregate into a well-ordered fibrillar structure in experiments. Our results show that randomly-oriented monomers can aggregate into fibrillar subunits, which agree not only with X-ray diffraction experiments but also with solid-state NMR studies. Our findings demonstrate that coarse-grained models and discrete molecular dynamics simulations can help researchers understand the aggregation mechanism of amyloid peptides.
In Situ FTIR Microspectroscopy of Brain Tissue from a Transgenic Mouse Model of Alzheimer Disease

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

Rak,M.; Del Bigio, M.; Mai, S.

2007-01-01

Plaques composed of the A{beta} peptide are the main pathological feature of Alzheimer's disease. Dense-core plaques are fibrillar deposits of A{beta}, showing all the classical properties of amyloid including {beta}-sheet secondary structure, while diffuse plaques are amorphous deposits. We studied both plaque types, using synchrotron infrared (IR) microspectroscopy, a technique that allows the chemical composition and average protein secondary structure to be investigated in situ. We examined plaques in hippocampal, cortical and caudal tissue from 5- to 21-month-old TgCRND8 mice, a transgenic model expressing doubly mutant amyloid precursor protein, and displaying impaired hippocampal function and robust pathology from an earlymore » age. Spectral analysis confirmed that the congophilic plaque cores were composed of protein in a {beta}-sheet conformation. The amide I maximum of plaque cores was at 1623 cm-1, and unlike for in vitro A{beta} fibrils, the high-frequency (1680-1690 cm-1) component attributed to antiparallel {beta}-sheet was not observed. A significant elevation in phospholipids was found around dense-core plaques in TgCRND8 mice ranging in age from 5 to 21 months. In contrast, diffuse plaques were not associated with IR detectable changes in protein secondary structure or relative concentrations of any other tissue components.« less
Genetic engineering combined with deep UV resonance Raman spectroscopy for structural characterization of amyloid-like fibrils.

PubMed

Sikirzhytski, Vitali; Topilina, Natalya I; Higashiya, Seiichiro; Welch, John T; Lednev, Igor K

2008-05-07

Elucidating the structure of the cross-beta core in large amyloid fibrils is a challenging problem in modern structural biology. For the first time, a set of de novo polypeptides was genetically engineered to form amyloid-like fibrils with similar morphology and yet different strand length. Differential ultraviolet Raman spectroscopy allowed for separation of the spectroscopic signatures of the highly ordered beta-sheet strands and turns of the fibril core. The relationship between Raman frequencies and Ramachandran dihedral angles of the polypeptide backbone indicates the nature of the beta-sheet and turn structural elements.
Interaction between two discontiguous chain segments from the beta-sheet of Escherichia coli thioredoxin suggests an initiation site for folding.

PubMed

Tasayco, M L; Fuchs, J; Yang, X M; Dyalram, D; Georgescu, R E

2000-09-05

The approach of comparing folding and folding/binding processes is exquisitely poised to narrow down the regions of the sequence that drive protein folding. We have dissected the small single alpha/beta domain of oxidized Escherichia coli thioredoxin (Trx) into three complementary fragments (N, residues 1-37; M, residues 38-73; and C, residues 74-108) to study them in isolation and upon recombination by far-UV CD and NMR spectroscopy. The isolated fragments show a minimum of ellipticity of ca. 197 nm in their far-UV CD spectra without concentration dependence, chemical shifts of H(alpha) that are close to the random coil values, and no medium- and long-range NOE connectivities in their three-dimensional NMR spectra. These fragments behave as disordered monomers. Only the far-UV CD spectra of binary or ternary mixtures that contain N- and C-fragments are different from the sum of their individual spectra, which is indicative of folding and/or binding of these fragments. Indeed, the cross-peaks corresponding to the rather hydrophobic beta(2) and beta(4) regions of the beta-sheet of Trx disappear from the (1)H-(15)N HSQC spectra of isolated labeled N- and C-fragments, respectively, upon addition of the unlabeled complementary fragments. The disappearing cross-peaks indicate interactions between the beta(2) and beta(4) regions, and their reappearance at lower temperatures indicates unfolding and/or dissociation of heteromers that are predominantly held by hydrophobic forces. Our results argue that the folding of Trx begins by zippering two discontiguous and rather hydrophobic chain segments (beta(2) and beta(4)) corresponding to neighboring strands of the native beta-sheet.
The paradox of MHC-DRB exon/intron evolution: alpha-helix and beta-sheet encoding regions diverge while hypervariable intronic simple repeats coevolve with beta-sheet codons.

PubMed

Schwaiger, F W; Weyers, E; Epplen, C; Brün, J; Ruff, G; Crawford, A; Epplen, J T

1993-09-01

Twenty-one different caprine and 13 ovine MHC-DRB exon 2 sequences were determined including part of the adjacent introns containing simple repetitive (gt)n(ga)m elements. The positions for highly polymorphic DRB amino acids vary slightly among ungulates and other mammals. From man and mouse to ungulates the basic (gt)n(ga)m structure is fixed in evolution for 7 x 10(7) years whereas ample variations exist in the tandem (gt)n and (ga)m dinucleotides and especially their "degenerated" derivatives. Phylogenetic trees for the alpha-helices and beta-pleated sheets of the ungulate DRB sequences suggest different evolutionary histories. In hoofed animals as well as in humans DRB beta-sheet encoding sequences and adjacent intronic repeats can be assembled into virtually identical groups suggesting coevolution of noncoding as well as coding DNA. In contrast alpha-helices and C-terminal parts of the first DRB domain evolve distinctly. In the absence of a defined mechanism causing specific, site-directed mutations, double-recombination or gene-conversion-like events would readily explain this fact. The role of the intronic simple (gt)n(ga)m repeat is discussed with respect to these genetic exchange mechanisms during evolution.
Low-Temperature Forming of Beta Titanium Alloys

NASA Technical Reports Server (NTRS)

Kaneko, R. S.; Woods, C. A.

1983-01-01

Low cost methods for titanium structural fabrication using advanced cold-formable beta alloys were investigated for application in a Mach 2.7 supersonic cruise vehicle. This work focuses on improving processing and structural efficiencies as compared with standard hot formed and riveted construction of alpha-beta alloy sheet structure. Mechanical property data and manufacturing parameters were developed for cold forming, brazing, welding, and processing Ti-15V-3Cr-3Sn-3Al sheet, and Ti-3Al-8V-6Cr-4Zr on a more limited basis. Cost and structural benefits were assessed through the fabrication and evaluation of large structural panels. The feasibility of increasing structural efficiency of beta titanium structure by selective reinforcement with metal matrix composite was also explored.
The specificity of polygalacturonase-inhibiting protein (PGIP): a single amino acid substitution in the solvent-exposed beta-strand/beta-turn region of the leucine-rich repeats (LRRs) confers a new recognition capability.

PubMed Central

Leckie, F; Mattei, B; Capodicasa, C; Hemmings, A; Nuss, L; Aracri, B; De Lorenzo, G; Cervone, F

1999-01-01

Two members of the pgip gene family (pgip-1 and pgip-2) of Phaseolus vulgaris L. were expressed separately in Nicotiana benthamiana and the ligand specificity of their products was analysed by surface plasmon resonance (SPR). Polygalacturonase-inhibiting protein-1 (PGIP-1) was unable to interact with PG from Fusarium moniliforme and interacted with PG from Aspergillus niger; PGIP-2 interacted with both PGs. Only eight amino acid variations distinguish the two proteins: five of them are confined within the beta-sheet/beta-turn structure and two of them are contiguous to this region. By site-directed mutagenesis, each of the variant amino acids of PGIP-2 was replaced with the corresponding amino acid of PGIP-1, in a loss-of-function approach. The mutated PGIP-2s were expressed individually in N.benthamiana, purified and subjected to SPR analysis. Each single mutation caused a decrease in affinity for PG from F.moniliforme; residue Q253 made a major contribution, and its replacement with a lysine led to a dramatic reduction in the binding energy of the complex. Conversely, in a gain-of-function approach, amino acid K253 of PGIP-1 was mutated into the corresponding amino acid of PGIP-2, a glutamine. With this single mutation, PGIP-1 acquired the ability to interact with F.moniliforme PG. PMID:10228150
Distinct spatio-temporal profiles of beta-oscillations within visual and sensorimotor areas during action recognition as revealed by MEG.

PubMed

Pavlidou, Anastasia; Schnitzler, Alfons; Lange, Joachim

2014-05-01

The neural correlates of action recognition have been widely studied in visual and sensorimotor areas of the human brain. However, the role of neuronal oscillations involved during the process of action recognition remains unclear. Here, we were interested in how the plausibility of an action modulates neuronal oscillations in visual and sensorimotor areas. Subjects viewed point-light displays (PLDs) of biomechanically plausible and implausible versions of the same actions. Using magnetoencephalography (MEG), we examined dynamic changes of oscillatory activity during these action recognition processes. While both actions elicited oscillatory activity in visual and sensorimotor areas in several frequency bands, a significant difference was confined to the beta-band (∼20 Hz). An increase of power for plausible actions was observed in left temporal, parieto-occipital and sensorimotor areas of the brain, in the beta-band in successive order between 1650 and 2650 msec. These distinct spatio-temporal beta-band profiles suggest that the action recognition process is modulated by the degree of biomechanical plausibility of the action, and that spectral power in the beta-band may provide a functional interaction between visual and sensorimotor areas in humans. Copyright © 2014 Elsevier Ltd. All rights reserved.
Synthesis of porous sheet-like Co{sub 3}O{sub 4} microstructure by precipitation method and its potential applications in the thermal decomposition of ammonium perchlorate

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

Lu Shanshan; Jing Xiaoyan; Liu Jingyuan

2013-01-15

Porous sheet-like cobalt oxide (Co{sub 3}O{sub 4}) were successfully synthesized by precipitation method combined with calcination of cobalt hydroxide precursors. The structure, morphology and porosity properties of the products were characterized by X-ray powder diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and nitrogen adsorption-desorption measurement. The as-prepared sheet-like microstructures were approximately 2-3 {mu}m in average diameter, and the morphology of the cobalt hydroxide precursors was retained after the calcination process. However, it appeared a large number of uniform pores in the sheets after calcination. In order to calculate the potential catalytic activity, the thermal decomposition of ammoniummore » perchlorate (AP) has been analyzed, in which cobalt oxide played a role of an additive and the porous sheet-like Co{sub 3}O{sub 4} microstructures exhibited high catalytic performance and considerable decrease in the thermal decomposition temperature of AP. Moreover, a formation mechanism for the sheet-like microstructures has been discussed. - Graphical abstract: Porous sheet-like Co{sub 3}O{sub 4} were synthesized by facile precipitation method combined with calcination of {beta}-Co(OH){sub 2} precursors. Thermogravimetric-differential scanning calorimetric analysis indicates potential catalytic activity in the thermal decomposition of ammonium perchlorate. Highlights: Black-Right-Pointing-Pointer Synthesis of sheet-like {beta}-Co(OH){sub 2} precursors by precipitation method. Black-Right-Pointing-Pointer Porous sheet-like Co{sub 3}O{sub 4} were obtained by calcining {beta}-Co(OH){sub 2} precursors. Black-Right-Pointing-Pointer The possible formation mechanism of porous sheet-like Co{sub 3}O{sub 4} has been discussed. Black-Right-Pointing-Pointer Porous sheet-like Co{sub 3}O{sub 4} decrease the thermal decomposition temperature of ammonium perchlorate.« less
Folding cooperativity in a three-stranded beta-sheet model.

PubMed

Roe, Daniel R; Hornak, Viktor; Simmerling, Carlos

2005-09-16

The thermodynamic behavior of a previously designed three-stranded beta-sheet was studied via several microseconds of standard and replica exchange molecular dynamics simulations. The system is shown to populate at least four thermodynamic minima, including two partially folded states in which only a single hairpin is formed. Simulated melting curves show different profiles for the C and N-terminal hairpins, consistent with differences in secondary structure content in published NMR and CD/FTIR measurements, which probed different regions of the chain. Individual beta-hairpins that comprise the three-stranded beta-sheet are observed to form cooperatively. Partial folding cooperativity between the component hairpins is observed, and good agreement between calculated and experimental values quantifying this cooperativity is obtained when similar analysis techniques are used. However, the structural detail in the ensemble of conformations sampled in the simulations permits a more direct analysis of this cooperativity than has been performed on the basis of experimental data. The results indicate the actual folding cooperativity perpendicular to strand direction is significantly larger than the lower bound obtained previously.
Proteopedia: Rossmann Fold: A Beta-Alpha-Beta Fold at Dinucleotide Binding Sites

ERIC Educational Resources Information Center

Hanukoglu, Israel

2015-01-01

The Rossmann fold is one of the most common and widely distributed super-secondary structures. It is composed of a series of alternating beta strand (ß) and alpha helical (a) segments wherein the ß-strands are hydrogen bonded forming a ß-sheet. The initial beta-alpha-beta (ßaß) fold is the most conserved segment of Rossmann folds. As this segment…
Mutational analysis of the folding transition state of the C-terminal domain of ribosomal protein L9: a protein with an unusual beta-sheet topology.

PubMed

Li, Ying; Gupta, Ruchi; Cho, Jae-Hyun; Raleigh, Daniel P

2007-01-30

The C-terminal domain of ribosomal protein L9 (CTL9) is a 92-residue alpha-beta protein which contains an unusual three-stranded mixed parallel and antiparallel beta-sheet. The protein folds in a two-state fashion, and the folding rate is slow. It is thought that the slow folding may be caused by the necessity of forming this unusual beta-sheet architecture in the transition state for folding. This hypothesis makes CTL9 an interesting target for folding studies. The transition state for the folding of CTL9 was characterized by phi-value analysis. The folding of a set of hydrophobic core mutants was analyzed together with a set of truncation mutants. The results revealed a few positions with high phi-values (> or = 0.5), notably, V131, L133, H134, V137, and L141. All of these residues were found in the beta-hairpin region, indicating that the formation of this structure is likely to be the rate-limiting step in the folding of CTL9. One face of the beta-hairpin docks against the N-terminal helix. Analysis of truncation mutants of this helix confirmed its importance in folding. Mutations at other sites in the protein gave small phi-values, despite the fact that some of them had major effects on stability. The analysis indicates that formation of the antiparallel hairpin is critical and its interactions with the first helix are also important. Thus, the slow folding is not a consequence of the need to fully form the unusual three-stranded beta-sheet in the transition state. Analysis of the urea dependence of the folding rates indicates that mutations modulate the unfolded state. The folding of CTL9 is broadly consistent with the nucleation-condensation model of protein folding.
Origin of life. Primordial genetics: Information transfer in a pre-RNA world based on self-replicating beta-sheet amyloid conformers.

PubMed

Maury, Carl Peter J

2015-10-07

The question of the origin of life on Earth can largely be reduced to the question of what was the first molecular replicator system that was able to replicate and evolve under the presumably very harsh conditions on the early Earth. It is unlikely that a functional RNA could have existed under such conditions and it is generally assumed that some other kind of information system preceded the RNA world. Here, I present an informational molecular system that is stable, self-replicative, environmentally responsive, and evolvable under conditions characterized by high temperatures, ultraviolet and cosmic radiation. This postulated pregenetic system is based on the amyloid fold, a functionally unique polypeptide fold characterized by a cross beta-sheet structure in which the beta strands are arranged perpendicular to the fiber axis. Beside an extraordinary structural robustness, the amyloid fold possesses a unique ability to transmit information by a three-dimensional templating mechanism. In amyloidogenesis short peptide monomers are added one by one to the growing end of the fiber. From the same monomeric subunits several structural variants of amyloid may be formed. Then, in a self-replicative mode, a specific amyloid conformer can act as a template and confer its spatially encoded information to daughter molecular entities in a repetitive way. In this process, the specific conformational information, the spatially changed organization, is transmitted; the coding element is the steric zipper structure, and recognition occurs by amino acid side chain complementarity. The amyloid information system fulfills several basic requirements of a primordial evolvable replicator system: (i) it is stable under the presumed primitive Earth conditions, (ii) the monomeric building blocks of the informational polymer can be formed from available prebiotic compounds, (iii) the system is self-assembling and self-replicative and (iv) it is adaptive to changes in the environment and evolvable. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.
The complete amino acid sequence of echinoidin, a lectin from the coelomic fluid of the sea urchin Anthocidaris crassispina. Homologies with mammalian and insect lectins.

PubMed

Giga, Y; Ikai, A; Takahashi, K

1987-05-05

The complete amino acid sequence of echinoidin, the proposed name for a lectin from the coelomic fluid of the sea urchin Anthocidaris crassispina, has been determined by sequencing the peptides obtained from tryptic, Staphylococcus aureus V8 protease, chymotryptic, and thermolysin digestions. Echinoidin is a multimeric protein (Giga, Y., Sutoh, K., and Ikai, A. (1985) Biochemistry 24, 4461-4467) whose subunit consists of a total of 147 amino acid residues and one carbohydrate chain attached to Ser38. The molecular weight of the polypeptide without carbohydrate was calculated to be 16,671. Each polypeptide chain contains seven half-cystines, and six of them form three disulfide bonds in the single polypeptide chain (Cys3-Cys14, Cys31-Cys141, and Cys116-Cys132), while Cys2 is involved in an interpolypeptide disulfide linkage. From secondary structure prediction by the method of Chou and Fasman (Chou, P. Y., and Fasman, G. D. (1974) Biochemistry 13, 211-222) the protein appears to be rich in beta-sheet and beta-turn structures and poor in alpha-helical structure. The sequence of the COOH-terminal half of echinoidin is highly homologous to those of the COOH-terminal carbohydrate recognition portions of rat liver mannose-binding protein and several other hepatic lectins. This COOH-terminal region of echinoidin is also homologous to the central portion of the lectin from the flesh fly Sarcophaga peregrina. Moreover, echinoidin contains an Arg-Gly-Asp sequence which has been proposed to be a basic functional unit in cellular recognition proteins.

Plasma convection and ion beam generation in the plasma sheet boundary layer

NASA Technical Reports Server (NTRS)

Moghaddam-Taaheri, E.; Goertz, C. K.; Smith, R. A.

1991-01-01

Because of the dawn-dusk electric field E(dd), plasma in the magnetotail convects from the lobe toward the central plasma sheet (CPS). In the absence of space or velocity diffusion due to plasma turbulence, convection would yield a steady state distribution function f = V exp (-2/3) g(v exp 2 V exp 2/3), where V is the flux tube volume. Starting with such a distribution function and a plasma beta which varies from beta greater than 1 in the CPS to beta much smaller than 1 in the lobe, the evolution of the ion distribution function was studied considering the combined effects of ion diffusion by kinetic Alfven waves (KAW) in the ULF frequency range (1-10 mHz) and convection due to E(dd) x B drift in the plasma sheet boundary layer (PSBL) and outer central plasma sheet (OCPS). The results show that, during the early stages after launching the KAWs, a beamlike ion distribution forms in the PSBL and at the same time the plasma density and temperature decrease in the OCPS. Following this stage, ions in the beams convect toward the CPS resulting in an increase of the plasma temperature in the OCPS.
Influence of Philosamia ricini silk fibroin components on morphology, secondary structure and thermal properties of chitosan biopolymer film.

PubMed

Prasong, S; Nuanchai, K; Wilaiwan, S

2009-09-15

This study aimed to prepare Eri (Philosamia ricini) Silk Fibroin (SF)/chitosan (CS) blend films by a solvent evaporation method and to compare the blend films with both native SF and CS films. Influence of SF ratios on the morphology, secondary structure and thermal decomposition of the CS blend films were investigated. The native SF and CS films were uniform and homogeneous without phase separation. For the blend films, the uniform can be found less than 60% of SF composition. All of SF/CS blend films showed both SF and CS characteristics. FT-IR results showed that the blend films composed of both random coil and beta-sheet with predominant of beta-sheet form. Interaction of intermolecular between SF and CS have occurred which were measured by thermogravimetric thermograms. Increasing of SF contents was leading to the increase of beta-sheet structures which were enhanced the thermal stability of the CS blend films.
Amyloidogenesis abolished by proline substitutions but enhanced by lipid binding.

PubMed

Jiang, Ping; Xu, Weixin; Mu, Yuguang

2009-04-01

The influence of lipid molecules on the aggregation of a highly amyloidogenic segment of human islet amyloid polypeptide, hIAPP20-29, and the corresponding sequence from rat has been studied by all-atom replica exchange molecular dynamics (REMD) simulations with explicit solvent model. hIAPP20-29 fragments aggregate into partially ordered beta-sheet oligomers and then undergo large conformational reorganization and convert into parallel/antiparallel beta-sheet oligomers in mixed in-register and out-of-register patterns. The hydrophobic interaction between lipid tails and residues at positions 23-25 is found to stabilize the ordered beta-sheet structure, indicating a catalysis role of lipid molecules in hIAPP20-29 self-assembly. The rat IAPP variants with three proline residues maintain unstructured micelle-like oligomers, which is consistent with non-amyloidogenic behavior observed in experimental studies. Our study provides the atomic resolution descriptions of the catalytic function of lipid molecules on the aggregation of IAPP peptides.
Rapid acquisition of beta-sheet structure in the prion protein prior to multimer formation.

PubMed

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

1998-11-01

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

PubMed

Lietzow, Michael A; Hubbell, Wayne L

2004-03-23

A goal in the development of site-directed spin labeling in proteins is to correlate the motion of a nitroxide side chain with local structure, interactions, and dynamics. Significant progress toward this goal has been made using alpha-helical proteins of known structure, and the present study is the first step in a similar exploration of a beta-sheet protein, cellular retinol-binding protein (CRBP). Nitroxide side chains were introduced along both interior and edge strands. At sites in interior strands, the side-chain motion is strongly influenced by interactions with side chains of neighboring strands, giving rise to a rich variety of dynamic modes (weakly ordered, strongly ordered, immobilized) and complex electron paramagnetic resonance spectra that are modulated by strand twist. The interactions giving rise to the dynamic modes are explored using mutagenesis, and the results demonstrate the particular importance of the non-hydrogen-bonded neighbor residue in giving rise to highly ordered states. Along edge strands of the beta-sheet, the motion of the side chain is simple and weakly ordered, resembling that at solvent-exposed surfaces of an alpha-helix. A simple working model is proposed that can account for the wide variety of dynamic modes encountered. Collectively, the results suggest that the nitroxide side chain is an effective probe of side-chain interactions, and that site-directed spin labeling should be a powerful means of monitoring conformational changes that involve changes in beta-sheet topology.
A cluster of diagnostic Hsp68 amino acid sites that are identified in Drosophila from the melanogaster species group are concentrated around beta-sheet residues involved with substrate binding.

PubMed

Kellett, Mark; McKechnie, Stephen W

2005-04-01

The coding region of the hsp68 gene has been amplified, cloned, and sequenced from 10 Drosophila species, 5 from the melanogaster subgroup and 5 from the montium subgroup. When the predicted amino acid sequences are compared with available Hsp70 sequences, patterns of conservation suggest that the C-terminal region should be subdivided according to predominant secondary structure. Conservation levels between Hsp68 and Hsp70 proteins were high in the N-terminal ATPase and adjacent beta-sheet domains, medium in the alpha-helix domain, and low in the C-terminal mobile domain (78%, 72%, 41%, and 21% identity, respectively). A number of amino acid sites were found to be "diagnostic" for Hsp68 (28 of approximately 635 residues). A few of these occur in the ATPase domain (385 residues) but most (75%) are concentrated in the beta-sheet and alpha-helix domains (34% of the protein) with none in the short mobile domain. Five of the diagnostic sites in the beta-sheet domain are clustered around, but not coincident with, functional sites known to be involved in substrate binding. Nearly all of the Hsp70 family length variation occurs in the mobile domain. Within montium subgroup species, 2 nearly identical hsp68 PCR products that differed in length are either different alleles or products of an ancestral hsp68 duplication.
Making Ordered DNA and Protein Structures from Computer-Printed Transparency Film Cut-Outs

ERIC Educational Resources Information Center

Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

2009-01-01

Instructions are given for building physical scale models of ordered structures of B-form DNA, protein [alpha]-helix, and parallel and antiparallel protein [beta]-pleated sheets made from colored computer printouts designed for transparency film sheets. Cut-outs from these sheets are easily assembled. Conventional color coding for atoms are used…
Structure and molecular dynamics simulation of archaeal prefoldin: the molecular mechanism for binding and recognition of nonnative substrate proteins.

PubMed

Ohtaki, Akashi; Kida, Hiroshi; Miyata, Yusuke; Ide, Naoki; Yonezawa, Akihiro; Arakawa, Takatoshi; Iizuka, Ryo; Noguchi, Keiichi; Kita, Akiko; Odaka, Masafumi; Miki, Kunio; Yohda, Masafumi

2008-02-29

Prefoldin (PFD) is a heterohexameric molecular chaperone complex in the eukaryotic cytosol and archaea with a jellyfish-like structure containing six long coiled-coil tentacles. PFDs capture protein folding intermediates or unfolded polypeptides and transfer them to group II chaperonins for facilitated folding. Although detailed studies on the mechanisms for interaction with unfolded proteins or cooperation with chaperonins of archaeal PFD have been performed, it is still unclear how PFD captures the unfolded protein. In this study, we determined the X-ray structure of Pyrococcus horikoshii OT3 PFD (PhPFD) at 3.0 A resolution and examined the molecular mechanism for binding and recognition of nonnative substrate proteins by molecular dynamics (MD) simulation and mutation analyses. PhPFD has a jellyfish-like structure with six long coiled-coil tentacles and a large central cavity. Each subunit has a hydrophobic groove at the distal region where an unfolded substrate protein is bound. During MD simulation at 330 K, each coiled coil was highly flexible, enabling it to widen its central cavity and capture various nonnative proteins. Docking MD simulation of PhPFD with unfolded insulin showed that the beta subunit is essentially involved in substrate binding and that the alpha subunit modulates the shape and width of the central cavity. Analyses of mutant PhPFDs with amino acid replacement of the hydrophobic residues of the beta subunit in the hydrophobic groove have shown that beta Ile107 has a critical role in forming the hydrophobic groove.
Protein-induced Photophysical Changes to the Amyloid Indicator Dye Thioflavin T

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

L Wolfe; M Calabrese; A Nath

2011-12-31

The small molecule thioflavin T (ThT) is a defining probe for the identification and mechanistic study of amyloid fiber formation. As such, ThT is fundamental to investigations of serious diseases such as Alzheimer's disease, Parkinson disease, and type II diabetes. For each disease, a different protein undergoes conformational conversion to a {beta}-sheet rich fiber. The fluorescence of ThT exhibits an increase in quantum yield upon binding these fibers. Despite its widespread use, the structural basis for binding specificity and for the changes to the photophysical properties of ThT remain poorly understood. Here, we report the co-crystal structures of ThT withmore » two alternative states of {beta}-2 microglobulin ({beta}2m); one monomeric, the other an amyloid-like oligomer. In the latter, the dye intercalates between {beta}-sheets orthogonal to the {beta}-strands. Importantly, the fluorophore is bound in such a manner that a photophysically relevant torsion is limited to a range of angles generally associated with low, not high, quantum yield. Quantum mechanical assessment of the fluorophore shows the electronic distribution to be strongly stabilized by aromatic interactions with the protein. Monomeric {beta}2m gives little increase in ThT fluorescence despite showing three fluorophores, at two binding sites, in configurations generally associated with high quantum yield. Our efforts fundamentally extend existing understanding about the origins of amyloid-induced photophysical changes. Specifically, the {beta}-sheet interface that characterizes amyloid acts both sterically and electronically to stabilize the fluorophore's ground state electronic distribution. By preventing the fluorophore from adopting its preferred excited state configuration, nonradiative relaxation pathways are minimized and quantum yield is increased.« less
Protein-induced photophysical changes to the amyloid indicator dye thioflavin T

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

Wolfe, Leslie S.; Calabrese, Matthew F.; Nath, Abhinav

2010-10-04

The small molecule thioflavin T (ThT) is a defining probe for the identification and mechanistic study of amyloid fiber formation. As such, ThT is fundamental to investigations of serious diseases such as Alzheimer's disease, Parkinson disease, and type II diabetes. For each disease, a different protein undergoes conformational conversion to a {beta}-sheet rich fiber. The fluorescence of ThT exhibits an increase in quantum yield upon binding these fibers. Despite its widespread use, the structural basis for binding specificity and for the changes to the photophysical properties of ThT remain poorly understood. Here, we report the co-crystal structures of ThT withmore » two alternative states of {beta}-2 microglobulin ({beta}2m); one monomeric, the other an amyloid-like oligomer. In the latter, the dye intercalates between {beta}-sheets orthogonal to the {beta}-strands. Importantly, the fluorophore is bound in such a manner that a photophysically relevant torsion is limited to a range of angles generally associated with low, not high, quantum yield. Quantum mechanical assessment of the fluorophore shows the electronic distribution to be strongly stabilized by aromatic interactions with the protein. Monomeric {beta}2m gives little increase in ThT fluorescence despite showing three fluorophores, at two binding sites, in configurations generally associated with high quantum yield. Our efforts fundamentally extend existing understanding about the origins of amyloid-induced photophysical changes. Specifically, the {beta}-sheet interface that characterizes amyloid acts both sterically and electronically to stabilize the fluorophore's ground state electronic distribution. By preventing the fluorophore from adopting its preferred excited state configuration, nonradiative relaxation pathways are minimized and quantum yield is increased.« less
High-Resolution Structure of a Self-Assembly-Competent Form of a Hydrophobic Peptide Captured in a Soluble [beta]-Sheet Scaffold

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

Makabe, Koki; Biancalana, Matthew; Yan, Shude

2010-02-08

{beta}-Rich self-assembly is a major structural class of polypeptides, but still little is known about its atomic structures and biophysical properties. Major impediments for structural and biophysical studies of peptide self-assemblies include their insolubility and heterogeneous composition. We have developed a model system, termed peptide self-assembly mimic (PSAM), based on the single-layer {beta}-sheet of Borrelia outer surface protein A. PSAM allows for the capture of a defined number of self-assembly-like peptide repeats within a water-soluble protein, making structural and energetic studies possible. In this work, we extend our PSAM approach to a highly hydrophobic peptide sequence. We show that amore » penta-Ile peptide (Ile{sub 5}), which is insoluble and forms {beta}-rich self-assemblies in aqueous solution, can be captured within the PSAM scaffold in a form capable of self-assembly. The 1.1-{angstrom} crystal structure revealed that the Ile{sub 5} stretch forms a highly regular {beta}-strand within this flat {beta}-sheet. Self-assembly models built with multiple copies of the crystal structure of the Ile5 peptide segment showed no steric conflict, indicating that this conformation represents an assembly-competent form. The PSAM retained high conformational stability, suggesting that the flat {beta}-strand of the Ile{sub 5} stretch primed for self-assembly is a low-energy conformation of the Ile{sub 5} stretch and rationalizing its high propensity for self-assembly. The ability of the PSAM to 'solubilize' an otherwise insoluble peptide stretch suggests the potential of the PSAM approach to the characterization of self-assembling peptides.« less
An exact collisionless equilibrium for the Force-Free Harris Sheet with low plasma beta

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

Allanson, O., E-mail: oliver.allanson@st-andrews.ac.uk; Neukirch, T., E-mail: tn3@st-andrews.ac.uk; Wilson, F., E-mail: fw237@st-andrews.ac.uk

We present a first discussion and analysis of the physical properties of a new exact collisionless equilibrium for a one-dimensional nonlinear force-free magnetic field, namely, the force-free Harris sheet. The solution allows any value of the plasma beta, and crucially below unity, which previous nonlinear force-free collisionless equilibria could not. The distribution function involves infinite series of Hermite polynomials in the canonical momenta, of which the important mathematical properties of convergence and non-negativity have recently been proven. Plots of the distribution function are presented for the plasma beta modestly below unity, and we compare the shape of the distribution functionmore » in two of the velocity directions to a Maxwellian distribution.« less
Fish β-parvalbumin acquires allergenic properties by amyloid assembly.

PubMed

Martínez, Javier; Sánchez, Rosa; Castellanos, Milagros; Fernández-Escamilla, Ana M; Vázquez-Cortés, Sonia; Fernández-Rivas, Montserrat; Gasset, María

2015-01-01

Amyloids are highly cross-β-sheet-rich aggregated states that confer protease resistance, membrane activity and multivalence properties to proteins, all essential features for the undesired preservation of food proteins transiting the gastrointestinal tract and causing type I allergy. Amyloid propensity of β-parvalbumin, the major fish allergen, was theoretically analysed and assayed under gastrointestinal-relevant conditions using the binding of thioflavin T, the formation of sodium dodecyl sulphate- (SDS-) resistant aggregates, circular dichroism spectroscopy and atomic force microscopy fibril imaging. Impact of amyloid aggregates on allergenicity was assessed with dot blot. Sequences of β-parvalbumin from species with commercial value contain several adhesive hexapeptides capable of driving amyloid formation. Using Atlantic cod β-parvalbumin (rGad m 1) displaying high IgE cross-reactivity, we found that formation of amyloid fibres under simulated gastrointestinal conditions accounts for the resistance to acid and neutral proteases, for the presence of membrane active species under gastrointestinal relevant conditions and for the IgE-recognition in the sera of allergic patients. Incorporation of the anti-amyloid compound epigallocatechin gallate prevents rGad m 1 fibrillation, facilitates its protease digestion and impairs its recognition by IgE. the formation of amyloid by rGad m 1 explains its degradation resistance, its facilitated passage across the intestinal epithelial barrier and its epitope architecture as allergen.
Using molecular recognition of beta-cyclodextrin to determine molecular weights of low-molecular-weight explosives by MALDI-TOF mass spectrometry.

PubMed

Zhang, Min; Shi, Zhen; Bai, Yinjuan; Gao, Yong; Hu, Rongzu; Zhao, Fenqi

2006-02-01

This study presents a novel method for determining the molecular weights of low molecular weight (MW) energetic compounds through their complexes of beta-cyclodextrin (beta-CD) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in a mass range of 500 to 1700 Da, avoiding matrix interference. The MWs of one composite explosive composed of 2,6-DNT, TNT, and RDX, one propellant with unknown components, and 14 single-compound explosives (RDX, HMX, 3,4-DNT, 2,6-DNT, 2,5-DNT, 2,4,6-TNT, TNAZ, DNI, BTTN, NG, TO, NTO, NP, and 662) were measured. The molecular recognition and inclusion behavior of beta-CD to energetic materials (EMs) were investigated. The results show that (1) the established method is sensitive, simple, accurate, and suitable for determining the MWs of low-MW single-compound explosives and energetic components in composite explosives and propellants; and (2) beta-CD has good inclusion and modular recognition abilities to the above EMs.
Reversal of temperature-induced conformational changes in the amyloid-beta peptide, Aβ40, by the β-sheet breaker peptides 16–23 and 17–24

PubMed Central

Hatip, Funda F Bölükbaşı; Suenaga, Midori; Yamada, Tatsuo; Matsunaga, Yoichi

2009-01-01

Background and purpose: Aggregates of the protein amyloid-beta (Aβ) play a crucial role in the pathogenesis of Alzheimer's disease (AD). Most therapeutic approaches to AD do not target Aβ, so determination of the factor(s) that facilitate aggregation and discovering agents that prevent aggregation have great potential therapeutic value. Experimental approach: We investigated ex vivo the temperature-sensitive regions of Aβ1–40 (Aβ40) and their interactions with octapeptides derived from sequences within Aβ40 –β-sheet breaker peptides (βSBP) – using enzyme-linked immunosorbent assay, and dot blot and far-UV circular dichroism (CD) spectroscopy. We measured changes within the physiological limits of temperature, using antibodies targeting epitopes 1–7, 5–10, 9–14 and 17–21 within Aβ40. Key results: Temperature-dependent conformational changes were observed in Aβ40 at epitopes 9–14 and 17–21 at 36–38 and 36–40°C respectively. The βSBPs 16–23 and 17–24, but not 15–22 and 18–25, could inhibit the changes. Moreover, βSBPs 16–23 and 17–24 increased digestion of Aβ40 by protease K, indicating a decreased aggregation of Aβ40, whereas βSBPs 15–22 and 18–25 did not increase this digestion. CD spectra revealed that β-sheet formation in Aβ40 at 38°C was reduced with βSBPs 16–23 and 17–24. Conclusions and implications: The epitopes 9–14 and 17–21 are the temperature-sensitive regions within Aβ40. The βSBPs, Aβ16–23 and 17–24 reversed temperature-induced β-sheet formation, and decreased Aβ40 aggregation. The results suggest that the 17–23 epitope of Aβ40 is crucially involved in preventing Aβ40 aggregation and consequent deposition of Aβ40 in AD brain. PMID:19785651
A molecular view of the role of chirality in charge-driven polypeptide complexation

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

Hoffmann, K. Q.; Perry, S. L.; Leon, L.

Polyelectrolyte molecules of opposite charge are known to form stable complexes in solution. Depending on the system conditions, such complexes can be solid or liquid. The latter are known as complex coacervates, and they appear as a second liquid phase in equilibrium with a polymer-dilute aqueous phase. This work considers the complexation between poly(glutamic acid) and poly(lysine), which is of particular interest because it enables examination of the role of chirality in ionic complexation, without changes to the overall chemical composition. Systematic atomic-level simulations are carried out for chains of poly(glutamic acid) and poly(lysine) with varying combinations of chirality alongmore » the backbone. Achiral chains form unstructured complexes. In contrast, homochiral chains lead to formation of stable beta-sheets between molecules of opposite charge, and experiments indicate that beta-sheet formation is correlated with the formation of solid precipitates. Changes in chirality along the peptide backbone are found to cause "kinks" in the beta-sheets. These are energetically unfavorable and result in irregular structures that are more difficult to pack together. Taken together, these results provide new insights that may be of use for the development of simple yet strong bioinspired materials consisting of beta-rich domains and amorphous regions.« less
Secondary structure of spiralin in solution, at the air/water interface, and in interaction with lipid monolayers.

PubMed

Castano, Sabine; Blaudez, Daniel; Desbat, Bernard; Dufourcq, Jean; Wróblewski, Henri

2002-05-03

The surface of spiroplasmas, helically shaped pathogenic bacteria related to the mycoplasmas, is crowded with the membrane-anchored lipoprotein spiralin whose structure and function are unknown. In this work, the secondary structure of spiralin under the form of detergent-free micelles (average Stokes radius, 87.5 A) in water and at the air/water interface, alone or in interaction with lipid monolayers was analyzed. FT-IR and circular dichroism (CD) spectroscopic data indicate that spiralin in solution contains about 25+/-3% of helices and 38+/-2% of beta sheets. These measurements are consistent with a consensus predictive analysis of the protein sequence suggesting about 28% of helices, 32% of beta sheets and 40% of irregular structure. Brewster angle microscopy (BAM) revealed that, in water, the micelles slowly disaggregate to form a stable and homogeneous layer at the air/water interface, exhibiting a surface pressure up to 10 mN/m. Polarization modulation infrared reflection absorption spectroscopy (PMIRRAS) spectra of interfacial spiralin display a complex amide I band characteristic of a mixture of beta sheets and alpha helices, and an intense amide II band. Spectral simulations indicate a flat orientation for the beta sheets and a vertical orientation for the alpha helices with respect to the interface. The combination of tensiometric and PMIRRAS measurements show that, when spiroplasma lipids are used to form a monolayer at the air/water interface, spiralin is adsorbed under this monolayer and its antiparallel beta sheets are mainly parallel to the polar-head layer of the lipids without deep perturbation of the fatty acid chains organization. Based upon these results, we propose a 'carpet model' for spiralin organization at the spiroplasma cell surface. In this model, spiralin molecules anchored into the outer leaflet of the lipid bilayer by their N-terminal lipid moiety are composed of two colinear domains (instead of a single globular domain) situated at the lipid/water interface. Owing to the very high amount of spiralin in the membrane, such carpets would cover most if not all the lipids present in the outer leaflet of the bilayer.
Structural Studies of Human Pyruvate Dehydrogenase

NASA Technical Reports Server (NTRS)

Ciszak, Ewa; Korotchkina, Lioubov G.; Dominiak, Paulina; Sidhu, Sukhdeep; Patel, Mulchand S.; Curreri, Peter A. (Technical Monitor)

2002-01-01

Human pyruvate dehydrogenase (E1) catalyzes the irreversible decarboxylation of pyruvate in the presence of Mg(2+) and thiamin pyrophosphate (TPP) followed by the rate-limiting reductive acetylation of the lipoyl moiety linked to dihydrolipoamide acetyltransferase. The three-dimensional structure of human E1 is elucidated using the methods of macromolecular X-ray crystallography. The structure is an alpha, alpha', beta and beta' tetramer with the protein units being in the tetrahedral arrangement. Each 361-residue alpha-subunit and 329-residue beta-subunit is composed of a beta-sheet core surrounded by alpha-helical domains. Each subunit is in extensive contact with all the three subunits involving TPP and magnesium cofactors, and potassium ions. The two binding sites for TPP are at the alpha-beta' and alpha'-beta interfaces, each involving a magnesium ion and Phe6l, His63, Tyr89, and Met200 from the alpha-subunit (or alpha'-subunit), and Met81 Phe85, His128 from the beta-subunit (or beta'-subunit). K+ ions are nestled between two beta-sheets and the end of an alpha-helix in each beta-subunit, where they are coordinated by four carbonyl oxygen groups from Ile12, Ala160, Asp163, and Asnl65, and a water molecule. The catalytic C2 carbon of thiazolium ring in this structure forms a 3.2 A contact with a water molecule involved in a series of H-bonds with other water molecules, and indirectly with amino acids including those involved in the catalysis and regulation of the enzyme.
Beta-hairpin formation in aqueous solution and in the presence of trifluoroethanol: a (1)H and (13)C nuclear magnetic resonance conformational study of designed peptides.

PubMed

Santiveri, Clara M; Pantoja-Uceda, David; Rico, Manuel; Jiménez, M Angeles

2005-10-15

In order to check our current knowledge on the principles involved in beta-hairpin formation, we have modified the sequence of a 3:5 beta-hairpin forming peptide with two different purposes, first to increase the stability of the formed 3:5 beta-hairpin, and second to convert the 3:5 beta-hairpin into a 2:2 beta-hairpin. The conformational behavior of the designed peptides was investigated in aqueous solution and in 30% trifluoroethanol (TFE) by analysis of the following nuclear magnetic resonance (NMR) parameters: nuclear Overhauser effect (NOE) data, and C(alpha)H, (13)C(alpha), and (13)C(beta) conformational shifts. From the differences in the ability to adopt beta-hairpin structures in these peptides, we have arrived to the following conclusions: (i) beta-Hairpin population increases with the statistical propensity of residues to occupy each turn position. (ii) The loop length, and in turn, the beta-hairpin type, can be modified as a function of the type of turn favored by the loop sequence. These two conclusions reinforce previous results about the importance of beta-turn sequence in beta-hairpin folding. (iii) Side-chain packing on each face of the beta-sheet may play a major role in beta-hairpin stability; hence simplified analysis in terms of isolated pair interactions and intrinsic beta-sheet propensities is insufficient. (iv) Contributions to beta-hairpin stability of turn and strand sequences are not completely independent. (v) The burial of hydrophobic surface upon beta-hairpin formation that, in turn, depends on side-chain packing also contributes to beta-hairpin stability. (vi) As previously observed, TFE stabilizes beta-hairpin structures, but the extent of the contribution of different factors to beta-hairpin formation is sometimes different in aqueous solution and in 30% TFE. (c) 2005 Wiley Periodicals, Inc. Biopolymers 79: 150-162, 2005.
Incorporating beta-turns and a turn mimetic out of context in loop 1 of the WW domain affords cooperatively folded beta-sheets.

PubMed

Kaul, R; Angeles, A R; Jäger, M; Powers, E T; Kelly, J W

2001-06-06

To probe the conformational requirements of loop 1 in the Pin1 WW domain, the residues at the i + 2 and i + 3 positions of a beta-turn within this loop were replaced by dPro-Gly and Asn-Gly, which are known to prefer the conformations required at the i + 1 and i + 2 positions of type II' and type I' beta-turns. Conformational specificity or lack thereof was further examined by incorporating into the i + 2 and i + 3 positions a non-alpha-amino acid-based beta-turn mimetic (4-(2'-aminoethyl)-6-dibenzofuran propionic acid residue, 1), which was designed to replace the i + 1 and i + 2 positions of beta-turns. All these Pin WW variants are monomeric and folded as discerned by analytical ultracentrifugation, NMR, and CD. They exhibit cooperative two-state transitions and display thermodynamic stability within 0.5 kcal/mol of the wild-type WW domain, demonstrating that the acquisition of native structure and stability does not require a specific sequence and, by extension, conformation within loop 1. However, it could be that these loop 1 mutations alter the kinetics of antiparallel beta-sheet folding, which will be addressed by subsequent kinetic studies.

Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.

PubMed

Satoh, Tadashi; Sato, Ken; Kanoh, Akira; Yamashita, Katsuko; Yamada, Yusuke; Igarashi, Noriyuki; Kato, Ryuichi; Nakano, Akihiko; Wakatsuki, Soichi

2006-04-14

Emp46p and Emp47p are type I membrane proteins, which cycle between the endoplasmic reticulum (ER) and the Golgi apparatus by vesicles coated with coat protein complexes I and II (COPI and COPII). They are considered to function as cargo receptors for exporting N-linked glycoproteins from the ER. We have determined crystal structures of the carbohydrate recognition domains (CRDs) of Emp46p and Emp47p of Saccharomyces cerevisiae, in the absence and presence of metal ions. Both proteins fold as a beta-sandwich, and resemble that of the mammalian ortholog, p58/ERGIC-53. However, the nature of metal binding is distinct from that of Ca(2+)-dependent p58/ERGIC-53. Interestingly, the CRD of Emp46p does not bind Ca(2+) ion but instead binds K(+) ion at the edge of a concave beta-sheet whose position is distinct from the corresponding site of the Ca(2+) ion in p58/ERGIC-53. Binding of K(+) ion to Emp46p appears essential for transport of a subset of glycoproteins because the Y131F mutant of Emp46p, which cannot bind K(+) ion fails to rescue the transport in disruptants of EMP46 and EMP47 genes. In contrast the CRD of Emp47p binds no metal ions at all. Furthermore, the CRD of Emp46p binds to glycoproteins carrying high mannosetype glycans and the is promoted by binding not the addition of Ca(2+) or K(+) ion in These results suggest that Emp46p can be regarded as a Ca(2+)-independent intracellular lectin at the ER exit sites.
Ribonucleocapsid Formation of SARS-COV Through Molecular Action of the N-Terminal Domain of N Protein

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

Saikatendu, K.S.; Joseph, J.S.; Subramanian, V.

Conserved amongst all coronaviruses are four structural proteins, the matrix (M), small envelope (E) and spike (S) that are embedded in the viral membrane and the nucleocapsid phosphoprotein (N), which exists in a ribonucleoprotein complex in their lumen. The N terminal domain of coronaviral N proteins (N-NTD) provides a scaffold for RNA binding while the C-terminal domain (N-CTD) mainly acts as oligomerization modules during assembly. The C-terminus of N protein anchors it to the viral membrane by associating with M protein. We characterized the structures of N-NTD from severe acute respiratory syndrome coronavirus (SARS-CoV) in two crystal forms, at 1.17Amore » (monoclinic) and 1.85 A (cubic) respectively, solved by molecular replacement using the homologous avian infectious bronchitis virus (IBV) structure. Flexible loops in the solution structure of SARS-CoV N-NTD are now shown to be well ordered around the beta-sheet core. The functionally important positively charged beta-hairpin protrudes out of the core and is oriented similar to that in the IBV N-NTD and is involved in crystal packing in the monoclinic form. In the cubic form, the monomers form trimeric units that stack in a helical array. Comparison of crystal packing of SARS-CoV and IBV N-NTDs suggest a common mode of RNA recognition, but probably associate differently in vivo during the formation of the ribonucleoprotein complex. Electrostatic potential distribution on the surface of homology models of related coronaviral N-NTDs hints that they employ different modes of both RNA recognition as well as oligomeric assembly, perhaps explaining why their nucleocapsids have different morphologies.« less
Structural Interplay - Tuning Mechanics in Peptide-Polyurea Hybrids

NASA Astrophysics Data System (ADS)

Korley, Lashanda

Utilizing cues from natural materials, we have been inspired to explore the hierarchical arrangement critical to energy absorption and mechanical enhancement in synthetic systems. Of particular interest is the soft domain ordering proposed as a contributing element to the observed toughness in spider silk. Multiblock copolymers, are ideal and dynamic systems in which to explore this approach via variations in secondary structure of nature's building blocks - peptides. We have designed a new class of polyurea hybrids that incorporate peptidic copolymers as the soft segment. The impact of hierarchical ordering on the thermal, mechanical, and morphological behavior of these bio-inspired polyurethanes with a siloxane-based, peptide soft segment was investigated. These peptide-polyurethane/urea hybrids were microphase segregated, and the beta-sheet secondary structure of the soft segment was preserved during polymerization and film casting. Toughness enhancement at low strains was achieved, but the overall extensibility of the peptide-incorporated systems was reduced due to the unique hard domain organization. To decouple the secondary structure influence in the siloxane-peptide soft segment from mechanics dominated by the hard domain, we also developed non-chain extended peptide-polyurea hybrids in which the secondary structure (beta sheet vs. alpha helix) was tuned via choice of peptide and peptide length. It was shown that this structural approach allowed tailoring of extensibility, toughness, and modulus. The sheet-dominant hybrid materials were typically tougher and more elastic due to intermolecular H-bonding facilitating load distribution, while the helical-prevalent systems generally exhibited higher stiffness. Recently, we have explored the impact of a molecular design strategy that overlays a covalent and physically crosslinked architecture in these peptide-polyurea hybrids, demonstrating that physical constraints in the network hybrids influences peptide hydrogen bonding and morphology. These structural features correlated well with systematic changes in modulus, extensibility, and hysteresis. Complementary to this effort is the design of PEG-based peptide-polyurea hybrids with tunable and responsive as structural and injectable hydrogels. The authors acknowledge funding support from the National Science Foundation (CAREER DMR-0953236).
Evidence for novel beta-sheet structures in Iowa mutant beta-amyloid fibrils.

PubMed

Tycko, Robert; Sciarretta, Kimberly L; Orgel, Joseph P R O; Meredith, Stephen C

2009-07-07

Asp23-to-Asn mutation within the coding sequence of beta-amyloid, called the Iowa mutation, is associated with early onset, familial Alzheimer's disease and cerebral amyloid angiopathy, in which patients develop neuritic plaques and massive vascular deposition predominantly of the mutant peptide. We examined the mutant peptide, D23N-Abeta40, by electron microscopy, X-ray diffraction, and solid-state NMR spectroscopy. D23N-Abeta40 forms fibrils considerably faster than the wild-type peptide (k = 3.77 x 10(-3) min(-1) and 1.07 x 10(-4) min(-1) for D23N-Abeta40 and the wild-type peptide WT-Abeta40, respectively) and without a lag phase. Electron microscopy shows that D23N-Abeta40 forms fibrils with multiple morphologies. X-ray fiber diffraction shows a cross-beta pattern, with a sharp reflection at 4.7 A and a broad reflection at 9.4 A, which is notably smaller than the value for WT-Abeta40 fibrils (10.4 A). Solid-state NMR measurements indicate molecular level polymorphism of the fibrils, with only a minority of D23N-Abeta40 fibrils containing the in-register, parallel beta-sheet structure commonly found in WT-Abeta40 fibrils and most other amyloid fibrils. Antiparallel beta-sheet structures in the majority of fibrils are indicated by measurements of intermolecular distances through (13)C-(13)C and (15)N-(13)C dipole-dipole couplings. An intriguing possibility exists that there is a relationship between the aberrant structure of D23N-Abeta40 fibrils and the unusual vasculotropic clinical picture in these patients.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Mosley, Ralph T.; Edwards, Thomas E.; Murakami, Eisuke

The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in a closed, polymerization-incompetent state. The removal of an autoinhibitory {beta}-hairpin loop from genotype 2a HCV NS5B increases de novo RNA synthesis by >100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs. These crystal structures demonstrate the structural realignment required for primer-template recognition and elongation, provide new insights into HCV RNA synthesismore » at the molecular level, and may prove useful in the structure-based design of novel antiviral compounds. Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase may be generally applicable to solving RNA-bound complexes for other viral RdRps that contain similar regulatory {beta}-hairpin loops, including bovine viral diarrhea virus, dengue virus, and West Nile virus.« less
Programmable DNA scaffolds for spatially-ordered protein assembly

NASA Astrophysics Data System (ADS)

Chandrasekaran, Arun Richard

2016-02-01

Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed.Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed. Dedicated to my advisor Ned Seeman on the occasion of his 70th birthday.
Recurrence of 49-base decamers, nonomers, and octamers within mouse C mu gene of Ig heavy chain and its primordial building block.

PubMed Central

Yazaki, A; Ohno, S

1983-01-01

Within the published 2,168-base-long mouse C mu gene of Ig heavy chain consisting of four coding and four noncoding segments, 2 base decamers, 8 nonomers, and 39 octamers recurred. Recurring base heptamers (about 100) and hexamers (about 350) were simply too numerous to merit individual identification. In spite of extensive overlaps between these recurring base decamers to hexamers, they occupied nearly the entire length of mouse Ig C mu gene. As with other genes of the beta-sheet-forming beta 2-microglobulin family, the Ig C mu gene (flanking and intervening noncoding sequences included) is not a unique sequence but rather it is degenerate repeats of the 45-base-long primordial building-block sequence uniquely its own. This primordial building block must originally have specified the 15-amino-acid-residue-long primordial arm of beta-sheet-forming loops, the characteristics of the beta 2-microglobulin family of polypeptides. PMID:6403948
Structure and function of small heat shock/alpha-crystallin proteins: established concepts and emerging ideas.

PubMed

MacRae, T H

2000-06-01

Small heat shock/alpha-crystallin proteins are defined by conserved sequence of approximately 90 amino acid residues, termed the alpha-crystallin domain, which is bounded by variable amino- and carboxy-terminal extensions. These proteins form oligomers, most of uncertain quaternary structure, and oligomerization is prerequisite to their function as molecular chaperones. Sequence modelling and physical analyses show that the secondary structure of small heat shock/alpha-crystallin proteins is predominately beta-pleated sheet. Crystallography, site-directed spin-labelling and yeast two-hybrid selection demonstrate regions of secondary structure within the alpha-crystallin domain that interact during oligomer assembly, a process also dependent on the amino terminus. Oligomers are dynamic, exhibiting subunit exchange and organizational plasticity, perhaps leading to functional diversity. Exposure of hydrophobic residues by structural modification facilitates chaperoning where denaturing proteins in the molten globule state associate with oligomers. The flexible carboxy-terminal extension contributes to chaperone activity by enhancing the solubility of small heat shock/alpha-crystallin proteins. Site-directed mutagenesis has yielded proteins where the effect of the change on structure and function depends upon the residue modified, the organism under study and the analytical techniques used. Most revealing, substitution of a conserved arginine residue within the alpha-crystallin domain has a major impact on quaternary structure and chaperone action probably through realignment of beta-sheets. These mutations are linked to inherited diseases. Oligomer size is regulated by a stress-responsive cascade including MAPKAP kinase 2/3 and p38. Phosphorylation of small heat shock/alpha-crystallin proteins has important consequences within stressed cells, especially for microfilaments.
Crystal structure of tandem type III fibronectin domains from Drosophila neuroglian at 2.0 A.

PubMed

Huber, A H; Wang, Y M; Bieber, A J; Bjorkman, P J

1994-04-01

We report the crystal structure of two adjacent fibronectin type III repeats from the Drosophila neural cell adhesion molecule neuroglian. Each domain consists of two antiparallel beta sheets and is folded topologically identically to single fibronectin type III domains from the extracellular matrix proteins tenascin and fibronectin. beta bulges and left-handed polyproline II helices disrupt the regular beta sheet structure of both neuroglian domains. The hydrophobic interdomain interface includes a metal-binding site, presumably involved in stabilizing the relative orientation between domains and predicted by sequence comparision to be present in the vertebrate homolog molecule L1. The neuroglian domains are related by a near perfect 2-fold screw axis along the longest molecular dimension. Using this relationship, a model for arrays of tandem fibronectin type III repeats in neuroglian and other molecules is proposed.
Distinct roles of beta1 metal ion-dependent adhesion site (MIDAS), adjacent to MIDAS (ADMIDAS), and ligand-associated metal-binding site (LIMBS) cation-binding sites in ligand recognition by integrin alpha2beta1.

PubMed

Valdramidou, Dimitra; Humphries, Martin J; Mould, A Paul

2008-11-21

Integrin-ligand interactions are regulated in a complex manner by divalent cations, and previous studies have identified ligand-competent, stimulatory, and inhibitory cation-binding sites. In collagen-binding integrins, such as alpha2beta1, ligand recognition takes place exclusively at the alpha subunit I domain. However, activation of the alphaI domain depends on its interaction with a structurally similar domain in the beta subunit known as the I-like or betaI domain. The top face of the betaI domain contains three cation-binding sites: the metal-ion dependent adhesion site (MIDAS), the ADMIDAS (adjacent to MIDAS), and LIMBS (ligand-associated metal-binding site). The role of these sites in controlling ligand binding to the alphaI domain has yet to be elucidated. Mutation of the MIDAS or LIMBS completely blocked collagen binding to alpha2beta1; in contrast mutation of the ADMIDAS reduced ligand recognition but this effect could be overcome by the activating monoclonal antibody TS2/16. Hence, the MIDAS and LIMBS appear to be essential for the interaction between alphaI and betaI, whereas occupancy of the ADMIDAS has an allosteric effect on the conformation of betaI. An activating mutation in the alpha2 I domain partially restored ligand binding to the MIDAS and LIMBS mutants. Analysis of the effects of Ca(2+), Mg(2+), and Mn(2+) on ligand binding to these mutants showed that the MIDAS is a ligand-competent site through which Mn(2+) stimulates ligand binding, whereas the LIMBS is a stimulatory Ca(2+)-binding site, occupancy of which increases the affinity of Mg(2+) for the MIDAS.
Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

PubMed

Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav

2002-12-01

The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.
Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

PubMed Central

Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav

2002-01-01

The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit. PMID:12515387
Entropic stabilization of isolated beta-sheets.

PubMed

Dugourd, Philippe; Antoine, Rodolphe; Breaux, Gary; Broyer, Michel; Jarrold, Martin F

2005-04-06

Temperature-dependent electric deflection measurements have been performed for a series of unsolvated alanine-based peptides (Ac-WA(n)-NH(2), where Ac = acetyl, W = tryptophan, A = alanine, and n = 3, 5, 10, 13, and 15). The measurements are interpreted using Monte Carlo simulations performed with a parallel tempering algorithm. Despite alanine's high helix propensity in solution, the results suggest that unsolvated Ac-WA(n)-NH(2) peptides with n > 10 adopt beta-sheet conformations at room temperature. Previous studies have shown that protonated alanine-based peptides adopt helical or globular conformations in the gas phase, depending on the location of the charge. Thus, the charge more than anything else controls the structure.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Driscoll, P.C.; Gronenborn, A.M.; Beress, L.

The three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata has been determined on the basis of 489 interproton and 24 hydrogen-bonding distance restraints supplemented by 23 {phi} backbone and 21 {sub {chi}1} side-chain torsion angle restraints derived from nuclear magnetic resonance (NMR) measurements. A total of 42 structures is calculated by a hybrid metric matrix distance geometry-dynamical simulated annealing approach. Both the backbone and side-chain atom positions are well defined. The average atomic rms difference between the 42 individual SA structures and the mean structure obtained by averaging their coordinates is 0.67more » {plus minus} 0.12 {angstrom} for the backbone atoms and 0.90 {plus minus} 0.17 {angstrom} for all atoms. The core of the protein is formed by a triple-stranded antiparallel {beta}-sheet composed of residues 14-16 (strand 1), 30-34 (strand 2), and 37-41 (strand 3) with an additional mini-antiparallel {beta}-sheet at the N-terminus (residues 6-9). The first and second strands of the triple-stranded antiparallel {beta}-sheet are connected by a long exposed loop. A number of side-chain interactions are discussed in light of the structure.« less
sup 1 H assignments and secondary structure determination of the soybean trypsin/chymotrypsin Bowman-Birk inhibitor

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

Werner, M.H.; Wemmer, D.E.

1991-04-09

The {sup 1}H resonance assignments and secondary structure of the trypsin/chymotrypsin Bowman-Birk inhibitor from soybeans were determined by nuclear magnetic resonance spectroscopy (NMR) at 600 MHz in an 18% acetonitrile-d{sub 3}/aqueous cosolvent. Resonances from 69 to 71 amino acids were assigned sequence specifically. Residues Q11-T15 form an antiparallel {beta}-sheet with residues Q21-S25 in the tryptic inhibitory domain and an analogous region of antiparallel sheet forms between residues S38-A42 and Q48-V52 in the chymotryptic inhibitory domain. The inhibitory sites of each fragment (K16-S17 for trypsin, L43-S44 for chymotrypsin) are each part of a type VI like turn at one end ofmore » their respective region of the antiparallel {beta}-sheet. These structural elements are compared to those found in other Bowman-Birk inhibitors.« less
The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins.

PubMed

Eisenberg, David

2003-09-30

PNAS papers by Linus Pauling, Robert Corey, and Herman Branson in the spring of 1951 proposed the alpha-helix and the beta-sheet, now known to form the backbones of tens of thousands of proteins. They deduced these fundamental building blocks from properties of small molecules, known both from crystal structures and from Pauling's resonance theory of chemical bonding that predicted planar peptide groups. Earlier attempts by others to build models for protein helices had failed both by including nonplanar peptides and by insisting on helices with an integral number of units per turn. In major respects, the Pauling-Corey-Branson models were astoundingly correct, including bond lengths that were not surpassed in accuracy for >40 years. However, they did not consider the hand of the helix or the possibility of bent sheets. They also proposed structures and functions that have not been found, including the gamma-helix.
Beta structures of alternating polypeptides and their possible prebiotic significance

NASA Technical Reports Server (NTRS)

Brack, A.; Orgel, L. E.

1975-01-01

A survey of the commonest amino acids formed in prebiotic conditions suggests that the earliest form of genetic coding may have specified polypeptides with a strong tendency to form stable beta-sheet structures. Poly(Val-Lys), like other polypeptides in which hydrophobic and hydrophilic residues alternate, tends to form beta structures. It is shown that bilayers with a hydrophobic interior and a hydrophilic exterior may be present in aqueous solution.
Parallel nucleic acid recognition by the LNA (locked nucleic acid) stereoisomers beta-L-LNA and alpha-D-LNA; studies in the mirror image world.

PubMed

Christensen, Nanna K; Bryld, Torsten; Sørensen, Mads D; Arar, Khalil; Wengel, Jesper; Nielsen, Poul

2004-02-07

Two LNA (locked nucleic acid) stereoisomers (beta-L-LNA and alpha-D-LNA) are evaluated in the mirror-image world, that is by the study of two mixed sequences of LNA and alpha-L-LNA and their L-DNA and L-RNA complements. Both are found to display high-affinity RNA-recognition by the formation of duplexes with parallel strand orientation.
Estrogens and their receptors in the medial amygdala rapidly facilitate social recognition in female mice.

PubMed

Lymer, Jennifer M; Sheppard, Paul A S; Kuun, Talya; Blackman, Andrea; Jani, Nilay; Mahbub, Sahnon; Choleris, Elena

2018-03-01

Estrogens have been shown to rapidly (within 1 h) affect learning and memory processes, including social recognition. Both systemic and hippocampal administration of 17β-estradiol facilitate social recognition in female mice within 40 min of administration. These effects were likely mediated by estrogen receptor (ER) α and the G-protein coupled estrogen receptor (GPER), as administration of the respective receptor agonists (PPT and G-1) also facilitated social recognition on a rapid time scale. The medial amygdala has been shown to be necessary for social recognition and long-term manipulations in rats have implicated medial amygdalar ERα. As such, our objective was to investigate whether estrogens and different ERs within the medial amygdala play a role in the rapid facilitation of social recognition in female mice. 17β-estradiol, G-1, PPT, or ERβ agonist DPN was infused directly into the medial amygdala of ovariectomized female mice. Mice were then tested in a social recognition paradigm, which was completed within 40 min, thus allowing the assessment of rapid effects of treatments. 17β-estradiol (10, 25, 50, 100 nM), PPT (300 nM), DPN (150 nM), and G-1 (50 nM) each rapidly facilitated social recognition. Therefore, estrogens in the medial amygdala rapidly facilitate social recognition in female mice, and the three main estrogen receptors: ERα, ERβ, and the GPER all are involved in these effects. This research adds to a network of brain regions, including the medial amygdala and the dorsal hippocampus, that are involved in mediating the rapid estrogenic facilitation of social recognition in female mice. Copyright © 2017 Elsevier Ltd. All rights reserved.
Careers "Fact Sheets" for clinical engineering & biomedical technology.

PubMed

Pacela, A F

1991-01-01

Three Careers "Fact Sheets" include information on CE and BMET job titles, job descriptions, and certification. These materials are intended to aid in furthering professional recognition for Clinical Engineers and BMETs, and may be useful in communicating with Administration or Human Resources departments.

Pain-Related Suppression of Beta Oscillations Facilitates Voluntary Movement

PubMed Central

Misra, Gaurav; Ofori, Edward; Chung, Jae Woo; Coombes, Stephen A.

2017-01-01

Abstract Increased beta oscillations over sensorimotor cortex are antikinetic. Motor- and pain-related processes separately suppress beta oscillations over sensorimotor cortex leading to the prediction that ongoing pain should facilitate movement. In the current study, we used a paradigm in which voluntary movements were executed during an ongoing pain-eliciting stimulus to test the hypothesis that a pain-related suppression of beta oscillations would facilitate the initiation of a subsequent voluntary movement. Using kinematic measures, electromyography, and high-density electroencephalography, we demonstrate that ongoing pain leads to shorter reaction times without affecting the kinematics or accuracy of movement. Reaction time was positively correlated with beta power prior to movement in contralateral premotor areas. Our findings corroborate the view that beta-band oscillations are antikinetic and provide new evidence that pain primes the motor system for action. Our observations provide the first evidence that a pain-related suppression of beta oscillations over contralateral premotor areas leads to shorter reaction times for voluntary movement. PMID:26965905
Topological side-chain classification of beta-turns: ideal motifs for peptidomimetic development.

PubMed

Tran, Tran Trung; McKie, Jim; Meutermans, Wim D F; Bourne, Gregory T; Andrews, Peter R; Smythe, Mark L

2005-08-01

Beta-turns are important topological motifs for biological recognition of proteins and peptides. Organic molecules that sample the side chain positions of beta-turns have shown broad binding capacity to multiple different receptors, for example benzodiazepines. Beta-turns have traditionally been classified into various types based on the backbone dihedral angles (phi2, psi2, phi3 and psi3). Indeed, 57-68% of beta-turns are currently classified into 8 different backbone families (Type I, Type II, Type I', Type II', Type VIII, Type VIa1, Type VIa2 and Type VIb and Type IV which represents unclassified beta-turns). Although this classification of beta-turns has been useful, the resulting beta-turn types are not ideal for the design of beta-turn mimetics as they do not reflect topological features of the recognition elements, the side chains. To overcome this, we have extracted beta-turns from a data set of non-homologous and high-resolution protein crystal structures. The side chain positions, as defined by C(alpha)-C(beta) vectors, of these turns have been clustered using the kth nearest neighbor clustering and filtered nearest centroid sorting algorithms. Nine clusters were obtained that cluster 90% of the data, and the average intra-cluster RMSD of the four C(alpha)-C(beta) vectors is 0.36. The nine clusters therefore represent the topology of the side chain scaffold architecture of the vast majority of beta-turns. The mean structures of the nine clusters are useful for the development of beta-turn mimetics and as biological descriptors for focusing combinatorial chemistry towards biologically relevant topological space.
A self-excising beta-recombinase/six cassette for repetitive gene deletion and homokaryon purification in Neurospora crassa

USDA-ARS?s Scientific Manuscript database

In a previous study we developed a cassette employing a bacterial beta-recombinase acting on six recognition sequences (beta-rec/six), which allowed repetitive site-specific gene deletion and marker recycling in Neurospora crassa. However, only one positive selection marker was used in the cassette...
Structure of the human protein kinase MPSK1 reveals an atypical activation loop architecture.

PubMed

Eswaran, Jeyanthy; Bernad, Antonio; Ligos, Jose M; Guinea, Barbara; Debreczeni, Judit E; Sobott, Frank; Parker, Sirlester A; Najmanovich, Rafael; Turk, Benjamin E; Knapp, Stefan

2008-01-01

The activation segment of protein kinases is structurally highly conserved and central to regulation of kinase activation. Here we report an atypical activation segment architecture in human MPSK1 comprising a beta sheet and a large alpha-helical insertion. Sequence comparisons suggested that similar activation segments exist in all members of the MPSK1 family and in MAST kinases. The consequence of this nonclassical activation segment on substrate recognition was studied using peptide library screens that revealed a preferred substrate sequence of X-X-P/V/I-phi-H/Y-T*-N/G-X-X-X (phi is an aliphatic residue). In addition, we identified the GTPase DRG1 as an MPSK1 interaction partner and specific substrate. The interaction domain in DRG1 was mapped to the N terminus, leading to recruitment and phosphorylation at Thr100 within the GTPase domain. The presented data reveal an atypical kinase structural motif and suggest a role of MPSK1 regulating DRG1, a GTPase involved in regulation of cellular growth.
Dynamics of beta-amyloid peptide in cholesterol superlattice domain

NASA Astrophysics Data System (ADS)

Smirnov, Anton; Zhu, Qing; Vaughn, Mark; Khare, Rajesh; Cheng, K.

2006-10-01

Presence of beta-amyloid peptide (beta-A) plagues in membranes of neuron cells is a clinical signature of Alzheimer disease. The onset of beta-A peptide aggregation occurs via a conformational transition from an alpha-helix state to a beta-sheet state. A gradual build-up of beta-A content in the neuronal extracellular space is another characteristic of the beta-A plague formation. Hypothetically, both the pathological conformation and the predominant localization of the beta-A can be a result of specific dynamic characteristics of the interphase between cellular membrane and extracellular milieu. In this study, the beta-A interphase problem has been investigated using a virtual membrane model implemented on the base of GROMACS molecular dynamics simulation package. The detailed folding pattern of beta-A has been examined using a novice interphase model comprised of a cholesterol supperlattice membrane and two water layers.
Off-lexicon online Arabic handwriting recognition using neural network

NASA Astrophysics Data System (ADS)

Yahia, Hamdi; Chaabouni, Aymen; Boubaker, Houcine; Alimi, Adel M.

2017-03-01

This paper highlights a new method for online Arabic handwriting recognition based on graphemes segmentation. The main contribution of our work is to explore the utility of Beta-elliptic model in segmentation and features extraction for online handwriting recognition. Indeed, our method consists in decomposing the input signal into continuous part called graphemes based on Beta-Elliptical model, and classify them according to their position in the pseudo-word. The segmented graphemes are then described by the combination of geometric features and trajectory shape modeling. The efficiency of the considered features has been evaluated using feed forward neural network classifier. Experimental results using the benchmarking ADAB Database show the performance of the proposed method.
Target recognition of beta2-glycoprotein I (beta2GPI)-dependent anticardiolipin antibodies: evidence for involvement of the fourth domain of beta2GPI in antibody binding.

PubMed

George, J; Gilburd, B; Hojnik, M; Levy, Y; Langevitz, P; Matsuura, E; Koike, T; Shoenfeld, Y

1998-04-15

Beta2-glycoprotein I (beta2GPI) is an absolute requirement for the binding of autoimmune anticardiolipin Abs (aCL) to cardiolipin (CL). We evaluated the target recognition of human beta2GPI by IgG derived from two patients with primary and two with secondary antiphospholipid syndrome. The total IgG serum fractions and beta2GPI affinity-purified IgGs were assessed by using various domain-deleted mutants (DM) of human beta2GPI (DMs: I-III, I-IV, II-V, III-V, IV-V, and V) and mouse mAbs against individual beta2GPI domains. The four IgGs bound slightly to CL in the absence of beta2GPI and showed increased binding in the beta2GPI presence. Following affinity purification of the IgGs on a beta2GPI column, reactivity toward CL was absent. DMs containing domain V inhibited the binding of biotinylated beta2GPI to CL. The addition to CL-coated plates of DM V, but not the other DMs, reduced the binding of all four IgGs. The anti-beta2GPI IgGs bound only to complete beta2GPI and DM I-IV coated on the plates. The binding to plate-adsorbed beta2GPI could be inhibited by complete beta2GPI and DM I-IV, the latter being a more efficient inhibitor. Further, the human anti-beta2GPI IgGs could compete with the binding to beta2GPI of Cof-21 mouse mAb (directed at domain IV), but not with the two other mouse mAbs. The results suggest that some "autoimmune:" beta2GPI-dependent anticardiolipin Abs recognize a beta2GPI target that is distinct from the CL-binding site in domain V. The target site for some antiphospholipid syndrome IgGs appear to reside in domain IV of beta2GPI.
Silk from crickets: a new twist on spinning.

PubMed

Walker, Andrew A; Weisman, Sarah; Church, Jeffrey S; Merritt, David J; Mudie, Stephen T; Sutherland, Tara D

2012-01-01

Raspy crickets (Orthoptera: Gryllacrididae) are unique among the orthopterans in producing silk, which is used to build shelters. This work studied the material composition and the fabrication of cricket silk for the first time. We examined silk-webs produced in captivity, which comprised cylindrical fibers and flat films. Spectra obtained from micro-Raman experiments indicated that the silk is composed of protein, primarily in a beta-sheet conformation, and that fibers and films are almost identical in terms of amino acid composition and secondary structure. The primary sequences of four silk proteins were identified through a mass spectrometry/cDNA library approach. The most abundant silk protein was large in size (300 and 220 kDa variants), rich in alanine, glycine and serine, and contained repetitive sequence motifs; these are features which are shared with several known beta-sheet forming silk proteins. Convergent evolution at the molecular level contrasts with development by crickets of a novel mechanism for silk fabrication. After secretion of cricket silk proteins by the labial glands they are fabricated into mature silk by the labium-hypopharynx, which is modified to allow the controlled formation of either fibers or films. Protein folding into beta-sheet structure during silk fabrication is not driven by shear forces, as is reported for other silks.
KM+, a mannose-binding lectin from Artocarpus integrifolia: amino acid sequence, predicted tertiary structure, carbohydrate recognition, and analysis of the beta-prism fold.

PubMed Central

Rosa, J. C.; De Oliveira, P. S.; Garratt, R.; Beltramini, L.; Resing, K.; Roque-Barreira, M. C.; Greene, L. J.

1999-01-01

The complete amino acid sequence of the lectin KM+ from Artocarpus integrifolia (jackfruit), which contains 149 residues/mol, is reported and compared to those of other members of the Moraceae family, particularly that of jacalin, also from jackfruit, with which it shares 52% sequence identity. KM+ presents an acetyl-blocked N-terminus and is not posttranslationally modified by proteolytic cleavage as is the case for jacalin. Rather, it possesses a short, glycine-rich linker that unites the regions homologous to the alpha- and beta-chains of jacalin. The results of homology modeling implicate the linker sequence in sterically impeding rotation of the side chain of Asp141 within the binding site pocket. As a consequence, the aspartic acid is locked into a conformation adequate only for the recognition of equatorial hydroxyl groups on the C4 epimeric center (alpha-D-mannose, alpha-D-glucose, and their derivatives). In contrast, the internal cleavage of the jacalin chain permits free rotation of the homologous aspartic acid, rendering it capable of accepting hydrogen bonds from both possible hydroxyl configurations on C4. We suggest that, together with direct recognition of epimeric hydroxyls and the steric exclusion of disfavored ligands, conformational restriction of the lectin should be considered to be a new mechanism by which selectivity may be built into carbohydrate binding sites. Jacalin and KM+ adopt the beta-prism fold already observed in two unrelated protein families. Despite presenting little or no sequence similarity, an analysis of the beta-prism reveals a canonical feature repeatedly present in all such structures, which is based on six largely hydrophobic residues within a beta-hairpin containing two classic-type beta-bulges. We suggest the term beta-prism motif to describe this feature. PMID:10210179
Multiple levels of regulation determine the role of the receptor for AGE (RAGE) as common soil in inflammation, immune responses and diabetes mellitus and its complications.

PubMed

Bierhaus, A; Nawroth, P P

2009-11-01

The pattern recognition receptor or receptor for AGE (RAGE) is constitutionally expressed in a few cell types only. However in almost all cells studied so far it is induced by reactions known to initiate inflammation. Its biological activity seems to be mainly dependent on the presence of its various ligands, including AGE, S100-calcium binding protein/calgranulins, high-mobility group protein 1, amyloid-beta-peptides and the family of beta-sheet fibrils, all known to be elevated in chronic metabolic, malignant and inflammatory diseases. The RAGE pathway interacts with cytokine-, lipopolysaccharide-, oxidised LDL- and glucose-triggered cellular reactions by turning a short-lasting inflammatory response into a sustained change of cellular function driven by perpetuated activation of the proinflammatory transcription factor, nuclear factor kappa-B. RAGE-mediated persistent cell activation is of pivotal importance in various experimental and clinical settings, including diabetes and its complications, neurodegeneration, ageing, tumour growth, and autoimmune and infectious inflammatory disease. Due to RAGE's central role in maintaining perpetuated cell activation, various therapeutic attempts to block RAGE or its ligands are currently under investigation. Despite broad experimental evidence for the role of RAGE in chronic disease, knowledge of its physiological function is still missing, limiting predictions about safety of long-term inhibition of RAGE x ligand interaction in chronic diseases.
A single-point mutation in the extreme heat- and pressure-resistant sso7d protein from sulfolobus solfataricus leads to a major rearrangement of the hydrophobic core.

PubMed

Consonni, R; Santomo, L; Fusi, P; Tortora, P; Zetta, L

1999-09-28

Sso7d is a basic 7-kDa DNA-binding protein from Sulfolobus solfataricus, also endowed with ribonuclease activity. The protein consists of a double-stranded antiparallel beta-sheet, onto which an orthogonal triple-stranded antiparallel beta-sheet is packed, and of a small helical stretch at the C-terminus. Furthermore, the two beta-sheets enclose an aromatic cluster displaying a fishbone geometry. We previously cloned the Sso7d-encoding gene, expressed it in Escherichia coli, and produced several single-point mutants, either of residues located in the hydrophobic core or of Trp23, which is exposed to the solvent and plays a major role in DNA binding. The mutation F31A was dramatically destabilizing, with a loss in thermo- and piezostabilities by at least 27 K and 10 kbar, respectively. Here, we report the solution structure of the F31A mutant, which was determined by NMR spectroscopy using 744 distance constraints obtained from analysis of multidimensional spectra in conjunction with simulated annealing protocols. The most remarkable finding is the change in orientation of the Trp23 side chain, which in the wild type is completely exposed to the solvent, whereas in the mutant is largely buried in the aromatic cluster. This prevents the formation of a cavity in the hydrophobic core of the mutant, which would arise in the absence of structural rearrangements. We found additional changes produced by the mutation, notably a strong distortion in the beta-sheets with loss in several hydrogen bonds, increased flexibility of some stretches of the backbone, and some local strains. On one hand, these features may justify the dramatic destabilization provoked by the mutation; on the other hand, they highlight the crucial role of the hydrophobic core in protein stability. To the best of our knowledge, no similar rearrangement has been so far described as a result of a single-point mutation.
PB1-F2 influenza A virus protein adopts a beta-sheet conformation and forms amyloid fibers in membrane environments.

PubMed

Chevalier, Christophe; Al Bazzal, Ali; Vidic, Jasmina; Février, Vincent; Bourdieu, Christiane; Bouguyon, Edwige; Le Goffic, Ronan; Vautherot, Jean-François; Bernard, Julie; Moudjou, Mohammed; Noinville, Sylvie; Chich, Jean-François; Da Costa, Bruno; Rezaei, Human; Delmas, Bernard

2010-04-23

The influenza A virus PB1-F2 protein, encoded by an alternative reading frame in the PB1 polymerase gene, displays a high sequence polymorphism and is reported to contribute to viral pathogenesis in a sequence-specific manner. To gain insights into the functions of PB1-F2, the molecular structure of several PB1-F2 variants produced in Escherichia coli was investigated in different environments. Circular dichroism spectroscopy shows that all variants have a random coil secondary structure in aqueous solution. When incubated in trifluoroethanol polar solvent, all PB1-F2 variants adopt an alpha-helix-rich structure, whereas incubated in acetonitrile, a solvent of medium polarity mimicking the membrane environment, they display beta-sheet secondary structures. Incubated with asolectin liposomes and SDS micelles, PB1-F2 variants also acquire a beta-sheet structure. Dynamic light scattering revealed that the presence of beta-sheets is correlated with an oligomerization/aggregation of PB1-F2. Electron microscopy showed that PB1-F2 forms amorphous aggregates in acetonitrile. In contrast, at low concentrations of SDS, PB1-F2 variants exhibited various abilities to form fibers that were evidenced as amyloid fibers in a thioflavin T assay. Using a recombinant virus and its PB1-F2 knock-out mutant, we show that PB1-F2 also forms amyloid structures in infected cells. Functional membrane permeabilization assays revealed that the PB1-F2 variants can perforate membranes at nanomolar concentrations but with activities found to be sequence-dependent and not obviously correlated with their differential ability to form amyloid fibers. All of these observations suggest that PB1-F2 could be involved in physiological processes through different pathways, permeabilization of cellular membranes, and amyloid fiber formation.
Biodegradable materials based on silk fibroin and keratin.

PubMed

Vasconcelos, Andreia; Freddi, Giuliano; Cavaco-Paulo, Artur

2008-04-01

Wool and silk were dissolved and used for the preparation of blended films. Two systems are proposed: (1) blend films of silk fibroin and keratin aqueous solutions and (2) silk fibroin and keratin dissolved in formic acid. The FTIR spectra of pure films cast from aqueous solutions indicated that the keratin secondary structure mainly consists of alpha-helix and random coil conformations. The IR spectrum of pure SF is characteristic of films with prevalently amorphous structure (random coil conformation). Pure keratin film cast from formic acid shows an increase in the amount of beta-sheet and disordered keratin structures. The FTIR pattern of SF dissolved in formic acid is characteristic of films with prevalently beta-sheet conformations with beta-sheet crystallites embedded in an amorphous matrix. The thermal behavior of the blends confirmed the FTIR results. DSC curve of pure SF is typical of amorphous SF and the curve of pure keratin show the characteristic melting peak of alpha-helices for the aqueous system. These patterns are no longer observed in the films cast from formic acid due to the ability of formic acid to induce crystallization of SF and to increase the amount of beta-sheet structures on keratin. The nonlinear trend of the different parameters obtained from FTIR analysis and DSC curves of both SF/keratin systems indicate that when proteins are mixed they do not follow additives rules but are able to establish intermolecular interactions. Degradable polymeric biomaterials are preferred candidates for medical applications. It was investigated the degradation behavior of both SF/keratin systems by in vitro enzymatic incubation with trypsin. The SF/keratin films cast from water underwent a slower biological degradation than the films cast from formic acid. The weight loss obtained is a function of the amount of keratin in the blend. This study encourages the further investigation of the type of matrices presented here to be applied whether in scaffolds for tissue engineering or as controlled release drug delivery vehicles.
Towards a Pharmacophore for Amyloid

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

Landau, Meytal; Sawaya, Michael R.; Faull, Kym F.

2011-09-16

Diagnosing and treating Alzheimer's and other diseases associated with amyloid fibers remains a great challenge despite intensive research. To aid in this effort, we present atomic structures of fiber-forming segments of proteins involved in Alzheimer's disease in complex with small molecule binders, determined by X-ray microcrystallography. The fiber-like complexes consist of pairs of {beta}-sheets, with small molecules binding between the sheets, roughly parallel to the fiber axis. The structures suggest that apolar molecules drift along the fiber, consistent with the observation of nonspecific binding to a variety of amyloid proteins. In contrast, negatively charged orange-G binds specifically to lysine sidemore » chains of adjacent sheets. These structures provide molecular frameworks for the design of diagnostics and drugs for protein aggregation diseases. The devastating and incurable dementia known as Alzheimer's disease affects the thinking, memory, and behavior of dozens of millions of people worldwide. Although amyloid fibers and oligomers of two proteins, tau and amyloid-{beta}, have been identified in association with this disease, the development of diagnostics and therapeutics has proceeded to date in a near vacuum of information about their structures. Here we report the first atomic structures of small molecules bound to amyloid. These are of the dye orange-G, the natural compound curcumin, and the Alzheimer's diagnostic compound DDNP bound to amyloid-like segments of tau and amyloid-{beta}. The structures reveal the molecular framework of small-molecule binding, within cylindrical cavities running along the {beta}-spines of the fibers. Negatively charged orange-G wedges into a specific binding site between two sheets of the fiber, combining apolar binding with electrostatic interactions, whereas uncharged compounds slide along the cavity. We observed that different amyloid polymorphs bind different small molecules, revealing that a cocktail of compounds may be required for future amyloid therapies. The structures described here start to define the amyloid pharmacophore, opening the way to structure-based design of improved diagnostics and therapeutics.« less
Pressure response of protein backbone structure. Pressure-induced amide 15N chemical shifts in BPTI.

PubMed Central

Akasaka, K.; Li, H.; Yamada, H.; Li, R.; Thoresen, T.; Woodward, C. K.

1999-01-01

The effect of pressure on amide 15N chemical shifts was studied in uniformly 15N-labeled basic pancreatic trypsin inhibitor (BPTI) in 90%1H2O/10%2H2O, pH 4.6, by 1H-15N heteronuclear correlation spectroscopy between 1 and 2,000 bar. Most 15N signals were low field shifted linearly and reversibly with pressure (0.468 +/- 0.285 ppm/2 kbar), indicating that the entire polypeptide backbone structure is sensitive to pressure. A significant variation of shifts among different amide groups (0-1.5 ppm/2 kbar) indicates a heterogeneous response throughout within the three-dimensional structure of the protein. A tendency toward low field shifts is correlated with a decrease in hydrogen bond distance on the order of 0.03 A/2 kbar for the bond between the amide nitrogen atom and the oxygen atom of either carbonyl or water. The variation of 15N shifts is considered to reflect site-specific changes in phi, psi angles. For beta-sheet residues, a decrease in psi angles by 1-2 degrees/2 kbar is estimated. On average, shifts are larger for helical and loop regions (0.553 +/- 0.343 and 0.519 +/- 0.261 ppm/2 kbar, respectively) than for beta-sheet (0.295 +/- 0.195 ppm/2 kbar), suggesting that the pressure-induced structural changes (local compressibilities) are larger in helical and loop regions than in beta-sheet. Because compressibility is correlated with volume fluctuation, the result is taken to indicate that the volume fluctuation is larger in helical and loop regions than in beta-sheet. An important aspect of the volume fluctuation inferred from pressure shifts is that they include motions in slower time ranges (less than milliseconds) in which many biological processes may take place. PMID:10548039
Gallstones containing bacteria are biofilms: bacterial slime production and ability to form pigment solids determines infection severity and bacteremia.

PubMed

Stewart, Lygia; Griffiss, J McLeod; Jarvis, Gary A; Way, Lawrence W

2007-08-01

Gallstone bacteria provide a reservoir for biliary infections. Slime production facilitates adherence, whereas beta-glucuronidase and phospholipase generate colonization surface. These factors facilitate gallstone formation, but their influence on infection severity is unknown. Two hundred ninety-two patients were studied. Gallstones, bile, and blood (as applicable) were cultured. Bacteria were tested for beta-glucuronidase/phospholipase production and quantitative slime production. Infection severity was correlated with bacterial factors. Bacteria were present in 43% of cases, 13% with bacteremia. Severe infections correlated directly with beta-glucuronidase/phospholipase (55% with vs 13% without, P < 0.0001), but inversely with slime production (55 vs 8%, slime <75 or >75, P = 0.008). Low slime production and beta-glucuronidase/phospholipase production were additive: Severe infections were present in 76% with both, but 10% with either or none (P < 0.0001). beta-Glucuronidase/phospholipase production facilitated bactibilia (86% with vs 62% without, P = 0.03). Slime production was 19 (+/-8) vs 50 (+/-10) for bacteria that did or did not cause bacteremia (P = 0.004). No bacteria with slime >75 demonstrated bacteremia. Bacteria-laden gallstones are biofilms whose characteristics influence illness severity. Factors creating colonization surface (beta-glucuronidase/phospholipase) facilitated bacteremia and severe infections; but abundant slime production, while facilitating colonization, inhibited detachment and cholangiovenous reflux. This shows how properties of the gallstone biofilm determine the severity of the associated illness.
Beta-propellers: associated functions and their role in human diseases.

PubMed

Pons, Tirso; Gómez, Raú; Chinea, Glay; Valencia, Alfonso

2003-03-01

The beta-propeller fold appears as a very fascinating architecture based on four-stranded antiparallel and twisted beta-sheets, radially arranged around a central tunnel. Similar to the alpha/beta-barrel (TIM-barrel) fold, the beta-propeller has a wide range of different functions, and is gaining substantial attention. Some proteins containing beta-propeller domains have been implicated in the pathogenesis of a variety of diseases such as cancer, Alzheimer, Huntington, arthritis, familial hypercholesterolemia, retinitis pigmentosa, osteogenesis, hypertension, and microbial and viral infections. This article reviews some aspects of 3D structure, amino acids sequence regularities, and biological functions of the proteins containing beta-propeller domains. Major emphasis has been laid on beta-propellers whose functions are associated to human diseases. Recent research efforts reported in the fields of protein engineering, drug design, and protein structure-function relationship studies, concerning the beta-propeller architecture, have also been discussed.
Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis.

PubMed

Han, S; Arvai, A S; Clancy, S B; Tainer, J A

2001-01-05

Clostridium botulinum C3 exoenzyme inactivates the small GTP-binding protein family Rho by ADP-ribosylating asparagine 41, which depolymerizes the actin cytoskeleton. C3 thus represents a major family of the bacterial toxins that transfer the ADP-ribose moiety of NAD to specific amino acids in acceptor proteins to modify key biological activities in eukaryotic cells, including protein synthesis, differentiation, transformation, and intracellular signaling. The 1.7 A resolution C3 exoenzyme structure establishes the conserved features of the core NAD-binding beta-sandwich fold with other ADP-ribosylating toxins despite little sequence conservation. Importantly, the central core of the C3 exoenzyme structure is distinguished by the absence of an active site loop observed in many other ADP-ribosylating toxins. Unlike the ADP-ribosylating toxins that possess the active site loop near the central core, the C3 exoenzyme replaces the active site loop with an alpha-helix, alpha3. Moreover, structural and sequence similarities with the catalytic domain of vegetative insecticidal protein 2 (VIP2), an actin ADP-ribosyltransferase, unexpectedly implicates two adjacent, protruding turns, which join beta5 and beta6 of the toxin core fold, as a novel recognition specificity motif for this newly defined toxin family. Turn 1 evidently positions the solvent-exposed, aromatic side-chain of Phe209 to interact with the hydrophobic region of Rho adjacent to its GTP-binding site. Turn 2 evidently both places the Gln212 side-chain for hydrogen bonding to recognize Rho Asn41 for nucleophilic attack on the anomeric carbon of NAD ribose and holds the key Glu214 catalytic side-chain in the adjacent catalytic pocket. This proposed bipartite ADP-ribosylating toxin turn-turn (ARTT) motif places the VIP2 and C3 toxin classes into a single ARTT family characterized by analogous target protein recognition via turn 1 aromatic and turn 2 hydrogen-bonding side-chain moieties. Turn 2 centrally anchors the catalytic Glu214 within the ARTT motif, and furthermore distinguishes the C3 toxin class by a conserved turn 2 Gln and the VIP2 binary toxin class by a conserved turn 2 Glu for appropriate target side-chain hydrogen-bonding recognition. Taken together, these structural results provide a molecular basis for understanding the coupled activity and recognition specificity for C3 and for the newly defined ARTT toxin family, which acts in the depolymerization of the actin cytoskeleton. This beta5 to beta6 region of the toxin fold represents an experimentally testable and potentially general recognition motif region for other ADP-ribosylating toxins that have a similar beta-structure framework. Copyright 2001 Academic Press.
Possible participation of transient sheets of 1. -->. 4-. beta. -glucans in the biosynthesis of cellulose I. [Acetobacter xylinum

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

Colvin, J.R.

1983-01-01

It is suggested that a primary, essential stage in the biologic formation of a microfibril of cellulose I is an extracellular, lateral association of presynthesized (1..-->..4)-..beta..-D-glucans, by hydrogen bonding, to form long, thin sheets. These sheets then superimpose themselves nonenzymatically by London forces to form the nascent microfibril. The ends of the constituent glucans of the nascent microfibril may undergo extension or rearrangement of the type indicated by Maclachlan and colleagues. The formation of the metastable, native structure (cellulose I) may be deduced from the above suggestion as a natural consequence of closest packing of the sheets. The irreversibility ofmore » the change from cellulose I to cellulose II, either by mercerization or regeneration, also follows from the postulate. The suggestion also explains why cellulose microfibrils and chitin microfibrils may be formed contiguously in cell walls without interfering with each other. High-resolution electron micrographs of the tips of newly formed microfibrils of bacterial cellulose which had been very lightly negatively stained with sodium phosphotungstate are consistent with the suggestion. 33 references, 3 figures.« less
Pain-Related Suppression of Beta Oscillations Facilitates Voluntary Movement.

PubMed

Misra, Gaurav; Ofori, Edward; Chung, Jae Woo; Coombes, Stephen A

2017-04-01

Increased beta oscillations over sensorimotor cortex are antikinetic. Motor- and pain-related processes separately suppress beta oscillations over sensorimotor cortex leading to the prediction that ongoing pain should facilitate movement. In the current study, we used a paradigm in which voluntary movements were executed during an ongoing pain-eliciting stimulus to test the hypothesis that a pain-related suppression of beta oscillations would facilitate the initiation of a subsequent voluntary movement. Using kinematic measures, electromyography, and high-density electroencephalography, we demonstrate that ongoing pain leads to shorter reaction times without affecting the kinematics or accuracy of movement. Reaction time was positively correlated with beta power prior to movement in contralateral premotor areas. Our findings corroborate the view that beta-band oscillations are antikinetic and provide new evidence that pain primes the motor system for action. Our observations provide the first evidence that a pain-related suppression of beta oscillations over contralateral premotor areas leads to shorter reaction times for voluntary movement. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Involvement of estrogen receptor alpha, beta and oxytocin in social discrimination: A detailed behavioral analysis with knockout female mice.

PubMed

Choleris, E; Ogawa, S; Kavaliers, M; Gustafsson, J-A; Korach, K S; Muglia, L J; Pfaff, D W

2006-10-01

Social recognition, processing, and retaining information about conspecific individuals is crucial for the development of normal social relationships. The neuropeptide oxytocin (OT) is necessary for social recognition in male and female mice, with its effects being modulated by estrogens in females. In previous studies, mice whose genes for the estrogen receptor-alpha (alpha-ERKO) and estrogen receptor-beta (beta-ERKO) as well as OTKO were knocked out failed to habituate to a repeatedly presented conspecific and to dishabituate when the familiar mouse is replaced by a novel animal (Choleris et al. 2003, Proc Natl Acad Sci USA 100, 6192-6197). However, a binary social discrimination assay, where animals are given a simultaneous choice between a familiar and a previously unknown individual, offers a more direct test of social recognition. Here, we used alpha-ERKO, beta-ERKO, and OTKO female mice in the binary social discrimination paradigm. Differently from their wild-type controls, when given a choice, the KO mice showed either reduced (beta-ERKO) or completely impaired (OTKO and alpha-ERKO) social discrimination. Detailed behavioral analyses indicate that all of the KO mice have reduced anxiety-related stretched approaches to the social stimulus with no overall impairment in horizontal and vertical activity, non-social investigation, and various other behaviors such as, self-grooming, digging, and inactivity. Therefore, the OT, ER-alpha, and ER-beta genes are necessary, to different degrees, for social discrimination and, thus, for the modulation of social behavior (e.g. aggression, affiliation).
Implementation and application of an interactive user-friendly validation software for RADIANCE

NASA Astrophysics Data System (ADS)

Sundaram, Anand; Boonn, William W.; Kim, Woojin; Cook, Tessa S.

2012-02-01

RADIANCE extracts CT dose parameters from dose sheets using optical character recognition and stores the data in a relational database. To facilitate validation of RADIANCE's performance, a simple user interface was initially implemented and about 300 records were evaluated. Here, we extend this interface to achieve a wider variety of functions and perform a larger-scale validation. The validator uses some data from the RADIANCE database to prepopulate quality-testing fields, such as correspondence between calculated and reported total dose-length product. The interface also displays relevant parameters from the DICOM headers. A total of 5,098 dose sheets were used to test the performance accuracy of RADIANCE in dose data extraction. Several search criteria were implemented. All records were searchable by accession number, study date, or dose parameters beyond chosen thresholds. Validated records were searchable according to additional criteria from validation inputs. An error rate of 0.303% was demonstrated in the validation. Dose monitoring is increasingly important and RADIANCE provides an open-source solution with a high level of accuracy. The RADIANCE validator has been updated to enable users to test the integrity of their installation and verify that their dose monitoring is accurate and effective.
Solution structure and interactions of the Escherichia coli cell division activator protein CedA.

PubMed

Chen, Ho An; Simpson, Peter; Huyton, Trevor; Roper, David; Matthews, Stephen

2005-05-10

CedA is a protein that is postulated to be involved in the regulation of cell division in Escherichia coli and related organisms; however, little biological data about its possible mode of action are available. Here we present a three-dimensional structure of this protein as determined by NMR spectroscopy. The protein is made up of four antiparallel beta-strands, an alpha-helix, and a large unstructured stretch of residues at the N-terminus. It shows structural similarity to a family of DNA-binding proteins which interact with dsDNA via a three-stranded beta-sheet, suggesting that CedA may be a DNA-binding protein. The putative binding surface of CedA is predominantly positively charged with a number of basic residues surrounding a groove largely dominated by aromatic residues. NMR chemical shift perturbations and gel-shift experiments performed with CedA confirm that the protein binds dsDNA, and its interaction is mediated primarily via the beta-sheet.
ATP-induced noncooperative thermal unfolding of hen lysozyme

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

Liu, Honglin; Yin, Peidong; He, Shengnan

To understand the role of ATP underlying the enhanced amyloidosis of hen egg white lysozyme (HEWL), the synchrotron radiation circular dichroism, combined with tryptophan fluorescence, dynamic light-scattering, and differential scanning calorimetry, is used to examine the alterations of the conformation and thermal unfolding pathway of the HEWL in the presence of ATP, Mg{sup 2+}-ATP, ADP, AMP, etc. It is revealed that the binding of ATP to HEWL through strong electrostatic interaction changes the secondary structures of HEWL and makes the exposed residue W62 move into hydrophobic environments. This alteration of W62 decreases the {beta}-domain stability of HEWL, induces a noncooperativemore » unfolding of the secondary structures, and produces a partially unfolded intermediate. This intermediate containing relatively rich {alpha}-helix and less {beta}-sheet structures has a great tendency to aggregate. The results imply that the ease of aggregating of HEWL is related to the extent of denaturation of the amyloidogenic region, rather than the electrostatic neutralizing effect or monomeric {beta}-sheet enriched intermediate.« less
Amino Acid Distribution Rules Predict Protein Fold: Protein Grammar for Beta-Strand Sandwich-Like Structures

PubMed Central

Kister, Alexander

2015-01-01

We present an alternative approach to protein 3D folding prediction based on determination of rules that specify distribution of “favorable” residues, that are mainly responsible for a given fold formation, and “unfavorable” residues, that are incompatible with that fold, in polypeptide sequences. The process of determining favorable and unfavorable residues is iterative. The starting assumptions are based on the general principles of protein structure formation as well as structural features peculiar to a protein fold under investigation. The initial assumptions are tested one-by-one for a set of all known proteins with a given structure. The assumption is accepted as a “rule of amino acid distribution” for the protein fold if it holds true for all, or near all, structures. If the assumption is not accepted as a rule, it can be modified to better fit the data and then tested again in the next step of the iterative search algorithm, or rejected. We determined the set of amino acid distribution rules for a large group of beta sandwich-like proteins characterized by a specific arrangement of strands in two beta sheets. It was shown that this set of rules is highly sensitive (~90%) and very specific (~99%) for identifying sequences of proteins with specified beta sandwich fold structure. The advantage of the proposed approach is that it does not require that query proteins have a high degree of homology to proteins with known structure. So long as the query protein satisfies residue distribution rules, it can be confidently assigned to its respective protein fold. Another advantage of our approach is that it allows for a better understanding of which residues play an essential role in protein fold formation. It may, therefore, facilitate rational protein engineering design. PMID:25625198
Characterization of arrangement and expression of the beta-2 microglobulin locus in the sandbar and nurse shark.

PubMed

Chen, Hao; Kshirsagar, Sarika; Jensen, Ingvill; Lau, Kevin; Simonson, Caitlin; Schluter, Samuel F

2010-02-01

Beta 2 microglobulin (beta2m) is an essential subunit of major histocompatibility complex (MHC) type I molecules. In this report, beta2m cDNAs were identified and sequenced from sandbar shark spleen cDNA library. Sandbar shark beta2m gene encodes one amino acid less than most teleost beta2m genes, and 3 amino acids less than mammal beta2m genes. Although sandbar shark beta2m protein contains one beta sheet less than that of human in the predicted protein structure, the overall structure of beta2m proteins is conserved during evolution. Germline gene for the beta2m in sandbar and nurse shark is present as a single locus. It contains three exons and two introns. CpG sites are evenly distributed in the shark beta2m loci. Several DNA repeat elements were also identified in the shark beta2m loci. Sequence analysis suggests that the beta2m locus is not linked to the MHC I loci in the shark genome.
Dispatcher Recognition of Stroke Using the National Academy Medical Priority Dispatch System

PubMed Central

Buck, Brian H; Starkman, Sidney; Eckstein, Marc; Kidwell, Chelsea S; Haines, Jill; Huang, Rainy; Colby, Daniel; Saver, Jeffrey L

2009-01-01

Background Emergency Medical Dispatchers (EMDs) play an important role in optimizing stroke care if they are able to accurately identify calls regarding acute cerebrovascular disease. This study was undertaken to assess the diagnostic accuracy of the current national protocol guiding dispatcher questioning of 911 callers to identify stroke, QA Guide v 11.1 of the National Academy Medical Priority Dispatch System (MPDS). Methods We identified all Los Angeles Fire Department paramedic transports of patients to UCLA Medical Center during the 12 month period from January to December 2005 in a prospectively maintained database. Dispatcher-assigned MPDS codes for each of these patient transports were abstracted from the paramedic run sheets and compared to final hospital discharge diagnosis. Results Among 3474 transported patients, 96 (2.8%) had a final diagnosis of stroke or transient ischemic attack. Dispatchers assigned a code of potential stroke to 44.8% of patients with a final discharge diagnosis of stroke or TIA. Dispatcher identification of stroke showed a sensitivity of 0.41, specificity of 0.96, positive predictive value of 0.45, and negative predictive value of 0.95. Conclusions Dispatcher recognition of stroke calls using the widely employed MPDS algorithm is suboptimal, with failure to identify more than half of stroke patients as likely stroke. Revisions to the current national dispatcher structured interview and complaint identification algorithm for stroke may facilitate more accurate recognition of stroke by EMDs. PMID:19390065
Wnt/beta-catenin pathway activation and myogenic differentiation are induced by cholesterol depletion.

PubMed

Mermelstein, Cláudia S; Portilho, Débora M; Mendes, Fábio A; Costa, Manoel L; Abreu, José Garcia

2007-03-01

Myogenic differentiation is a multistep process that begins with the commitment of mononucleated precursors that withdraw from cell cycle. These myoblasts elongate while aligning to each other, guided by the recognition between their membranes. This step is followed by cell fusion and the formation of long and striated multinucleated myotubes. We have recently shown that cholesterol depletion by methyl-beta-cyclodextrin (MbetaCD) induces myogenic differentiation by enhancing myoblast recognition and fusion. Here, we further studied the signaling pathways responsible for early steps of myogenesis. As it is known that Wnt plays a role in muscle differentiation, we used the chemical MbetaCD to deplete membrane cholesterol and investigate the involvement of the Wnt/beta-catenin pathway during myogenesis. We show that cholesterol depletion promoted a significant increase in expression of beta-catenin, its nuclear translocation and activation of the Wnt pathway. Moreover, we show that the activation of the Wnt pathway after cholesterol depletion can be inhibited by the soluble protein Frzb-1. Our data suggest that membrane cholesterol is involved in Wnt/beta-catenin signaling in the early steps of myogenic differentiation.
Yeast prion architecture explains how proteins can be genes

NASA Astrophysics Data System (ADS)

Wickner, Reed

2013-03-01

Prions (infectious proteins) transmit information without an accompanying DNA or RNA. Most yeast prions are self-propagating amyloids that inactivate a normally functional protein. A single protein can become any of several prion variants, with different manifestations due to different amyloid structures. We showed that the yeast prion amyloids of Ure2p, Sup35p and Rnq1p are folded in-register parallel beta sheets using solid state NMR dipolar recoupling experiments, mass-per-filament-length measurements, and filament diameter measurements. The extent of beta sheet structure, measured by chemical shifts in solid-state NMR and acquired protease-resistance on amyloid formation, combined with the measured filament diameters, imply that the beta sheets must be folded along the long axis of the filament. We speculate that prion variants of a single protein sequence differ in the location of these folds. Favorable interactions between identical side chains must hold these structures in-register. The same interactions must guide an unstructured monomer joining the end of a filament to assume the same conformation as molecules already in the filament, with the turns at the same locations. In this way, a protein can template its own conformation, in analogy to the ability of a DNA molecule to template its sequence by specific base-pairing. Bldg. 8, Room 225, NIH, 8 Center Drive MSC 0830, Bethesda, MD 20892-0830, wickner@helix.nih.gov, 301-496-3452
Estradiol prevents ozone-induced increases in brain lipid peroxidation and impaired social recognition memory in female rats.

PubMed

Guevara-Guzmán, R; Arriaga, V; Kendrick, K M; Bernal, C; Vega, X; Mercado-Gómez, O F; Rivas-Arancibia, S

2009-03-31

There is increasing concern about the neurodegenerative and behavioral consequences of ozone pollution in industrialized urban centers throughout the world and that women may be more susceptible to brain neurodegenerative disorders. In the present study we have investigated the effects of chronic (30 or 60 days) exposure to ozone on olfactory perception and memory and on levels of lipid peroxidation, alpha and beta estrogen receptors and dopamine beta-hydroxylase in the olfactory bulb in ovariectomized female rats. The ability of 17beta-estradiol to prevent these effects was then assessed. Results showed that ozone exposure for 30 or 60 days impaired formation/retention of a selective olfactory recognition memory 120 min after exposure to a juvenile stimulus animal with the effect at 60 days being significantly greater than at 30 days. They also showed impaired speed in locating a buried chocolate reward after 60 days of ozone exposure indicating some loss of olfactory perception. These functional impairments could all be prevented by coincident estradiol treatment. In the olfactory bulb, levels of lipid peroxidation were increased at both 30- and 60-day time-points and numbers of cells with immunohistochemical staining for alpha and beta estrogen receptors, and dopamine beta-hydroxylase were reduced as were alpha and beta estrogen receptor protein levels. These effects were prevented by estradiol treatment. Oxidative stress damage caused by chronic exposure to ozone does therefore impair olfactory perception and social recognition memory and may do so by reducing noradrenergic and estrogen receptor activity in the olfactory bulb. That these effects can be prevented by estradiol treatment suggests increased susceptibility to neurodegenerative disorders in aging women may be contributed to by reduced estrogen levels post-menopause.
Current and high-β sheets in CIR streams: statistics and interaction with the HCS and the magnetosphere

NASA Astrophysics Data System (ADS)

Potapov, A. S.

2018-04-01

Thirty events of CIR streams (corotating interaction regions between fast and slow solar wind) were analyzed in order to study statistically plasma structure within the CIR shear zones and to examine the interaction of the CIRs with the heliospheric current sheet (HCS) and the Earth's magnetosphere. The occurrence of current layers and high-beta plasma sheets in the CIR structure has been estimated. It was found that on average, each of the CIR streams had four current layers in its structure with a current density of more than 0.12 A/m2 and about one and a half high-beta plasma regions with a beta value of more than five. Then we traced how and how often the high-speed stream associated with the CIR can catch up with the heliospheric current sheet (HCS) and connect to it. The interface of each fourth CIR stream coincided in time within an hour with the HCS, but in two thirds of cases, the CIR connection with the HCS was completely absent. One event of the simultaneous observation of the CIR stream in front of the magnetosphere by the ACE satellite in the vicinity of the L1 libration point and the Wind satellite in the remote geomagnetic tail was considered in detail. Measurements of the components of the interplanetary magnetic field and plasma parameters showed that the overall structure of the stream is conserved. Moreover, some details of the fine structure are also transferred through the magnetosphere. In particular, the so-called "magnetic hole" almost does not change its shape when moving from L1 point to a neighborhood of L2 point.
Protein Secondary Structures (alpha-helix and beta-sheet) at a Cellular Levle and Protein Fractions in Relation to Rumen Degradation Behaviours of Protein: A New Approach

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

Yu,P.

2007-01-01

Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the {alpha}-helix and {beta}-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of {beta}-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present studymore » were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution ({approx}10 {mu}m). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of {alpha}-helixes and {beta}-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of {alpha}-helixes (from 47.1% to 36.1%: S-FTIR absorption intensity), increased the percentage of {beta}-sheets (from 37.2% to 49.8%: S-FTIR absorption intensity) and reduced the {alpha}-helix to {beta}-sheet ratio (from 0.3 to 0.7) in the golden flaxseeds, which indicated a negative effect of the roasting on protein values, utilisation and bioavailability. These results were proved by the Cornell Net Carbohydrate Protein System in situ animal trial, which also revealed that roasting increased the amount of protein bound to lignin, and well as of the Maillard reaction protein (both of which are poorly used by ruminants), and increased the level of indigestible and undegradable protein in ruminants. The present results demonstrate the potential of highly spatially resolved synchrotron-based infrared microspectroscopy to locate 'pure' protein in feed tissues, and reveal protein secondary structures and digestive behaviour, making a significant step forward in and an important contribution to protein nutritional research. Further study is needed to determine the sensitivities of protein secondary structures to various heat-processing conditions, and to quantify the relationship between protein secondary structures and the nutrient availability and digestive behaviour of various protein sources. Information from the present study arising from the synchrotron-based IR probing of the protein secondary structures of protein sources at the cellular level will be valuable as a guide to maintaining protein quality and predicting digestive behaviours.« less
Crystal Structures of T Cell Receptor (Beta) Chains Related to Rheumatoid Arthritis

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

Li,H.; van Vranken, S.; Zhao, Y.

The crystal structures of the V{beta}17+ {beta} chains of two human T cell receptors (TCRs), originally derived from the synovial fluid (SF4) and tissue (C5-1) of a patient with rheumatoid arthritis (RA), have been determined in native (SF4) and mutant (C5-1{sub F104{yields}Y/C187{yields}S}) forms, respectively. These TCR {beta} chains form homo-dimers in solution and in crystals. Structural comparison reveals that the main-chain conformations in the CDR regions of the C5-1 and SF4 V{beta}17 closely resemble those of a V{beta}17 JM22 in a bound form; however, the CDR3 region shows different conformations among these three V{beta}17 structures. At the side-chain level, conformationalmore » differences were observed at the CDR2 regions between our two ligand-free forms and the bound JM22 form. Other significant differences were observed at the V{beta} regions 8-12, 40-44, and 82-88 between C5-1/SF4 and JM22 V{beta}17, implying that there is considerable variability in the structures of very similar {beta} chains. Structural alignments also reveal a considerable variation in the V{beta}-C{beta} associations, and this may affect ligand recognition. The crystal structures also provide insights into the structure basis of T cell recognition of Mycoplasma arthritidis mitogen (MAM), a superantigen that may be implicated in the development of human RA. Structural comparisons of the V{beta} domains of known TCR structures indicate that there are significant similarities among V{beta} regions that are MAM-reactive, whereas there appear to be significant structural differences among those V{beta} regions that lack MAM-reactivity. It further reveals that CDR2 and framework region (FR) 3 are likely to account for the binding of TCR to MAM.« less
The evaluation of a mental health facilitator in general practice: effects on recognition, management, and outcome of mental illness.

PubMed

Bashir, K; Blizard, B; Bosanquet, A; Bosanquet, N; Mann, A; Jenkins, R

2000-08-01

Facilitation uses personal contact between the facilitator and the professional to encourage good practice and better service organisation. The model has been applied to physical illness but not to psychiatric disorders. To determine if a non-specialist facilitator can improve the recognition, management, and outcome of psychiatric illness presenting to general practitioners (GPs). Six practices were visited over an 18-month period by a facilitator whose activities included providing guidelines and organising training initiatives. Six other practices acted as controls. Recognition (identification index of family doctors), management (psychotropic prescribing, psychological consultations with the GP, specialist mental health treatment, and the use of medical interventions and investigations), and patient outcome at four months were assessed before and after intervention. The mean identification index of facilitator GPs rose from 0.51 to 0.64 following intervention, while that of the control GPs fell from 0.67 to 0.59 (P = 0.046). The facilitator had no detectable effect on management or patient outcome. The facilitator improved recognition of psychiatric illness by GPs. Generic facilitators can be trained to take on a mental health role; however, the failure to achieve more fundamental changes in treatment and outcome implies that facilitator intervention requires development.
A comparative evaluation of laser and GTA welds in a high-strength titanium alloy -- Ti-6-22-22S

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

Baeslack, W.A. III; Hurley, J.; Paskell, T.

1994-12-31

Titanium alloy Ti-6Al-2Sn-2Zr-2Mo-2Cr-025Si (hereafter designated Ti-6-22-22S)is an alpha-beta titanium alloy developed for deep hardenability, high strength, intermediate temperature creep resistance, and moderate toughness. As a potential structural material for next-generation aircraft and aerospace systems, the weldability of Ti-6-22-22S has recently become a subject of increasing importance and concern. In the welding of titanium sheet, achieving satisfactory ductility is the principal limitation to alloy weldability, with poor ductility promoted by a coarse beta grain structure in the weld fusion and near-heat-affected zones. Square-butt welds were produced in 1.6 mm thick Ti-6-22-22S sheet using automatic GTA and CO{sub 2} laser welding systems.more » Microstructure analysis and DPH hardness traverses were performed on mounted. polished and etched specimens. Three-point bend and tensile tests were performed on transverse-weld and longitudinal-weld oriented specimens. Microstructure analysis of the laser welds revealed a fine, columnar fusion zone beta grain macrostructure and a fully-martensitic transformed-beta microstructure. Consistent with the microstructural similarities, fusion zone hardnesses of the laser welds were comparable (385 and 390 DPG, respectively) and greater than that of the base metal (330 DPH). In general, laser welds did not exhibit markedly superior ductilities relative to the GTAW, which was attributed to differences in the nature of the intragranular transformed-beta microstructures, being coarser and softer for the GTAW, the response of these as-welded microstructures to heat treatment, and interactions between the transformed-beta microstructure and the beta grain macrostructure.« less
Ternary Aligned Nanofibers of RGD Peptide-Displaying M13 Bacteriophage/PLGA/Graphene Oxide for Facilitated Myogenesis

PubMed Central

Shin, Yong Cheol; Kim, Chuntae; Song, Su-Jin; Jun, Seungwon; Kim, Chang-Seok; Hong, Suck Won; Hyon, Suong-Hyu; Han, Dong-Wook; Oh, Jin-Woo

2018-01-01

Recently, there have been tremendous efforts to develop the biofunctional scaffolds by incorporating various biochemical factors. In the present study, we fabricated poly(lactic-co-glycolic acid) (PLGA) nanofiber sheets decorated with graphene oxide (GO) and RGD peptide. The decoration of GO and RGD peptide was readily achieved by using RGD peptide-displaying M13 bacteriophage (RGD-M13 phage) and electrospinning. Furthermore, the aligned GO-decorated PLGA/RGD peptide (GO-PLGA/RGD) ternary nanofiber sheets were prepared by magnetic field-assisted electrospinning, and their potentials as bifunctional scaffolds for facilitating myogenesis were explored. We characterized the physicochemical and mechanical properties of the sheets by scanning electron microscopy, Raman spectroscopy, contact angle measurement, and tensile test. In addition, the C2C12 skeletal myoblasts were cultured on the aligned GO-PLGA/RGD nanofiber sheets, and their cellular behaviors, including initial attachment, proliferation and myogenic differentiation, were evaluated. Our results revealed that the GO-PLGA/RGD nanofiber sheets had suitable physicochemical and mechanical properties for supporting cell growth, and could significantly promote the spontaneous myogenic differentiation of C2C12 skeletal myoblasts. Moreover, it was revealed that the myogenic differentiation was further accelerated on the aligned GO-PLGA/RGD nanofiber sheets due to the synergistic effects of RGD peptide, GO and aligned nanofiber structure. Therefore, , it is suggested that the aligned GO-PLGA/RGD ternary nanofiber sheets are one of the most promising approaches for facilitating myogenesis and promoting skeletal tissue regeneration. PMID:29577018
Ternary Aligned Nanofibers of RGD Peptide-Displaying M13 Bacteriophage/PLGA/Graphene Oxide for Facilitated Myogenesis.

PubMed

Shin, Yong Cheol; Kim, Chuntae; Song, Su-Jin; Jun, Seungwon; Kim, Chang-Seok; Hong, Suck Won; Hyon, Suong-Hyu; Han, Dong-Wook; Oh, Jin-Woo

2018-01-01

Recently, there have been tremendous efforts to develop the biofunctional scaffolds by incorporating various biochemical factors. In the present study, we fabricated poly(lactic- co -glycolic acid) (PLGA) nanofiber sheets decorated with graphene oxide (GO) and RGD peptide. The decoration of GO and RGD peptide was readily achieved by using RGD peptide-displaying M13 bacteriophage (RGD-M13 phage) and electrospinning. Furthermore, the aligned GO-decorated PLGA/RGD peptide (GO-PLGA/RGD) ternary nanofiber sheets were prepared by magnetic field-assisted electrospinning, and their potentials as bifunctional scaffolds for facilitating myogenesis were explored. We characterized the physicochemical and mechanical properties of the sheets by scanning electron microscopy, Raman spectroscopy, contact angle measurement, and tensile test. In addition, the C2C12 skeletal myoblasts were cultured on the aligned GO-PLGA/RGD nanofiber sheets, and their cellular behaviors, including initial attachment, proliferation and myogenic differentiation, were evaluated. Our results revealed that the GO-PLGA/RGD nanofiber sheets had suitable physicochemical and mechanical properties for supporting cell growth, and could significantly promote the spontaneous myogenic differentiation of C2C12 skeletal myoblasts. Moreover, it was revealed that the myogenic differentiation was further accelerated on the aligned GO-PLGA/RGD nanofiber sheets due to the synergistic effects of RGD peptide, GO and aligned nanofiber structure. Therefore, , it is suggested that the aligned GO-PLGA/RGD ternary nanofiber sheets are one of the most promising approaches for facilitating myogenesis and promoting skeletal tissue regeneration.
Learning From Tests: Facilitation of Delayed Recall by Initial Recognition Alternatives.

ERIC Educational Resources Information Center

Whitten, William B., II; Leonard, Janet Mauriello

1980-01-01

Two experiments were designed to determine the effects of multiple-choice recognition test alternatives on subsequent memory for the correct answers. Results of both experiments are interpreted as demonstrations of the principle that long-term retention is facilitated such that memory evaluation occurs during initial recognition tests. (Author/RD)
DOE Office of Scientific and Technical Information (OSTI.GOV)

Okada, Shoko; Weisman, Sarah; Trueman, Holly E.

Aposthonia gurneyi, an Australian webspinner species, is a primitive insect that constructs and lives in a silken tunnel which screens it from the attentions of predators. The insect spins silk threads from many tiny spines on its forelegs to weave a filmy sheet. We found that the webspinner silk fibers have a mean diameter of only 65 nm, an order of magnitude smaller than any previously reported insect silk. The purpose of such fine silk may be to reduce the metabolic cost of building the extensive tunnels. At the molecular level, the A. gurneyi silk has a predominantly beta-sheet proteinmore » structure. The most abundant clone in a cDNA library produced from the webspinner silk glands encoded a protein with extensive glycine-serine repeat regions. The GSGSGS repeat motif of the A. gurneyi silk protein is similar to the well-known GAGAGS repeat motif found in the heavy fibroin of silkworm silk, which also has beta-sheet structure. As the webspinner silk gene is unrelated to the silk gene of the phylogenetically distant silkworm, this is a striking example of convergent evolution.« less
Role of IL-1 beta and 5-HT2 receptors in midbrain periaqueductal gray (PAG) in potentiating defensive rage behavior in cat.

PubMed

Bhatt, Suresh; Bhatt, Rekha; Zalcman, Steven S; Siegel, Allan

2008-02-01

Feline defensive rage, a form of aggressive behavior that occurs in response to a threat can be elicited by electrical stimulation of the medial hypothalamus or midbrain periaqueductal gray (PAG). Our laboratory has recently begun a systematic examination of the role of cytokines in the regulation of rage and aggressive behavior. It was shown that the cytokine, interleukin-2 (IL-2), differentially modulates defensive rage when microinjected into the medial hypothalamus and PAG by acting through separate neurotransmitter systems. The present study sought to determine whether a similar relationship exists with respect to interleukin 1-beta (IL-1 beta), whose receptor activation in the medial hypothalamus potentiates defensive rage. Thus, the present study identified the effects of administration of IL-1 beta into the PAG upon defensive rage elicited from the medial hypothalamus. Microinjections of IL-1 beta into the dorsal PAG significantly facilitated defensive rage behavior elicited from the medial hypothalamus in a dose and time dependent manner. In addition, the facilitative effects of IL-1 beta were blocked by pre-treatment with anti-IL-1 beta receptor antibody, while IL-1 beta administration into the PAG had no effect upon predatory attack elicited from the lateral hypothalamus. The findings further demonstrated that IL-1 beta's effects were mediated through 5-HT(2) receptors since pretreatment with a 5-HT(2C) receptors antagonist blocked the facilitating effects of IL-1 beta. An extensive pattern of labeling of IL-1 beta and 5-HT(2C) receptors in the dorsal PAG supported these findings. The present study demonstrates that IL-beta in the dorsal PAG, similar to the medial hypothalamus, potentiates defensive rage behavior and is mediated through a 5-HT(2C) receptor mechanism.

Why S, Not X, Marks the Spot for CME/Flare Eruptions

NASA Technical Reports Server (NTRS)

Moore, Ronald L.; Sterling, Alphonse; Gary, Allen; Cirtain, Jonathan; Falconer, David

2010-01-01

For any major CME/flare eruption: I. The field that erupts is an arcade in which the interior is greatly sheared and twisted. Most of the free magnetic energy to be released: a) Is in the shear and twist of the interior field. b) Is Not due to a big current sheet. The eruption is unleashed by reconnection at a growing current sheet. The current sheet is still little when the reconnection turns on. The unleashed eruption then makes the current sheet much bigger by building it up faster than the reconnection can tear it down. II. Most X-ray jets work the opposite way: a) Tapped free energy is in the field of a pre-jet current sheet. b) Current sheet built by small arcade emerging into ambient field. c) Current sheet still much smaller than the arcade when reconnection turns on and tears it down, producing a jet. III. These rules reflect the low-beta condition in the eruptive magnetic field
REM sleep and emotional face memory in typically-developing children and children with autism.

PubMed

Tessier, Sophie; Lambert, Andréane; Scherzer, Peter; Jemel, Boutheina; Godbout, Roger

2015-09-01

Relationship between REM sleep and memory was assessed in 13 neurotypical and 13 children with Autistic Spectrum Disorder (ASD). A neutral/positive/negative face recognition task was administered the evening before (learning and immediate recognition) and the morning after (delayed recognition) sleep. The number of rapid eye movements (REMs), beta and theta EEG activity over the visual areas were measured during REM sleep. Compared to neurotypical children, children with ASD showed more theta activity and longer reaction time (RT) for correct responses in delayed recognition of neutral faces. Both groups showed a positive correlation between sleep and performance but different patterns emerged: in neurotypical children, accuracy for recalling neutral faces and overall RT improvement overnight was correlated with EEG activity and REMs; in children with ASD, overnight RT improvement for positive and negative faces correlated with theta and beta activity, respectively. These results suggest that neurotypical and children with ASD use different sleep-related brain networks to process faces. Copyright © 2015 Elsevier B.V. All rights reserved.
Topological switching between an alpha-beta parallel protein and a remarkably helical molten globule.

PubMed

Nabuurs, Sanne M; Westphal, Adrie H; aan den Toorn, Marije; Lindhoud, Simon; van Mierlo, Carlo P M

2009-06-17

Partially folded protein species transiently exist during folding of most proteins. Often these species are molten globules, which may be on- or off-pathway to native protein. Molten globules have a substantial amount of secondary structure but lack virtually all the tertiary side-chain packing characteristic of natively folded proteins. These ensembles of interconverting conformers are prone to aggregation and potentially play a role in numerous devastating pathologies, and thus attract considerable attention. The molten globule that is observed during folding of apoflavodoxin from Azotobacter vinelandii is off-pathway, as it has to unfold before native protein can be formed. Here we report that this species can be trapped under nativelike conditions by substituting amino acid residue F44 by Y44, allowing spectroscopic characterization of its conformation. Whereas native apoflavodoxin contains a parallel beta-sheet surrounded by alpha-helices (i.e., the flavodoxin-like or alpha-beta parallel topology), it is shown that the molten globule has a totally different topology: it is helical and contains no beta-sheet. The presence of this remarkably nonnative species shows that single polypeptide sequences can code for distinct folds that swap upon changing conditions. Topological switching between unrelated protein structures is likely a general phenomenon in the protein structure universe.
Time-resolved spectroscopy of dye-labeled photoactive yellow protein suggests a pathway of light-induced structural changes in the N-terminal cap.

PubMed

Hoersch, Daniel; Otto, Harald; Cusanovich, Michael A; Heyn, Maarten P

2009-07-14

The photoreceptor PYP responds to light activation with global conformational changes. These changes are mainly located in the N-terminal cap of the protein, which is approximately 20 A away from the chromophore binding pocket and separated from it by the central beta-sheet. The question of the propagation of the structural change across the central beta-sheet is of general interest for the superfamily of PAS domain proteins, for which PYP is the structural prototype. Here we measured the kinetics of the structural changes in the N-terminal cap by transient absorption spectroscopy on the ns to second timescale. For this purpose the cysteine mutants A5C and N13C were prepared and labeled with thiol reactive 5-iodoacetamidofluorescein (IAF). A5 is located close to the N-terminus, while N13 is part of helix alpha1 near the functionally important salt bridge E12-K110 between the N-terminal cap and the central anti-parallel beta-sheet. The absorption spectrum of the dye is sensitive to its environment, and serves as a sensor for conformational changes near the labeling site. In both labeled mutants light activation results in a transient red-shift of the fluorescein absorption spectrum. To correlate the conformational changes with the photocycle intermediates of the protein, we compared the kinetics of the transient absorption signal of the dye with that of the p-hydroxycinnamoyl chromophore. While the structural change near A5 is synchronized with the rise of the I(2) intermediate, which is formed in approximately 200 mus, the change near N13 is delayed and rises with the next intermediate I(2)', which forms in approximately 2 ms. This indicates that different parts of the N-terminal cap respond to light activation with different kinetics. For the signaling pathway of photoactive yellow protein we propose a model in which the structural signal propagates from the chromophore binding pocket across the central beta-sheet via the N-terminal region to helix alpha1, resulting in a large change in the protein conformation.
Catalytic growth and structural characterization of semiconducting beta-Ga2O3 nanowires.

PubMed

Choi, Kyo-Hong; Cho, Kwon-Koo; Kim, Ki-Won; Cho, Gyu-Bong; Ahn, Hyo-Jun; Nam, Tae-Hyun

2009-06-01

We have successfully synthesized beta-Ga2O3 nanomaterials with various morphologies, such as wire, rod, belt and sheet-like, through simple thermal evaporation of metal gallium powder in the presence of nickel oxide catalyst. beta-Ga2O3 nanomaterials with different morphology were observed as a function of synthesis time and temperature. In this report, generation sites of the beta-Ga2O3 nanomaterials have been delicately surveyed by FESEM. The growth mechanisms of nanomaterials are distinguished by the view of its generation site. The growth of nanowire follows both VLS and VS mechanism and other kinds of materials such as nanorod, nanobelt and nanosheet follows VS mechanism.
The Min Oscillator Uses MinD-Dependent Conformational Changes in MinE to Spatially Regulate Cytokinesis.

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

Park, Kyung-Tase; Wu, Wei; Battaile, Kevin P.

In E. coli, MinD recruits MinE to the membrane, leading to a coupled oscillation required for spatial regulation of the cytokinetic Z ring. How these proteins interact, however, is not clear because the MinD-binding regions of MinE are sequestered within a six-stranded {beta} sheet and masked by N-terminal helices. minE mutations that restore interaction between some MinD and MinE mutants were isolated. These mutations alter the MinE structure leading to release of the MinD-binding regions and the N-terminal helices that bind the membrane. Crystallization of MinD-MinE complexes revealed a four-stranded {beta} sheet MinE dimer with the released {beta} strands (MinD-bindingmore » regions) converted to {alpha} helices bound to MinD dimers. These results identify the MinD-dependent conformational changes in MinE that convert it from a latent to an active form and lead to a model of how MinE persists at the MinD-membrane surface.« less
Effects of beta-adrenergic antagonist, propranolol on spatial memory and exploratory behavior in mice.

PubMed

Sun, Huaying; Mao, Yu; Wang, Jianhong; Ma, Yuanye

2011-07-08

The beta-adrenergic system has been suggested to be involved in novelty detection and memory modulation. The present study aimed to investigate the role of beta-adrenergic receptors on novelty-based spatial recognition memory and exploratory behavior in mice using Y-maze test and open-field respectively. Mice were injected with three doses of beta-adrenergic receptor antagonist, propranolol (2, 10 and 20 mg/kg) or saline at three different time points (15 min prior to training, immediately after training and 15 min before test). The results showed that higher doses of propranolol (10 and 20 mg/kg) given before the training trial impaired spatial recognition memory while those injected at other two time points did not. A detailed analysis of exploratory behavior in open-field showed that lower dose (2 mg/kg) of propranolol reduced exploratory behavior of mice. Our findings indicate that higher dose of propranolol can impair acquisition of spatial information in the Y-maze without altering locomotion, suggesting that the beta-adrenergic system may be involved in modulating memory processes at the time of learning. Copyright © 2011. Published by Elsevier Ireland Ltd.
Chiral discrimination in cyclodextrin complexes of amino acid derivatives: beta-cyclodextrin/N-acetyl-L-phenylalanine and N-acetyl-D-phenylalanine complexes.

PubMed

Alexander, Jennifer M; Clark, Joanna L; Brett, Tom J; Stezowski, John J

2002-04-16

In a systematic study of molecular recognition of amino acid derivatives in solid-state beta-cyclodextrin (beta-CD) complexes, we have determined crystal structures for complexes of beta-cyclodextrin/N-acetyl-L-phenylalanine at 298 and 20 K and for N-acetyl-D-phenylalanine at 298 K. The crystal structures for the N-acetyl-L-phenylalanine complex present disordered inclusion complexes for which the distribution of guest molecules at room temperature is not resolvable; however, they can be located with considerable confidence at low temperature. In contrast, the complex with N-acetyl-D-phenylalanine is well ordered at room temperature. The latter complex presents an example of a complex in this series in which a water molecule is included deeply in the hydrophobic torus of the extended dimer host. In an effort to understand the mechanisms of molecular recognition giving rise to the dramatic differences in crystallographic order in these crystal structures, we have examined the intermolecular interactions in detail and have examined insertion of the enantiomer of the D-complex into the chiral beta-CD complex crystal lattice.
Binaural auditory beats affect long-term memory.

PubMed

Garcia-Argibay, Miguel; Santed, Miguel A; Reales, José M

2017-12-08

The presentation of two pure tones to each ear separately with a slight difference in their frequency results in the perception of a single tone that fluctuates in amplitude at a frequency that equals the difference of interaural frequencies. This perceptual phenomenon is known as binaural auditory beats, and it is thought to entrain electrocortical activity and enhance cognition functions such as attention and memory. The aim of this study was to determine the effect of binaural auditory beats on long-term memory. Participants (n = 32) were kept blind to the goal of the study and performed both the free recall and recognition tasks after being exposed to binaural auditory beats, either in the beta (20 Hz) or theta (5 Hz) frequency bands and white noise as a control condition. Exposure to beta-frequency binaural beats yielded a greater proportion of correctly recalled words and a higher sensitivity index d' in recognition tasks, while theta-frequency binaural-beat presentation lessened the number of correctly remembered words and the sensitivity index. On the other hand, we could not find differences in the conditional probability for recall given recognition between beta and theta frequencies and white noise, suggesting that the observed changes in recognition were due to the recollection component. These findings indicate that the presentation of binaural auditory beats can affect long-term memory both positively and negatively, depending on the frequency used.
Extension arm facilitated pegylation of alphaalpha-hemoglobin with modifications targeted exclusively to amino groups: functional and structural advantages of free Cys-93(beta) in the PEG-Hb adduct.

PubMed

Li, Dongxia; Hu, Tao; Manjula, Belur N; Acharya, Seetharama A

2009-11-01

Cys-93(beta) of hemoglobin (Hb) was reversibly protected as a mixed disulfide with thiopyridine during extension arm facilitated (EAF) PEGylation and its influence on the structural and functional properties of the EAF-PEG-Hb has been investigated. Avoiding PEGylation of Cys-93(beta) in the EAF-PEG-Hb lowers the level of perturbation of heme pocket, alpha1beta2 interface, autoxidation, heme loss, and the O(2) affinity, as compared to the EAF-PEG-Hb with PEGylation of Cys-93(beta).The structural and functional advantages of reversible protection of Cys-93(beta) during EAF PEGylation of oxy-Hb has been compared with Euro PEG-Hb generated by EAF PEGylation of deoxy Hb where Cys-93(beta) is free in the final product. The alphaalpha-fumaryl cross-linking and EAF PEGylation targeted exclusively to Lys residues has been combined together for generation of second-generation EAF-PEG-Hb with lower oxygen affinity. The PEG chains engineered on Lys as well as PEGylation of Cys-93(beta) independently contribute to the stabilization of oxy conformation of Hb and hence increase the oxygen affinity of Hb. However, oxygen affinity of the EAF-PEG-alphaalpha-Hb is more sensitive to the presence of PEGylation on Cys-93(beta) than that of the EAF-PEG-Hb. The present modified EAF PEGylation platform is expected to facilitate the design of novel versions of the EAF-PEG-Hbs that can now integrate the advantages of avoiding PEGylation of Cys-93(beta).
Two distinct β-sheet structures in Italian-mutant amyloid-beta fibrils: a potential link to different clinical phenotypes.

PubMed

Hubin, Ellen; Deroo, Stéphanie; Schierle, Gabriele Kaminksi; Kaminski, Clemens; Serpell, Louise; Subramaniam, Vinod; van Nuland, Nico; Broersen, Kerensa; Raussens, Vincent; Sarroukh, Rabia

2015-12-01

Most Alzheimer's disease (AD) cases are late-onset and characterized by the aggregation and deposition of the amyloid-beta (Aβ) peptide in extracellular plaques in the brain. However, a few rare and hereditary Aβ mutations, such as the Italian Glu22-to-Lys (E22K) mutation, guarantee the development of early-onset familial AD. This type of AD is associated with a younger age at disease onset, increased β-amyloid accumulation, and Aβ deposition in cerebral blood vessel walls, giving rise to cerebral amyloid angiopathy (CAA). It remains largely unknown how the Italian mutation results in the clinical phenotype that is characteristic of CAA. We therefore investigated how this single point mutation may affect the aggregation of Aβ1-42 in vitro and structurally characterized the resulting fibrils using a biophysical approach. This paper reports that wild-type and Italian-mutant Aβ both form fibrils characterized by the cross-β architecture, but with distinct β-sheet organizations, resulting in differences in thioflavin T fluorescence and solvent accessibility. E22K Aβ1-42 oligomers and fibrils both display an antiparallel β-sheet structure, in comparison with the parallel β-sheet structure of wild-type fibrils, characteristic of most amyloid fibrils described in the literature. Moreover, we demonstrate structural plasticity for Italian-mutant Aβ fibrils in a pH-dependent manner, in terms of their underlying β-sheet arrangement. These findings are of interest in the ongoing debate that (1) antiparallel β-sheet structure might represent a signature for toxicity, which could explain the higher toxicity reported for the Italian mutant, and that (2) fibril polymorphism might underlie differences in disease pathology and clinical manifestation.
Structure of the E2 DNA-binding domain from human papillomavirus serotype 31 at 2.4 A.

PubMed

Bussiere, D E; Kong, X; Egan, D A; Walter, K; Holzman, T F; Lindh, F; Robins, T; Giranda, V L

1998-11-01

The papillomaviruses are a family of small double-stranded DNA viruses which exclusively infect epithelial cells and stimulate the proliferation of those cells. A key protein within the papillomavirus life-cycle is known as the E2 (Early 2) protein and is responsible for regulating viral transcription from all viral promoters as well as for replication of the papillomavirus genome in tandem with another protein known as E1. The E2 protein itself consists of three functional domains: an N-terminal trans-activation domain, a proline-rich linker, and a C-terminal DNA-binding domain. The first crystal structure of the human papillomavirus, serotype 31 (HPV-31), E2 DNA-binding domain has been determined at 2.4 A resolution. The HPV DNA-binding domain monomer consists of two beta-alpha-beta repeats of approximately equal length and is arranged as to have an anti-parallel beta-sheet flanked by the two alpha-helices. The monomers form the functional in vivo dimer by association of the beta-sheets of each monomer so as to form an eight-stranded anti-parallel beta-barrel at the center of the dimer, with the alpha-helices lining the outside of the barrel. The overall structure of HVP-31 E2 DNA-binding domain is similar to both the bovine papillomavirus E2-binding domain and the Epstein-Barr nuclear antigen-1 DNA-binding domain.
Structural model of the amyloid fibril formed by beta(2)-microglobulin #21-31 fragment based on vibrational spectroscopy.

PubMed

Hiramatsu, Hirotsugu; Goto, Yuji; Naiki, Hironobu; Kitagawa, Teizo

2005-06-08

A structural model of amyloid fibril formed by the #21-31 fragment of beta2-microglobulin is proposed from microscope IR measurements on specifically 13C-labeled peptide fibrils and Raman spectra of the dispersed fibril solution. The 13C-shifted amide frequency indicated the secondary structure of the labeled residues. The IR spectra have demonstrated that the region between F22 and V27 forms the core part with the extended beta-sheet structure. Raman spectra indicated the formation of a dimer with a disulfide bridge between C25 residues.
A picture is worth a thousand words? Not when it comes to associative memory of older adults.

PubMed

Guez, Jonathan; Lev, Dror

2016-02-01

Properties of the binding mechanism in associative recognition were studied by examining the influence of the pictorial superiority effect on the age-related associative deficit. The informative aspect of associative recognition is the recollection of the pairing. Previous findings indicate that recollection is susceptible to aging and that pictorial presentation can enhance recollection and facilitate associative recognition. Pictorial presentation was found to facilitate item recognition by both young and older adults, associative recognition by young adults, but not associative recognition by older adults. Our findings support the hypothesis that the binding mechanism in associative recognition is content independent. Theoretical implications are discussed. (c) 2016 APA, all rights reserved).
L2 Gender Facilitation and Inhibition in Spoken Word Recognition

ERIC Educational Resources Information Center

Behney, Jennifer N.

2011-01-01

This dissertation investigates the role of grammatical gender facilitation and inhibition in second language (L2) learners' spoken word recognition. Native speakers of languages that have grammatical gender are sensitive to gender marking when hearing and recognizing a word. Gender facilitation refers to when a given noun that is preceded by an…
Semantic Ambiguity: Do Multiple Meanings Inhibit or Facilitate Word Recognition?

ERIC Educational Resources Information Center

Haro, Juan; Ferré, Pilar

2018-01-01

It is not clear whether multiple unrelated meanings inhibit or facilitate word recognition. Some studies have found a disadvantage for words having multiple meanings with respect to unambiguous words in lexical decision tasks (LDT), whereas several others have shown a facilitation for such words. In the present study, we argue that these…
Interaction of amino acids with the Au(111) surface: adsorption free energies from molecular dynamics simulations.

PubMed

Hoefling, Martin; Iori, Francesco; Corni, Stefano; Gottschalk, Kay-Eberhard

2010-06-01

Interactions of proteins with inorganic surfaces are of high importance in biological events and in modern biotechnological applications. Therefore, peptides have been engineered to recognize inorganic surfaces with high specificity. However, the underlying interactions are still not well understood. Here, we investigated the adsorption of amino acids as protein building blocks onto a Au(111) surface. In particular, using molecular dynamics simulations, we calculated the potential of mean force between all the 20 amino acids and the gold surface. We found a strong dependence of the binding affinities on the chemical character of the amino acids. Additionally, the interaction free energy is correlated with the propensity of amino acids to form beta-sheets, hinting at design principles for gold binding peptides and induction of beta-sheet formation near surfaces.
Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure.

PubMed

Chiusano, M L; D'Onofrio, G; Alvarez-Valin, F; Jabbari, K; Colonna, G; Bernardi, G

1999-09-30

We investigated the relationships between the nucleotide substitution rates and the predicted secondary structures in the three states representation (alpha-helix, beta-sheet, and coil). The analysis was carried out on 34 alignments, each of which comprised sequences belonging to at least four different mammalian orders. The rates of synonymous substitution were found to be significantly different in regions predicted to be alpha-helix, beta-sheet, or coil. Likewise, the nonsynonymous rates also differ, although expectedly at a lower extent, in the three types of secondary structure, suggesting that different selective constraints associated with the different structures are affecting in a similar way the synonymous and nonsynonymous rates. Moreover, the base composition of the third codon positions is different in coding sequence regions corresponding to different secondary structures of proteins.
Induced secondary structure and polymorphism in an intrinsically disordered structural linker of the CNS: solid-state NMR and FTIR spectroscopy of myelin basic protein bound to actin.

PubMed

Ahmed, Mumdooh A M; Bamm, Vladimir V; Shi, Lichi; Steiner-Mosonyi, Marta; Dawson, John F; Brown, Leonid; Harauz, George; Ladizhansky, Vladimir

2009-01-01

The 18.5 kDa isoform of myelin basic protein (MBP) is a peripheral membrane protein that maintains the structural integrity of the myelin sheath of the central nervous system by conjoining the cytoplasmic leaflets of oligodendrocytes and by linking the myelin membrane to the underlying cytoskeleton whose assembly it strongly promotes. It is a multifunctional, intrinsically disordered protein that behaves primarily as a structural stabilizer, but with elements of a transient or induced secondary structure that represent binding sites for calmodulin or SH3-domain-containing proteins, inter alia. In this study we used solid-state NMR (SSNMR) and Fourier transform infrared (FTIR) spectroscopy to study the conformation of 18.5 kDa MBP in association with actin microfilaments and bundles. FTIR spectroscopy of fully (13)C,(15)N-labeled MBP complexed with unlabeled F-actin showed induced folding of both protein partners, viz., some increase in beta-sheet content in actin, and increases in both alpha-helix and beta-sheet content in MBP, albeit with considerable extended structure remaining. Solid-state NMR spectroscopy revealed that MBP in MBP-actin assemblies is structurally heterogeneous but gains ordered secondary structure elements (both alpha-helical and beta-sheet), particularly in the terminal fragments and in a central immunodominant epitope. The overall conformational polymorphism of MBP is consistent with its in vivo roles as both a linker (membranes and cytoskeleton) and a putative signaling hub.
Dissociation of rapid response learning and facilitation in perceptual and conceptual networks of person recognition.

PubMed

Valt, Christian; Klein, Christoph; Boehm, Stephan G

2015-08-01

Repetition priming is a prominent example of non-declarative memory, and it increases the accuracy and speed of responses to repeatedly processed stimuli. Major long-hold memory theories posit that repetition priming results from facilitation within perceptual and conceptual networks for stimulus recognition and categorization. Stimuli can also be bound to particular responses, and it has recently been suggested that this rapid response learning, not network facilitation, provides a sound theory of priming of object recognition. Here, we addressed the relevance of network facilitation and rapid response learning for priming of person recognition with a view to advance general theories of priming. In four experiments, participants performed conceptual decisions like occupation or nationality judgments for famous faces. The magnitude of rapid response learning varied across experiments, and rapid response learning co-occurred and interacted with facilitation in perceptual and conceptual networks. These findings indicate that rapid response learning and facilitation in perceptual and conceptual networks are complementary rather than competing theories of priming. Thus, future memory theories need to incorporate both rapid response learning and network facilitation as individual facets of priming. © 2014 The British Psychological Society.

Structure of the transcriptional regulator LmrR and its mechanism of multidrug recognition.

PubMed

Madoori, Pramod Kumar; Agustiandari, Herfita; Driessen, Arnold J M; Thunnissen, Andy-Mark W H

2009-01-21

LmrR is a PadR-related transcriptional repressor that regulates the production of LmrCD, a major multidrug ABC transporter in Lactococcus lactis. Transcriptional regulation is presumed to follow a drug-sensitive induction mechanism involving the direct binding of transporter ligands to LmrR. Here, we present crystal structures of LmrR in an apo state and in two drug-bound states complexed with Hoechst 33342 and daunomycin. LmrR shows a common topology containing a typical beta-winged helix-turn-helix domain with an additional C-terminal helix involved in dimerization. Its dimeric organization is highly unusual with a flat-shaped hydrophobic pore at the dimer centre serving as a multidrug-binding site. The drugs bind in a similar manner with their aromatic rings sandwiched in between the indole groups of two dimer-related tryptophan residues. Multidrug recognition is facilitated by conformational plasticity and the absence of drug-specific hydrogen bonds. Combined analyses using site-directed mutagenesis, fluorescence-based drug binding and protein-DNA gel shift assays reveal an allosteric coupling between the multidrug- and DNA-binding sites of LmrR that most likely has a function in the induction mechanism.
Programmable DNA scaffolds for spatially-ordered protein assembly.

PubMed

Chandrasekaran, Arun Richard

2016-02-28

Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed.
Structural domains required for channel function of the mouse transient receptor potential protein homologue TRP1beta.

PubMed

Engelke, Michael; Friedrich, Olaf; Budde, Petra; Schäfer, Christina; Niemann, Ursula; Zitt, Christof; Jüngling, Eberhard; Rocks, Oliver; Lückhoff, Andreas; Frey, Jürgen

2002-07-17

Transient receptor potential proteins (TRP) are supposed to participate in the formation of store-operated Ca(2+) influx channels by co-assembly. However, little is known which domains facilitate the interaction of subunits. Contribution of the N-terminal coiled-coil domain and ankyrin-like repeats and the putative pore region of the mouse TRP1beta (mTRP1beta) variant to the formation of functional cation channels were analyzed following overexpression in HEK293 (human embryonic kidney) cells. MTRP1beta expressing cells exhibited enhanced Ca(2+) influx and enhanced whole-cell membrane currents compared to mTRP1beta deletion mutants. Using a yeast two-hybrid assay only the coiled-coil domain facilitated homodimerization of the N-terminus. These results suggest that the N-terminus of mTRP1beta is required for structural organization thus forming functional channels.
Structural mechanism of Smad4 recognition by the nuclear oncoprotein Ski: insights on Ski-mediated repression of TGF-beta signaling.

PubMed

Wu, Jia Wei; Krawitz, Ariel R; Chai, Jijie; Li, Wenyu; Zhang, Fangjiu; Luo, Kunxin; Shi, Yigong

2002-11-01

The Ski family of nuclear oncoproteins represses TGF-beta signaling through interactions with the Smad proteins. The crystal structure of the Smad4 binding domain of human c-Ski in complex with the MH2 domain of Smad4 reveals specific recognition of the Smad4 L3 loop region by a highly conserved interaction loop (I loop) from Ski. The Ski binding surface on Smad4 significantly overlaps with that required for binding of the R-Smads. Indeed, Ski disrupts the formation of a functional complex between the Co- and R-Smads, explaining how it could lead to repression of TGF-beta, activin, and BMP responses. Intriguingly, the structure of the Ski fragment, stabilized by a bound zinc atom, resembles the SAND domain, in which the corresponding I loop is responsible for DNA binding.
Rapid effects of estrogens on short-term memory: Possible mechanisms.

PubMed

Paletta, Pietro; Sheppard, Paul A S; Matta, Richard; Ervin, Kelsy S J; Choleris, Elena

2018-06-01

Estrogens affect learning and memory through rapid and delayed mechanisms. Here we review studies on rapid effects on short-term memory. Estradiol rapidly improves social and object recognition memory, spatial memory, and social learning when administered systemically. The dorsal hippocampus mediates estrogen rapid facilitation of object, social and spatial short-term memory. The medial amygdala mediates rapid facilitation of social recognition. The three estrogen receptors, α (ERα), β (ERβ) and the G-protein coupled estrogen receptor (GPER) appear to play different roles depending on the task and brain region. Both ERα and GPER agonists rapidly facilitate short-term social and object recognition and spatial memory when administered systemically or into the dorsal hippocampus and facilitate social recognition in the medial amygdala. Conversely, only GPER can facilitate social learning after systemic treatment and an ERβ agonist only rapidly improved short-term spatial memory when given systemically or into the hippocampus, but also facilitates social recognition in the medial amygdala. Investigations into the mechanisms behind estrogens' rapid effects on short term memory showed an involvement of the extracellular signal-regulated kinase (ERK) and the phosphoinositide 3-kinase (PI3K) kinase pathways. Recent evidence also showed that estrogens interact with the neuropeptide oxytocin in rapidly facilitating social recognition. Estrogens can increase the production and/or release of oxytocin and other neurotransmitters, such as dopamine and acetylcholine. Therefore, it is possible that estrogens' rapid effects on short-term memory may occur through the regulation of various neurotransmitters, although more research is need on these interactions as well as the mechanisms of estrogens' actions on short-term memory. Copyright © 2018 Elsevier Inc. All rights reserved.
Isolation, characterization, and purification to homogeneity of an endogenous polypeptide with agonistic action on benzodiazepine receptors.

PubMed Central

Guidotti, A; Forchetti, C M; Corda, M G; Konkel, D; Bennett, C D; Costa, E

1983-01-01

A brain polypeptide termed diazepam-binding inhibitor (DBI) and thought to be chemically and functionally related to the endogenous effector of the benzodiazepine recognition site was purified to homogeneity. This peptide gives a single band of protein on NaDodSO4 and acidic urea gel electrophoresis. A single UV-absorbing peak was obtained by HPLC using three different columns and solvent systems. DBI has a molecular mass of approximately equal to 11,000 daltons. Carboxyl-terminus analysis shows that tyrosine is the only residue while the amino-terminus was blocked. Cyanogen bromide treatment of DBI yields three polypeptide fragments, and the sequences of two of them have been determined for a total of 45 amino acids. DBI is a competitive inhibitor for the binding of [3H]diazepam, [3H]flunitrazepam, beta-[3H]carboline propyl esters, and 3H-labeled Ro 15-1788. The Ki for [3H]-diazepam and beta-[3H]carboline binding were 4 and 1 microM, respectively. Doses of DBI that inhibited [3H]diazepam binding by greater than 50% fail to change [3H]etorphine, gamma-amino[3H]butyric acid, [3H]-quinuclidinyl benzilate, [3H]dihydroalprenolol, [3H]adenosine, and [3H]imipramine binding tested at their respective Kd values. DBI injected intraventricularly at doses of 5-10 nmol completely reversed the anticonflict action of diazepam on unpunished drinking and, similar to the anxiety-inducing beta-carboline derivative FG 7142 (beta-carboline-3-carboxylic acid methyl ester), facilitated the shock-induced suppression of drinking by lowering the threshold for this response. Images PMID:6304714
Special Analysis for the Disposal of the Lawrence Livermore National Laboratory Low Activity Beta/Gamma Sources Waste Stream at the Area 5 Radioactive Waste Management Site, Nevada National Security Site, Nye County, Nevada

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

Shott, Gregory J.

This special analysis (SA) evaluates whether the Lawrence Livermore National Laboratory (LLNL) Low Activity Beta/Gamma Sources waste stream (BCLALADOEOSRP, Revision 0) is suitable for disposal by shallow land burial (SLB) at the Area 5 Radioactive Waste Management Site (RWMS) at the Nevada National Security Site (NNSS). The LLNL Low Activity Beta/Gamma Sources waste stream consists of sealed sources that are no longer needed. The LLNL Low Activity Beta/Gamma Sources waste stream required a special analysis because cobalt-60 (60Co), strontium-90 (90Sr), cesium-137 (137Cs), and radium-226 (226Ra) exceeded the NNSS Waste Acceptance Criteria (WAC) Action Levels (U.S. Department of Energy, National Nuclearmore » Security Administration Nevada Field Office [NNSA/NFO] 2015). The results indicate that all performance objectives can be met with disposal of the LLNL Low Activity Beta/Gamma Sources in a SLB trench. The LLNL Low Activity Beta/Gamma Sources waste stream is suitable for disposal by SLB at the Area 5 RWMS. However, the activity concentration of 226Ra listed on the waste profile sheet significantly exceeds the action level. Approval of the waste profile sheet could potentially allow the disposal of high activity 226Ra sources. To ensure that the generator does not include large 226Ra sources in this waste stream without additional evaluation, a control is need on the maximum 226Ra inventory. A limit based on the generator’s estimate of the total 226Ra inventory is recommended. The waste stream is recommended for approval with the control that the total 226Ra inventory disposed shall not exceed 5.5E10 Bq (1.5 Ci).« less
Nefiracetam facilitates hippocampal neurotransmission by a mechanism independent of the piracetam and aniracetam action.

PubMed

Nomura, T; Nishizaki, T

2000-07-07

Nefiracetam, a nootropic (cognition-enhancing) agent, facilitated neurotransmission in the dentate gyrus of rat hippocampal slices in a dose-dependent manner at concentrations ranged from 1 nM to 1 microM, being evident at 60-min washing-out of the drug. The facilitatory action was blocked by the nicotinic acetylcholine (ACh) receptor antagonists, alpha-bungarotoxin and mecamylamine. A similar facilitation was induced by the other nootropic agents, piracetam and aniracetam, but the facilitation was not inhibited by nicotinic ACh receptor antagonists and it did not occlude the potentiation induced by nefiracetam. In the Xenopus oocyte expression systems, nefiracetam potentiated currents through a variety of neuronal nicotinic ACh receptors (alpha 3beta 2, alpha 3beta 4, alpha 4 beta 2, alpha 4 beta 4, and alpha 7) to a different extent. In contrast, neither piracetam nor aniracetam had any potentiating action on alpha 7 receptor currents. While aniracetam delayed the decay time of currents through the alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor, GluR1, -2, -3, expressed in oocytes, nefiracetam or piracetam had no effect on the currents. Nefiracetam, thus, appears to facilitate hippocampal neurotransmission by functionally targeting nicotinic ACh receptors, independently of the action of piracetam and aniracetam.
Apply lightweight recognition algorithms in optical music recognition

NASA Astrophysics Data System (ADS)

Pham, Viet-Khoi; Nguyen, Hai-Dang; Nguyen-Khac, Tung-Anh; Tran, Minh-Triet

2015-02-01

The problems of digitalization and transformation of musical scores into machine-readable format are necessary to be solved since they help people to enjoy music, to learn music, to conserve music sheets, and even to assist music composers. However, the results of existing methods still require improvements for higher accuracy. Therefore, the authors propose lightweight algorithms for Optical Music Recognition to help people to recognize and automatically play musical scores. In our proposal, after removing staff lines and extracting symbols, each music symbol is represented as a grid of identical M ∗ N cells, and the features are extracted and classified with multiple lightweight SVM classifiers. Through experiments, the authors find that the size of 10 ∗ 12 cells yields the highest precision value. Experimental results on the dataset consisting of 4929 music symbols taken from 18 modern music sheets in the Synthetic Score Database show that our proposed method is able to classify printed musical scores with accuracy up to 99.56%.
A novel member of the split betaalphabeta fold: Solution structure of the hypothetical protein YML108W from Saccharomyces cerevisiae.

PubMed

Pineda-Lucena, Antonio; Liao, Jack C C; Cort, John R; Yee, Adelinda; Kennedy, Michael A; Edwards, Aled M; Arrowsmith, Cheryl H

2003-05-01

As part of the Northeast Structural Genomics Consortium pilot project focused on small eukaryotic proteins and protein domains, we have determined the NMR structure of the protein encoded by ORF YML108W from Saccharomyces cerevisiae. YML108W belongs to one of the numerous structural proteomics targets whose biological function is unknown. Moreover, this protein does not have sequence similarity to any other protein. The NMR structure of YML108W consists of a four-stranded beta-sheet with strand order 2143 and two alpha-helices, with an overall topology of betabetaalphabetabetaalpha. Strand beta1 runs parallel to beta4, and beta2:beta1 and beta4:beta3 pairs are arranged in an antiparallel fashion. Although this fold belongs to the split betaalphabeta family, it appears to be unique among this family; it is a novel arrangement of secondary structure, thereby expanding the universe of protein folds.
Fluctuation dynamics in reconnecting current sheets

NASA Astrophysics Data System (ADS)

von Stechow, Adrian; Grulke, Olaf; Ji, Hantao; Yamada, Masaaki; Klinger, Thomas

2015-11-01

During magnetic reconnection, a highly localized current sheet forms at the boundary between opposed magnetic fields. Its steep perpendicular gradients and fast parallel drifts can give rise to a range of instabilities which can contribute to the overall reconnection dynamics. In two complementary laboratory reconnection experiments, MRX (PPPL, Princeton) and VINETA.II (IPP, Greifswald, Germany), magnetic fluctuations are observed within the current sheet. Despite the large differences in geometries (toroidal vs. linear), plasma parameters (high vs. low beta) and magnetic configuration (low vs. high magnetic guide field), similar broadband fluctuation characteristics are observed in both experiments. These are identified as Whistler-like fluctuations in the lower hybrid frequency range that propagate along the current sheet in the electron drift direction. They are intrinsic to the localized current sheet and largely independent of the slower reconnection dynamics. This contribution characterizes these magnetic fluctuations within the wide parameter range accessible by both experiments. Specifically, the fluctuation spectra and wave dispersion are characterized with respect to the magnetic topology and plasma parameters of the reconnecting current sheet.
The J beta segment of the T cell receptor contributes to the V beta-specific T cell expansion caused by staphylococcal enterotoxin B and Urtica dioica superantigens.

PubMed

Musette, P; Galelli, A; Truffa-Bachi, P; Peumans, W; Kourilsky, P; Gachelin, G

1996-03-01

We have used a new polymerase chain reaction-based technique to analyze at the clonal level the CDR3 diversity and the J beta usage associated with the V beta-dependent T cell receptor (TCR) recognition of two superantigens: the staphylococcal enterotoxin B and the Urtica dioica agglutinin. Our results show that subset of J beta elements is preferentially expanded in a given V beta family, independently of the nature of the superantigen. By contrast, the CDR3 loop does not contribute significantly to the T cell expansion induced by the superantigens. We conclude that the J beta segment of the TCR beta chain, but not the CDR3 region, participates in superantigen binding, presumably by influencing the quaternary structure of the TCR beta chain.
Facile and efficient electrochemical enantiomer recognition of phenylalanine using β-Cyclodextrin immobilized on reduced graphene oxide.

PubMed

Zaidi, Shabi Abbas

2017-08-15

This work demonstrates the facile and efficient preparation protocol of β-Cyclodextrin-reduced graphene oxide modified glassy carbon electrode (β-CD/RGO/GCE) sensor for an impressive chiral selectivity analysis for phenylalanine enantiomers. In this work, the immobilization of β-CD over graphene sheets allows the excellent enantiomer recognition due to the large surface area and high conductivity of graphene sheets and extraordinary supramolecular (host-guest interaction) property of β-CD. The proposed sensor was well characterized by scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and electrochemical impedance spectroscopy (EIS) techniques. The analytical studies demonstrated that the β-CD/RGO/GCE exhibit superior chiral recognition toward L-phenylalanine as compared to D-phenylalanine. Under optimum conditions, the developed sensor displayed a good linear range from 0.4 to 40µM with the limit of detection (LOD) values of 0.10µM and 0.15µM for l- and D-phenylalanine, respectively. Furthermore, the proposed sensor exhibits good stability and regeneration capacity. Thus, the as-synthesized material can be exploited for electrochemical enantiomer recognition successfully. Copyright © 2017 Elsevier B.V. All rights reserved.
Anticipatory coarticulation facilitates word recognition in toddlers.

PubMed

Mahr, Tristan; McMillan, Brianna T M; Saffran, Jenny R; Ellis Weismer, Susan; Edwards, Jan

2015-09-01

Children learn from their environments and their caregivers. To capitalize on learning opportunities, young children have to recognize familiar words efficiently by integrating contextual cues across word boundaries. Previous research has shown that adults can use phonetic cues from anticipatory coarticulation during word recognition. We asked whether 18-24 month-olds (n=29) used coarticulatory cues on the word "the" when recognizing the following noun. We performed a looking-while-listening eyetracking experiment to examine word recognition in neutral vs. facilitating coarticulatory conditions. Participants looked to the target image significantly sooner when the determiner contained facilitating coarticulatory cues. These results provide the first evidence that novice word-learners can take advantage of anticipatory sub-phonemic cues during word recognition. Copyright © 2015 Elsevier B.V. All rights reserved.
Structural and functional characterization of the NHR1 domain of the Drosophila neuralized E3 ligase in the notch signaling pathway.

PubMed

He, Fahu; Saito, Kohei; Kobayashi, Naohiro; Harada, Takushi; Watanabe, Satoru; Kigawa, Takanori; Güntert, Peter; Ohara, Osamu; Tanaka, Akiko; Unzai, Satoru; Muto, Yutaka; Yokoyama, Shigeyuki

2009-10-23

The Notch signaling pathway is critical for many developmental processes and requires complex trafficking of both Notch receptor and its ligands, Delta and Serrate. In Drosophila melanogaster, the endocytosis of Delta in the signal-sending cell is essential for Notch receptor activation. The Neuralized protein from D. melanogaster (Neur) is a ubiquitin E3 ligase, which binds to Delta through its first neuralized homology repeat 1 (NHR1) domain and mediates the ubiquitination of Delta for endocytosis. Tom, a Bearded protein family member, inhibits the Neur-mediated endocytosis through interactions with the NHR1 domain. We have identified the domain boundaries of the novel NHR1 domain, using a screening system based on our cell-free protein synthesis method, and demonstrated that the identified Neur NHR1 domain had binding activity to the 20-residue peptide corresponding to motif 2 of Tom by isothermal titration calorimetry experiments. We also determined the solution structure of the Neur NHR1 domain by heteronuclear NMR methods, using a (15)N/(13)C-labeled sample. The Neur NHR1 domain adopts a characteristic beta-sandwich fold, consisting of a concave five-stranded antiparallel beta-sheet and a convex seven-stranded antiparallel beta-sheet. The long loop (L6) between the beta6 and beta7 strands covers the hydrophobic patch on the concave beta-sheet surface, and the Neur NHR1 domain forms a compact globular fold. Intriguingly, in spite of the slight, but distinct, differences in the topology of the secondary structure elements, the structure of the Neur NHR1 domain is quite similar to those of the B30.2/SPRY domains, which are known to mediate specific protein-protein interactions. Further NMR titration experiments of the Neur NHR1 domain with the 20-residue Tom peptide revealed that the resonances originating from the bottom area of the beta-sandwich (the L3, L5, and L11 loops, as well as the tip of the L6 loop) were affected. In addition, a structural comparison of the Neur NHR1 domain with the first NHR domain of the human KIAA1787 protein, which is from another NHR subfamily and does not bind to the 20-residue Tom peptide, suggested the critical amino acid residues for the interactions between the Neur NHR1 domain and the Tom peptide. The present structural study will shed light on the role of the Neur NHR1 domain in the Notch signaling pathway.
Folding dynamics of a family of beta-sheet proteins

NASA Astrophysics Data System (ADS)

Rousseau, Denis

2008-03-01

Fatty acid binding proteins (FABP) consist of ten anti-parallel beta strands and two small alpha helices. The beta strands are arranged into two nearly orthogonal five-strand beta sheets that surround the interior cavity, which binds unsaturated long-chain fatty acids. In the brain isoform (BFABP), these are very important for the development of the central nervous system and neuron differentiation. Furthermore, BFABP is implicated in the pathogenesis of a variety of human diseases including cancer and neuronal degenerative disorders. In this work, site-directed spin labeling combined with EPR techniques have been used to study the folding mechanism of BFABP. In the first series of studies, we labeled the two Cys residues at position 5 and 80 in the wild type protein with an EPR spin marker; in addition, two singly labeled mutants at positions 5 and 80 in the C80A and C5A mutants, respectively, were also produced and used as controls. The changes in the distances between the two residues were examined by a pulsed EPR method, DEER (Double Electron Electron Resonance), as a function of guanidinium hydrochloride concentration. The results were compared with those from CW EPR, circular dichroism and fluorescence measurements, which provide the information regarding sidechain mobility, secondary structure and tertiary structure, respectively. The results will be discussed in the context of the folding mechanism of the family of fatty acid binding proteins.
Aligned carbon nanotube-silicon sheets: a novel nano-architecture for flexible lithium ion battery electrodes.

PubMed

Fu, Kun; Yildiz, Ozkan; Bhanushali, Hardik; Wang, Yongxin; Stano, Kelly; Xue, Leigang; Zhang, Xiangwu; Bradford, Philip D

2013-09-25

Aligned carbon nanotube sheets provide an engineered scaffold for the deposition of a silicon active material for lithium ion battery anodes. The sheets are low-density, allowing uniform deposition of silicon thin films while the alignment allows unconstrained volumetric expansion of the silicon, facilitating stable cycling performance. The flat sheet morphology is desirable for battery construction. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Folding control in cyclic peptides through N-methylation pattern selection: formation of antiparallel beta-sheet dimers, double reverse turns and supramolecular helices by 3alpha,gamma cyclic peptides.

PubMed

Amorín, Manuel; Castedo, Luis; Granja, Juan R

2008-01-01

Peptide foldamers constitute a growing class of nanomaterials with potential applications in a wide variety of chemical, medical and technological fields. Here we describe the preparation and structural characteristics of a new class of cyclic peptide foldamers (3alpha,gamma-CPs) that, depending on their backbone N-methylation patterns and the medium, can either remain as flat rings that dimerize through arrays of hydrogen bonds of antiparallel beta-sheet type, or can fold into twisted double reverse turns that, in the case of double gamma-turns, associate in nonpolar solvents to form helical supramolecular structures. A 3alpha,gamma-CP consists of a number of multiples of a repeat unit made up of four amino acid residues of alternating chirality: three corresponding to alpha-amino acids and one to a gamma-amino acid (a cis-3-aminocycloalkanecarboxylic acid).
Inhibition of beta-amyloid aggregation by fluorescent dye labels

NASA Astrophysics Data System (ADS)

Amaro, Mariana; Wellbrock, Thorben; Birch, David J. S.; Rolinski, Olaf J.

2014-02-01

The fluorescence decay of beta-amyloid's (Aβ) intrinsic fluorophore tyrosine has been used for sensing the oligomer formation of dye-labelled Aβ monomers and the results compared with previously studied oligomerization of the non-labelled Aβ peptides. It has been demonstrated that two different sized, covalently bound probes 7-diethylaminocoumarin-3-carbonyl and Hilyte Fluor 488 (HLF), alter the rate and character of oligomerization to different extents. The ability of HLF to inhibit formation of highly ordered structures containing beta-sheets was also shown. The implications of our findings for using fluorescence methods in amyloidosis research are discussed and the advantages of this auto-fluorescence approach highlighted.
Development of anti-adhesive spongy sheet composed of hyaluronic acid and collagen containing epidermal growth factor.

PubMed

Kuroyanagi, Misato; Yamamoto, Akiko; Shimizu, Nahoko; Toi, Ayako; Inomata, Tomonori; Takeda, Akira; Kuroyanagi, Yoshimitsu

2014-01-01

Anti-adhesive products need to be designed while considering the concept of wound healing. Two main events must proceed simultaneously: facilitating wound healing in surgically excised tissue, as well as preventing injured tissue from adhering to the surrounding tissue. The present study aimed to develop an anti-adhesive spongy sheet composed of hyaluronic acid and collagen (Col) containing epidermal growth factor, and to investigate the potential of this spongy sheet using an in vitro wound surface model (placing a spongy sheet on a fibroblast-incorporating Col gel sheet) and an in vitro inter-tissue model (placing a spongy sheet between two fibroblast-incorporating Col gel sheets). These in vitro experiments demonstrated that this spongy sheet effectively stimulates fibroblasts to release an increased amount of vascular endothelial growth factor and hepatocyte growth factor, which are essential for wound healing to proceed succesfully. In addition, anti-adhesive performance of this spongy sheet was evaluated in animal experiments using Sprague Dawley rats. Under anesthesia, a 1 cm × 2 cm segment of peritoneum was superficially excised from walls, and the cecum was then abraded by scraping with a scalpel blade over a 1 cm × 2 cm area. A piece of spongy sheet was placed on the peritoneal defect. Both defects were placed in contact, and the incision was closed by suturing. Peritoneal condition was evaluated after one week. This spongy sheet was capable of facilitating the wound healing of surgically excised tissue and preventing surgically excised tissue from adhering to surrounding tissues.

Simultaneous measurements of magnetotail dynamics by IMP spacecraft

NASA Technical Reports Server (NTRS)

Fairfield, D. H.; Lepping, R. P.; Hones, E. W., Jr.; Bame, S. J.; Asbridge, J. R.

1980-01-01

Changes in tail energy density during substorms in the magnetotail are given. In addition to plasma sheet thinnings seen prior to substorm onsets, a gradual decrease in plasma beta was detected in the deep tail which precedes onset and the more prominent plasma disappearance that typically accompanies it. The frequency of thinnings and the regions over which they occurred indicate that drastic changes in plasma sheet thickness are common features of substorms which occur at all locations across the tail.
Three 3D hybrid networks based on octamolybdates and different Cu{sup I}/Cu{sup II}-bis(triazole) motifs

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

Zhang, Chun-Jing; Pang, Hai-Jun; Tang, Qun

2010-12-15

Three 3D compounds based on octamolybdate clusters and various Cu{sup I}/Cu{sup II}-bis(triazole) motifs, [Cu{sup I}{sub 2}btb][{beta}-Mo{sub 8}O{sub 26}]{sub 0.5} (1), [Cu{sup I}{sub 2}btpe][{beta}-Mo{sub 8}O{sub 26}]{sub 0.5} (2), and [Cu{sup II}(btpe){sub 2}][{beta}-Mo{sub 8}O{sub 26}]{sub 0.5} (3) [btb=1,4-bis(1,2,4-triazol-1-yl)butane, btpe=1,5-bis(1,2,4-triazol-1-yl)pentane], were isolated via tuning flexible ligand spacer length and metal coordination preferences. In 1, the copper(I)-btb motif is a one-dimensional (1D) chain which is further linked by hexadentate {beta}-[Mo{sub 8}O{sub 26}]{sup 4-} clusters via coordinating to Cu{sup I} cations giving a 3D structure. In 2, the copper(I)-btpe motif exhibits a 'stairs'-like [Cu{sup I}{sub 2}btpe]{sup 2+} sheet, and the tetradentate {beta}-[Mo{sub 8}O{sub 26}]{sup 4-}more » clusters interact with two neighboring [Cu{sup I}{sub 2}btpe]{sup 2+} sheets constructing a 3D framework. In 3, the copper(II)-btpe motif possesses a novel (2D{yields}3D) interdigitated structure, which is further connected by the tetradentate {beta}-[Mo{sub 8}O{sub 26}]{sup 4-} clusters forming a 3D framework. The thermal stability and luminescent properties of 1-3 are investigated in the solid state. -- Graphical abstract: Three 3D compounds based on {beta}-[Mo{sub 8}O{sub 26}]{sup 4-} clusters with different Cu{sup I}/Cu{sup II}-bis(triazole) motifs were synthesized by regularly tuning flexible ligand spacer length and metal coordination preferences. Display Omitted« less
Comparison of the adsorbed conformation of barley lipid transfer protein at the decane-water and vacuum-water interface: a molecular dynamics simulation.

PubMed

Euston, S R; Hughes, P; Naser, Md A; Westacott, R E

2008-05-01

Molecular dynamics simulation is used to model the adsorption of the barley lipid transfer protein (LTP) at the decane-water and vacuum-water interfaces. Adsorption at both surfaces is driven by displacement of water molecules from the interfacial region. LTP adsorbed at the decane surface exhibits significant changes in its tertiary structure, and penetrates a considerable distance into the decane phase. At the vacuum-water interface LTP shows small conformational changes away from its native structure and does not penetrate into the vacuum space. Modification of the conformational stability of LTP by reduction of its four disulphide bonds leads to an increase in conformational entropy of the molecules, which reduces the driving force for adsorption. Evidence for changes in the secondary structure are also observed for native LTP at the decane-water interface and reduced LTP at the vacuum-water interface. In particular, intermittent formation of short (six-residue) regions of beta-sheet is found in these two systems. Formation of interfacial beta-sheet in adsorbed proteins has been observed experimentally, notably in the globular milk protein beta-lactoglobulin and lysozyme.
Structure of the Minor Pseudopilin EpsH From the Type 2 Secretion System of Vibrio Cholerae

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

Yanez, M.E.; Korotkov, K.V.; Abendroth, J.

2009-05-28

Many Gram-negative bacteria use the multi-protein type II secretion system (T2SS) to selectively translocate virulence factors from the periplasmic space into the extracellular environment. In Vibrio cholerae the T2SS is called the extracellular protein secretion (Eps) system, which translocates cholera toxin and several enzymes in their folded state across the outer membrane. Five proteins of the T2SS, the pseudopilins, are thought to assemble into a pseudopilus, which may control the outer membrane pore EpsD, and participate in the active export of proteins in a 'piston-like' manner. We report here the 2.0 {angstrom} resolution crystal structure of an N-terminally truncated variantmore » of EpsH, a minor pseudopilin from Vibrio cholerae. While EpsH maintains an N-terminal {alpha}-helix and C-terminal {beta}-sheet consistent with the type 4a pilin fold, structural comparisons reveal major differences between the minor pseudopilin EpsH and the major pseudopilin GspG from Klebsiella oxytoca: EpsH contains a large {beta}-sheet in the variable domain, where GspG contains an {alpha}-helix. Most importantly, EpsH contains at its surface a hydrophobic crevice between its variable and conserved {beta}-sheets, wherein a majority of the conserved residues within the EpsH family are clustered. In a tentative model of a T2SS pseudopilus with EpsH at its tip, the conserved crevice faces away from the helix axis. This conserved surface region may be critical for interacting with other proteins from the T2SS machinery.« less
Group Recommendation in Social Networks

DTIC Science & Technology

2011-01-01

APPROVAL SHEET Title of Thesis: Group recognition in social networks Name of Candidate: Nagapradeep Chinnam Master of...2011 4. TITLE AND SUBTITLE Group recognition in social networks 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d...for public release; distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Recent years have seen an exponential growth in the use of social
Composite cell sheet for periodontal regeneration: crosstalk between different types of MSCs in cell sheet facilitates complex periodontal-like tissue regeneration.

PubMed

Zhang, Hao; Liu, Shiyu; Zhu, Bin; Xu, Qiu; Ding, Yin; Jin, Yan

2016-11-14

Tissue-engineering strategies based on mesenchymal stem cells (MSCs) and cell sheets have been widely used for periodontal tissue regeneration. However, given the complexity in periodontal structure, the regeneration methods using a single species of MSC could not fulfill the requirement for periodontal regeneration. We researched the interaction between the periodontal ligament stem cells (PDLSCs) and jaw bone marrow-derived mesenchymal stem cells (JBMMSCs), and constructed a composite cell sheet comprising both of the above MSCs to regenerate complex periodontium-like structures in nude mice. Our results show that by co-culturing PDLSCs and JBMMSCs, the expressions of bone and extracellular matrix (ECM)-related genes and proteins were significantly improved in both MSCs. Further investigations showed that, compared to the cell sheet using PDLSCs or JBMMSCs, the composite stem cell sheet (CSCS), which comprises these two MSCs, expressed higher levels of bone- and ECM-related genes and proteins, and generated a composite structure more similar to the native periodontal tissue physiologically in vivo. In conclusion, our results demonstrate that the crosstalk between PDLSCs and JBMMSCs in cell sheets facilitate regeneration of complex periodontium-like structures, providing a promising new strategy for physiological and functional regeneration of periodontal tissue.
Mechanical properties of coated titanium Beta-21S after exposure to air at 700 and 800 C

NASA Technical Reports Server (NTRS)

Wiedemann, Karl E.; Bird, R. Keith; Wallace, Terryl A.; Clark, Ronald K.

1992-01-01

Mechanical properties of Beta-21S (Ti-15Mo-3Al-2.7Nb-0.2Si, wt percent) with glass, aluminide, and glass-on-aluminide coatings less than 3-micron thick were studied. Coatings were deposited by sol-gel processing or electron-beam evaporation onto 4.5-mil (113-micron) thick Beta-21S sheet from which, after oxidizing in air at 700 or 800 C, tensile test specimens were machined. Plastic elongation was the most severely degraded of the tensile properties; the glass-on-aluminide coatings were the most effective in preventing degradation. It was found that oxygen trapping by forming oxides in the coating, and reactions between the coatings and the Beta-21S alloy played significant roles.
Slow Mode Waves in the Heliospheric Plasma Sheet

NASA Technical Reports Server (NTRS)

Smith, Edward. J.; Zhou, Xiaoyan

2007-01-01

We report the results of a search for waves/turbulence in the Heliospheric Plasma Sheet (HPS) surrounding the Heliospheric Current Sheet (HCS). The HPS is treated as a distinctive heliospheric structure distinguished by relatively high Beta, slow speed plasma. The data used in the investigation are from a previously published study of the thicknesses of the HPS and HCS that were obtained in January to May 2004 when Ulysses was near aphelion at 5 AU. The advantage of using these data is that the HPS is thicker at large radial distances and the spacecraft spends longer intervals inside the plasma sheet. From the study of the magnetic field and solar wind velocity components, we conclude that, if Alfven waves are present, they are weak and are dominated by variations in the field magnitude, B, and solar wind density, NP, that are anti-correlated.
Early Stages of Microstructure and Texture Evolution during Beta Annealing of Ti-6Al-4V

NASA Astrophysics Data System (ADS)

Pilchak, A. L.; Sargent, G. A.; Semiatin, S. L.

2018-03-01

The early stages of microstructure evolution during annealing of Ti-6Al-4V in the beta phase field were established. For this purpose, a series of short-time heat treatments was performed using sheet samples that had a noticeable degree of alpha-phase microtexture in the as-received condition. Reconstruction of the beta-grain structure from electron-backscatter-diffraction measurements of the room-temperature alpha-phase texture revealed that microstructure evolution at short times was controlled not by general grain growth, but rather by nucleation-and-growth events analogous to discontinuous recrystallization. The nuclei comprised a small subset of beta grains that were highly misoriented relative to those comprising the principal texture component of the beta matrix. From a quantitative standpoint, the transformation kinetics were characterized by an Avrami exponent of approximately unity, thus suggestive of metadynamic recrystallization. The recrystallization process led to the weakening and eventual elimination of the initial beta texture through the growth of a population of highly misoriented grains.
Activation of Supraoptic Oxytocin Neurons by Secretin Facilitates Social Recognition.

PubMed

Takayanagi, Yuki; Yoshida, Masahide; Takashima, Akihide; Takanami, Keiko; Yoshida, Shoma; Nishimori, Katsuhiko; Nishijima, Ichiko; Sakamoto, Hirotaka; Yamagata, Takanori; Onaka, Tatsushi

2017-02-01

Social recognition underlies social behavior in animals, and patients with psychiatric disorders associated with social deficits show abnormalities in social recognition. Oxytocin is implicated in social behavior and has received attention as an effective treatment for sociobehavioral deficits. Secretin receptor-deficient mice show deficits in social behavior. The relationship between oxytocin and secretin concerning social behavior remains to be determined. Expression of c-Fos in oxytocin neurons and release of oxytocin from their dendrites after secretin application were investigated. Social recognition was examined after intracerebroventricular or local injection of secretin, oxytocin, or an oxytocin receptor antagonist in rats, oxytocin receptor-deficient mice, and secretin receptor-deficient mice. Electron and light microscopic immunohistochemical analysis was also performed to determine whether oxytocin neurons extend their dendrites into the medial amygdala. Supraoptic oxytocin neurons expressed the secretin receptor. Secretin activated supraoptic oxytocin neurons and facilitated oxytocin release from dendrites. Secretin increased acquisition of social recognition in an oxytocin receptor-dependent manner. Local application of secretin into the supraoptic nucleus facilitated social recognition, and this facilitation was blocked by an oxytocin receptor antagonist injected into, but not outside of, the medial amygdala. In the medial amygdala, dendrite-like thick oxytocin processes were found to extend from the supraoptic nucleus. Furthermore, oxytocin treatment restored deficits of social recognition in secretin receptor-deficient mice. The results of our study demonstrate that secretin-induced dendritic oxytocin release from supraoptic neurons enhances social recognition. The newly defined secretin-oxytocin system may lead to a possible treatment for social deficits. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.
A photoaffinity scan maps regions of the p85 SH2 domain involved in phosphoprotein binding.

PubMed

Williams, K P; Shoelson, S E

1993-03-15

Src homology 2 (SH2) domains are modular phosphotyrosine binding pockets found within a wide variety of cytoplasmic signaling molecules. Here we develop a new approach to analyzing protein-protein interfaces termed photoaffinity scanning, and apply the method to map regions of the phosphatidylinositol 3-kinase p85 SH2 domain that participate in phospho-protein binding. Each residue except phosphotyrosine (pY) within a tightly binding, IRS-1-derived phosphopeptide (GNGDpYMPMSPKS) was substituted with the photoactive amino acid, benzoylphenylalanine (Bpa). Whereas most substitutions had little effect on binding affinity, Bpa substitution of either Met (+1 and +3 with respect to pY) reduced affinity 50-100-fold to confirm their importance in the pYMXM recognition motif. In three cases photolysis of SH2 domain/Bpa phosphopeptide complexes led to cross-linking of > 50% of the SH2 domain; cross-link positions were identified by microsequence, amino acid composition, and electrospray mass spectrometric analyses. Bpa-1 cross-links within alpha-helix I, whereas Bpa+1 and Bpa+4 cross-link the SH2 domain within the flexible loop C-terminal to alpha-helix II. Moreover, cross-linking at any position prevents SH2 domain cleavage at a trypsin-sensitive site within the flexible loop between beta-strands 1 and 2. Therefore, at least three distinct SH2 regions in addition to the beta-sheet participate in phosphoprotein binding; the loop cross-linked by phosphopeptide residues C-terminal to pY appears to confer specificity to the phosphoprotein/SH2 domain interaction.
Secbase: database module to retrieve secondary structure elements with ligand binding motifs.

PubMed

Koch, Oliver; Cole, Jason; Block, Peter; Klebe, Gerhard

2009-10-01

Secbase is presented as a novel extension module of Relibase. It integrates the information about secondary structure elements into the retrieval facilities of Relibase. The data are accessible via the extended Relibase user interface, and integrated retrieval queries can be addressed using an extended version of Reliscript. The primary information about alpha-helices and beta-sheets is used as provided by the PDB. Furthermore, a uniform classification of all turn families, based on recent clustering methods, and a new helix assignment that is based on this turn classification has been included. Algorithms to analyze the geometric features of helices and beta-strands were also implemented. To demonstrate the performance of the Secbase implementation, some application examples are given. They provide new insights into the involvement of secondary structure elements in ligand binding. A survey of water molecules detected next to the N-terminus of helices is analyzed to show their involvement in ligand binding. Additionally, the parallel oriented NH groups at the alpha-helix N-termini provide special binding motifs to bind particular ligand functional groups with two adjacent oxygen atoms, e.g., as found in negatively charged carboxylate or phosphate groups, respectively. The present study also shows that the specific structure of the first turn of alpha-helices provides a suitable explanation for stabilizing charged structures. The magnitude of the overall helix macrodipole seems to have no or only a minor influence on binding. Furthermore, an overview of the involvement of secondary structure elements with the recognition of some important endogenous ligands such as cofactors shows some distinct preference for particular binding motifs and amino acids.
Beta amyloid and hyperphosphorylated tau deposits in the pancreas in type 2 diabetes

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

Miklossy, J.; Miller, L.; Qing, H.

2008-08-25

Strong epidemiologic evidence suggests an association between Alzheimer disease (AD) and type 2 diabetes. To determine if amyloid beta (A{beta}) and hyperphosphorylated tau occurs in type 2 diabetes, pancreas tissues from 21 autopsy cases (10 type 2 diabetes and 11 controls) were analyzed. APP and tau mRNAs were identified in human pancreas and in cultured insulinoma beta cells (INS-1) by RT-PCR. Prominent APP and tau bands were detected by Western blotting in pancreatic extracts. Aggregated A{beta}, hyperphosphorylated tau, ubiquitin, apolipoprotein E, apolipoprotein(a), IB1/JIP-1 and JNK1 were detected in Langerhans islets in type 2 diabetic patients. A{beta} was co-localized with amylinmore » in islet amyloid deposits. In situ beta sheet formation of islet amyloid deposits was shown by infrared microspectroscopy (SIRMS). LPS increased APP in non-neuronal cells as well. We conclude that A{beta} deposits and hyperphosphorylated tau are also associated with type 2 diabetes, highlighting common pathogenetic features in neurodegenerative disorders, including AD and type 2 diabetes and suggesting that A{beta} deposits and hyperphosphorylated tau may also occur in other organs than the brain.« less
Structural and Functional Properties of Peptides Based on the N-terminus of HIV-1 gp41 and the C-terminus of the Amyloid-Beta Protein

PubMed Central

Gordon, Larry M.; Nisthal, Alex; Lee, Andy B.; Eskandari, Sepehr; Ruchala, Piotr; Jung, Chun-Ling; Waring, Alan J.; Mobley, Patrick W.

2008-01-01

Given their high alanine and glycine levels, plaque formation, α-helix to β-sheet interconversion and fusogenicity, FP (i.e., the N-terminal fusion peptide of HIV-1 gp41; 23 residues) and amyloids were proposed as belonging to the same protein superfamily. Here, we further test whether FP may exhibit ‘amyloid-like’ characteristics, by contrasting its structural and functional properties with those of Aβ(26–42), a 17-residue peptide from the C-terminus of the amyloid-beta protein responsible for Alzheimer’s. FTIR spectroscopy, electron microscopy, light scattering and predicted amyloid structure aggregation (PASTA) indicated that aqueous FP and Aβ(26–42) formed similar networked β-sheet fibrils, although the FP fibril interactions were weaker. FP and Aβ(26–42) both lysed and aggregated human erythrocytes, with the hemolysis-onsets correlated with the conversion of α-helix to β-sheet for each peptide in liposomes. Congo red (CR), a marker of amyloid plaques in situ, similarly inhibited either FP- or Aβ(26–42)-induced hemolysis, and surface plasmon resonance indicated that this may be due to direct CR-peptide binding. These findings suggest that membrane-bound β-sheets of FP may contribute to the cytopathicity of HIV in vivo through an amyloid-type mechanism, and support the classification of HIV-1 FP as an ‘amyloid homolog’ (or ‘amylog’). PMID:18515070
Semantic Ambiguity: Do Multiple Meanings Inhibit or Facilitate Word Recognition?

PubMed

Haro, Juan; Ferré, Pilar

2018-06-01

It is not clear whether multiple unrelated meanings inhibit or facilitate word recognition. Some studies have found a disadvantage for words having multiple meanings with respect to unambiguous words in lexical decision tasks (LDT), whereas several others have shown a facilitation for such words. In the present study, we argue that these inconsistent findings may be due to the approach employed to select ambiguous words across studies. To address this issue, we conducted three LDT experiments in which we varied the measure used to classify ambiguous and unambiguous words. The results suggest that multiple unrelated meanings facilitate word recognition. In addition, we observed that the approach employed to select ambiguous words may affect the pattern of experimental results. This evidence has relevant implications for theoretical accounts of ambiguous words processing and representation.
New mathematic model for predicting chiral separation using molecular docking: mechanism of chiral recognition of triadimenol analogues.

PubMed

Zhang, Guoqing; Sun, Qingyan; Hou, Ying; Hong, Zhanying; Zhang, Jun; Zhao, Liang; Zhang, Hai; Chai, Yifeng

2009-07-01

The purpose of this paper was to study the enantioseparation mechanism of triadimenol compounds by carboxymethylated (CM)-beta-CD mediated CE. All the enantiomers were separated under the same experimental conditions to study the chiral recognition mechanism using a 30 mM sodium dihydrogen phosphate buffer at pH 2.2 adjusted by phosphoric acid. The inclusion courses between CM-beta-CD and enantiomers were investigated by the means of molecular docking technique. It was found that there were at least three points (one hydrophobic bond and two hydrogen bonds) involved in the interaction of each enantiomer with the chiral selectors. A new mathematic model has been built up based on the results of molecular mechanics calculations, which could analyze the relationship between the resolution of enantioseparation and the interaction energy in the docking area. Comparing the results of the separation by CE, the established mathematic model demonstrated good capability to predict chiral separation of triadimenol enantiomers using CM-beta-CD mediated CE.
Sequence swapping does not result in conformation swapping for the beta4/beta5 and beta8/beta9 beta-hairpin turns in human acidic fibroblast growth factor.

PubMed

Kim, Jaewon; Lee, Jihun; Brych, Stephen R; Logan, Timothy M; Blaber, Michael

2005-02-01

The beta-turn is the most common type of nonrepetitive structure in globular proteins, comprising ~25% of all residues; however, a detailed understanding of effects of specific residues upon beta-turn stability and conformation is lacking. Human acidic fibroblast growth factor (FGF-1) is a member of the beta-trefoil superfold and contains a total of five beta-hairpin structures (antiparallel beta-sheets connected by a reverse turn). beta-Turns related by the characteristic threefold structural symmetry of this superfold exhibit different primary structures, and in some cases, different secondary structures. As such, they represent a useful system with which to study the role that turn sequences play in determining structure, stability, and folding of the protein. Two turns related by the threefold structural symmetry, the beta4/beta5 and beta8/beta9 turns, were subjected to both sequence-swapping and poly-glycine substitution mutations, and the effects upon stability, folding, and structure were investigated. In the wild-type protein these turns are of identical length, but exhibit different conformations. These conformations were observed to be retained during sequence-swapping and glycine substitution mutagenesis. The results indicate that the beta-turn structure at these positions is not determined by the turn sequence. Structural analysis suggests that residues flanking the turn are a primary structural determinant of the conformation within the turn.
The structure and dynamics of tandem WW domains in a negative regulator of notch signaling, Suppressor of deltex.

PubMed

Fedoroff, Oleg Y; Townson, Sharon A; Golovanov, Alexander P; Baron, Martin; Avis, Johanna M

2004-08-13

WW domains mediate protein recognition, usually though binding to proline-rich sequences. In many proteins, WW domains occur in tandem arrays. Whether or how individual domains within such arrays cooperate to recognize biological partners is, as yet, poorly characterized. An important question is whether functional diversity of different WW domain proteins is reflected in the structural organization and ligand interaction mechanisms of their multiple domains. We have determined the solution structure and dynamics of a pair of WW domains (WW3-4) from a Drosophila Nedd4 family protein called Suppressor of deltex (Su(dx)), a regulator of Notch receptor signaling. We find that the binding of a type 1 PPPY ligand to WW3 stabilizes the structure with effects propagating to the WW4 domain, a domain that is not active for ligand binding. Both WW domains adopt the characteristic triple-stranded beta-sheet structure, and significantly, this is the first example of a WW domain structure to include a domain (WW4) lacking the second conserved Trp (replaced by Phe). The domains are connected by a flexible linker, which allows a hinge-like motion of domains that may be important for the recognition of functionally relevant targets. Our results contrast markedly with those of the only previously determined three-dimensional structure of tandem WW domains, that of the rigidly oriented WW domain pair from the RNA-splicing factor Prp40. Our data illustrate that arrays of WW domains can exhibit a variety of higher order structures and ligand interaction mechanisms.
Recognition of conformational changes in beta-lactoglobulin by molecularly imprinted thin films.

PubMed

Turner, Nicholas W; Liu, Xiao; Piletsky, Sergey A; Hlady, Vladimir; Britt, David W

2007-09-01

Pathogenesis in protein conformational diseases is initiated by changes in protein secondary structure. This molecular restructuring presents an opportunity for novel shape-based detection approaches, as protein molecular weight and chemistry are otherwise unaltered. Here we apply molecular imprinting to discriminate between distinct conformations of the model protein beta-lactoglobulin (BLG). Thermal- and fluoro-alcohol-induced BLG isoforms were imprinted in thin films of 3-aminophenylboronic acid on quartz crystal microbalance chips. Enhanced rebinding of the template isoform was observed in all cases when compared to the binding of nontemplate isoforms over the concentration range of 1-100 microg mL(-1). Furthermore, it was observed that the greater the changes in the secondary structure of the template protein the lower the binding of native BLG challenges to the imprint, suggesting a strong steric influence in the recognition system. This feasibility study is a first demonstration of molecular imprints for recognition of distinct conformations of the same protein.
Molecular Mechanism of Thioflavin-T Binding to the Surface of [beta]-Rich Peptide Self-Assemblies

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

Biancalana, Matthew; Makabe, Koki; Koide, Akiko

A number of small organic molecules have been developed that bind to amyloid fibrils, a subset of which also inhibit fibrillization. Among these, the benzothiol dye Thioflavin-T (ThT) has been used for decades in the diagnosis of protein-misfolding diseases and in kinetic studies of self-assembly (fibrillization). Despite its importance, efforts to characterize the ThT-binding mechanism at the atomic level have been hampered by the inherent insolubility and heterogeneity of peptide self-assemblies. To overcome these challenges, we have developed a minimalist approach to designing a ThT-binding site in a 'peptide self-assembly mimic' (PSAM) scaffold. PSAMs are engineered water-soluble proteins that mimicmore » a segment of beta-rich peptide self-assembly, and they are amenable to standard biophysical techniques and systematic mutagenesis. The PSAM beta-sheet contains rows of repetitive amino acid patterns running perpendicular to the strands (cross-strand ladders) that represent a ubiquitous structural feature of fibril-like surfaces. We successfully designed a ThT-binding site that recapitulates the hallmarks of ThT-fibril interactions by constructing a cross-strand ladder consisting of contiguous tyrosines. The X-ray crystal structures suggest that ThT interacts with the beta-sheet by docking onto surfaces formed by a single tyrosine ladder, rather than in the space between adjacent ladders. Systematic mutagenesis further demonstrated that tyrosine surfaces across four or more beta-strands formed the minimal binding site for ThT. Our work thus provides structural insights into how this widely used dye recognizes a prominent subset of peptide self-assemblies, and proposes a strategy to elucidate the mechanisms of fibril-ligand interactions.« less

pH-directed self-assembling helical peptide conformation

USDA-ARS?s Scientific Manuscript database

The beta-sheet and alpha-helix peptide conformation are two of the most fundamentally ordered secondary structures found in proteins and peptides. They also give rise to self-assembling motifs that form macromolecular channels and nanostructures. Through design these conformations can yield enhance...
Engineering of an Extremely Thermostable Alpha/Beta Barrel Scaffold to Serve as a High Affinity Molecular Recognition Element for Use in Sensor Applications

DTIC Science & Technology

2015-12-23

papers submitted or published that acknowledge ARO support from the start of the project to the date of this printing. List the papers, including...1. Koide, S. & Sidhu, S.S. The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins. ACS
Estradiol-Induced Object Recognition Memory Consolidation Is Dependent on Activation of mTOR Signaling in the Dorsal Hippocampus

ERIC Educational Resources Information Center

Fortress, Ashley M.; Fan, Lu; Orr, Patrick T.; Zhao, Zaorui; Frick, Karyn M.

2013-01-01

The mammalian target of rapamycin (mTOR) signaling pathway is an important regulator of protein synthesis and is essential for various forms of hippocampal memory. Here, we asked whether the enhancement of object recognition memory consolidation produced by dorsal hippocampal infusion of 17[Beta]-estradiol (E[subscript 2]) is dependent on mTOR…
Adrenergic enhancement of consolidation of object recognition memory.

PubMed

Dornelles, Arethuza; de Lima, Maria Noemia Martins; Grazziotin, Manoela; Presti-Torres, Juliana; Garcia, Vanessa Athaide; Scalco, Felipe Siciliani; Roesler, Rafael; Schröder, Nadja

2007-07-01

Extensive evidence indicates that epinephrine (EPI) modulates memory consolidation for emotionally arousing tasks in animals and human subjects. However, previous studies have not examined the effects of EPI on consolidation of recognition memory. Here we report that systemic administration of EPI enhances consolidation of memory for a novel object recognition (NOR) task under different training conditions. Control male rats given a systemic injection of saline (0.9% NaCl) immediately after NOR training showed significant memory retention when tested at 1.5 or 24, but not 96h after training. In contrast, rats given a post-training injection of EPI showed significant retention of NOR at all delays. In a second experiment using a different training condition, rats treated with EPI, but not SAL-treated animals, showed significant NOR retention at both 1.5 and 24-h delays. We next showed that the EPI-induced enhancement of retention tested at 96h after training was prevented by pretraining systemic administration of the beta-adrenoceptor antagonist propranolol. The findings suggest that, as previously observed in experiments using aversively motivated tasks, epinephrine modulates consolidation of recognition memory and that the effects require activation of beta-adrenoceptors.
The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain.

PubMed Central

Housset, D; Mazza, G; Grégoire, C; Piras, C; Malissen, B; Fontecilla-Camps, J C

1997-01-01

The crystal structure of a mouse T-cell antigen receptor (TCR) Fv fragment complexed to the Fab fragment of a specific anti-clonotypic antibody has been determined to 2.6 A resolution. The polypeptide backbone of the TCR V alpha domain is very similar to those of other crystallographically determined V alphas, whereas the V beta structure is so far unique among TCR V beta domains in that it displays a switch of the c" strand from the inner to the outer beta-sheet. The beta chain variable region of this TCR antigen-binding site is characterized by a rather elongated third complementarity-determining region (CDR3beta) that packs tightly against the CDR3 loop of the alpha chain, without leaving any intervening hydrophobic pocket. Thus, the conformation of the CDR loops with the highest potential diversity distinguishes the structure of this TCR antigen-binding site from those for which crystallographic data are available. On the basis of all these results, we infer that a significant conformational change of the CDR3beta loop found in our TCR is required for binding to its cognate peptide-MHC ligand. PMID:9250664
Control of fibroin conformation: Toward the development of a biomimetic spinning process for silk fibers

NASA Astrophysics Data System (ADS)

Carlson, Kimberly Ann Trabbic

1999-09-01

Nature has shown that silks are sophisticated structural materials with remarkable mechanical properties; however, they are produced using far milder conditions than high-performance synthetic polymer fibers. While recent advances in molecular biotechnology have taken great strides toward the production of proteinaceous biopolymers, little is known about the processing conditions needed to spin fibers with the correct microstructures and mechanical properties. It is the purpose of this research to gain a fundamental understanding about how processing conditions affect the molecular structure of a model protein biopolymer, Bombyx mori silkworm fibroin, the structural protein of cocoon silk. Fibers of B. mori fibroin were wet spun from 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) into a methanol coagulation bath. X-ray fiber diffraction and quantitative Raman spectroscopy were used to determine that both naturally- and synthetically-spun fibers contain a high degree of beta-sheet (~50%). Fibers subjected to a post-spinning draw exhibited a preferential molecular alignment parallel to the fiber axis resulting in increased strength, stiffness, and extensibility. Fibers with microstructures and mechanical properties most similar to those of naturally-spun fibers were reproduced in synthetically-spun fibers with a draw ratio of 3.5. The transformation of helical fibroin in HFIP to beta-sheet sheet fibroin in synthetically-spun fibers was determined to be caused by the methanol coagulation bath. The kinetics beta-sheet fibroin crystallization from aqueous solution was investigated by monitoring the sigmoidal progression of gel formation using turbidity and Raman spectroscopy. Gelation kinetics were evaluated by measuring lag time, maximum gelation rate, and optical density to determine the effects of protein concentration, detergent concentration (nucleating agent), headgroup chemistry, ionic strength, pH, and temperature. An optimal molar ratio between SDS and fibroin (100:1) was found to produce gels with minimum lag times and maximum gelation rates. Fluorescence spectroscopy and a two-step denaturation and aggregation model for gelation were used to explore the mechanism of fibroin gelation. Conditions that lead to fibroin expansion (dilute fibroin, low ionic strength, highly charged fibroin, or increased temperature) result in decreased lag times. The results presented in this dissertation should aid in developing biomimetic spinning techniques for proteinaceous, biopolymers through the use of amphiphilic sheet nucleating agents.
Structure-function relationship in the globular type III antifreeze protein: identification of a cluster of surface residues required for binding to ice.

PubMed Central

Chao, H.; Sönnichsen, F. D.; DeLuca, C. I.; Sykes, B. D.; Davies, P. L.

1994-01-01

Antifreeze proteins (AFPs) depress the freezing point of aqueous solutions by binding to and inhibiting the growth of ice. Whereas the ice-binding surface of some fish AFPs is suggested by their linear, repetitive, hydrogen bonding motifs, the 66-amino-acid-long Type III AFP has a compact, globular fold without any obvious periodicity. In the structure, 9 beta-strands are paired to form 2 triple-stranded antiparallel sheets and 1 double-stranded antiparallel sheet, with the 2 triple sheets arranged as an orthogonal beta-sandwich (Sönnichsen FD, Sykes BD, Chao H, Davies PL, 1993, Science 259:1154-1157). Based on its structure and an alignment of Type III AFP isoform sequences, a cluster of conserved, polar, surface-accessible amino acids (N14, T18, Q44, and N46) was noted on and around the triple-stranded sheet near the C-terminus. At 3 of these sites, mutations that switched amide and hydroxyl groups caused a large decrease in antifreeze activity, but amide to carboxylic acid changes produced AFPs that were fully active at pH 3 and pH 6. This is consistent with the observation that Type III AFP is optimally active from pH 2 to pH 11. At a concentration of 1 mg/mL, Q44T, N14S, and T18N had 50%, 25%, and 10% of the activity of wild-type antifreeze, respectively. The effects of the mutations were cumulative, such that the double mutant N14S/Q44T had 10% of the wild-type activity and the triple mutant N14S/T18N/Q44T had no activity. All mutants with reduced activity were shown to be correctly folded by NMR spectroscopy. Moreover, a complete characterization of the triple mutant by 2-dimensional NMR spectroscopy indicated that the individual and combined mutations did not significantly alter the structure of these proteins. These results suggest that the C-terminal beta-sheet of Type III AFP is primarily responsible for antifreeze activity, and they identify N14, T18, and Q44 as key residues for the AFP-ice interaction. PMID:7849594
Structural Basis for Recognition and Sequestration of UUUOH 3 ' Temini of Nascent RNA Polymerase III Transcripts by La, a Rheumatic Disease Autoantigen

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

Teplova,M.; Yuan, Y.; Phan, A.

2006-01-01

The nuclear phosphoprotein La was identified as an autoantigen in patients with systemic lupus erythematosus and Sjogren's syndrome. La binds to and protects the UUUOH 3' terminii of nascent RNA polymerase III transcripts from exonuclease digestion. We report the 1.85 Angstroms crystal structure of the N-terminal domain of human La, consisting of La and RRM1 motifs, bound to r(U1-G2-C3-U4-G5-U6-U7-U8-U9OH). The U7-U8-U9OH 3' end, in a splayed-apart orientation, is sequestered within a basic and aromatic amino acid-lined cleft between the La and RRM1 motifs. The specificity-determining U8 residue bridges both motifs, in part through unprecedented targeting of the {beta} sheet edge,more » rather than the anticipated face, of the RRM1 motif. Our structural observations, supported by mutation studies of both La and RNA components, illustrate the principles behind RNA sequestration by a rheumatic disease autoantigen, whereby the UUUOH 3' ends of nascent RNA transcripts are protected during downstream processing and maturation events.« less
Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen.

PubMed

Teplova, Marianna; Yuan, Yu-Ren; Phan, Anh Tuân; Malinina, Lucy; Ilin, Serge; Teplov, Alexei; Patel, Dinshaw J

2006-01-06

The nuclear phosphoprotein La was identified as an autoantigen in patients with systemic lupus erythematosus and Sjogren's syndrome. La binds to and protects the UUU(OH) 3' terminii of nascent RNA polymerase III transcripts from exonuclease digestion. We report the 1.85 angstroms crystal structure of the N-terminal domain of human La, consisting of La and RRM1 motifs, bound to r(U1-G2-C3-U4-G5-U6-U7-U8-U9OH). The U7-U8-U9OH 3' end, in a splayed-apart orientation, is sequestered within a basic and aromatic amino acid-lined cleft between the La and RRM1 motifs. The specificity-determining U8 residue bridges both motifs, in part through unprecedented targeting of the beta sheet edge, rather than the anticipated face, of the RRM1 motif. Our structural observations, supported by mutation studies of both La and RNA components, illustrate the principles behind RNA sequestration by a rheumatic disease autoantigen, whereby the UUU(OH) 3' ends of nascent RNA transcripts are protected during downstream processing and maturation events.
Self-Assembled Hydrogels from Poly[N-(2-hydroxypropyl)methacrylamide] Grafted with β-Sheet Peptides

PubMed Central

Radu-Wu, Larisa C.; Yang, Jiyuan; Wu, Kuangshi; Kopeček, Jindřich

2009-01-01

A new hybrid hydrogel based on poly[N-(2-hydroxypropyl)methacrylamide] grafted with a β-sheet peptide, Beta11, was designed. Circular dichroism spectroscopy indicated that the folding ability of β-sheet peptide was retained in the hybrid system, whereas the sensitivity of the peptide towards temperature and pH variations was hindered. The polymer backbone also prevented the twisting of the fibrils that resulted from the antiparallel arrangement of the β-strands, as proved by Fourier transform infrared spectroscopy. Thioflavin T binding experiments and transmission electron microscopy showed fibril formation with minimal lateral aggregation. As a consequence, the graft copolymer self-assembled into a hydrogel in aqueous environment. This process was mediated by association of β-sheet domains. Scanning electron microscopy revealed a particular morphology of the network, characterized by long-range order and uniformly aligned lamellae. Microrheology results confirmed that concentration-dependent gelation occurred. PMID:19591463
Different disease-causing mutations in transthyretin trigger the same conformational conversion.

PubMed

Steward, Robert E; Armen, Roger S; Daggett, Valerie

2008-03-01

Transthyretin (TTR)-containing amyloid fibrils are deposited in cardiac tissue as a natural consequence of aging. A large number of inherited mutations lead to amyloid diseases by accelerating TTR deposition in other organs. Amyloid formation is preceded by a disruption of the quaternary structure of TTR and conformational changes in the monomer. To study conformational changes preceding the formation of amyloid, we performed molecular dynamics simulations of the wild-type monomer, amyloidogenic variants (V30M, L55P, V122I) and a protective variant (T119M) at neutral and low pH. At low pH, the D strand dissociated from the beta-sheet to expose the A strand, consistent with experimental studies. In amyloidogenic variants and in the wild-type at low pH, there was a conformational change in the beta-sheets into alpha-sheet via peptide bond flips that was not observed at neutral pH in the wild-type monomer. The same residues participated in conversion in each amyloidogenic variant simulation, originating in the G strand between residues 106 and 109, with accelerated conversion at low pH. The T119M protective variant changed the local conformation of the H strand and suppressed the conversion observed in amyloidogenic variants.
Development of Epstein-Barr virus-specific memory T cell receptor clonotypes in acute infectious mononucleosis

PubMed Central

1996-01-01

The importance of cytotoxic T lymphocytes (CTLs) in the immunosurveillance of Epstein-Barr virus (EBV)-infected B cells is firmly established, and the viral antigens of CTL recognition in latent infection are well defined. The epitopes targeted by CTLs during primary infection have not been identified, however, and there is only limited information about T cell receptor (TCR) selection. In the present report, we have monitored the development of memory TCR-beta clonotypes selected in response to natural EBV infection in a longitudinal study of an HLA-B8+ individual with acute infectious mononucleosis (IM). By stimulating peripheral blood lymphocytes with HLA-B8+ EBV-transformed B lymphoblastoid cells, the primary virus- specific CTL response was shown to include specificities for two HLA-B8- restricted antigenic determinants, FLRGRAYGL and QAKWRLQTL, which are encoded within the latent EBV nuclear antigen EBNA-3. TCR-beta sequence analysis of CTL clones specific for each epitope showed polyclonal TCR- beta repertoire selection, with structural restrictions on recognition that indicated antigen-driven selection. Furthermore, longitudinal repertoire analysis revealed long-term preservation of a multiclonal effector response throughout convalescence, with the reemergence of distinct memory T cell clonotypes sharing similar structural restrictions. Tracking the progression of specific TCR-beta clonotypes and antigen-specific TCR-V beta family gene expression in the peripheral repertoire ex vivo using semiquantitative PCR strongly suggested that selective TCR-beta expansions were present at the clonotype level, but not at the TCR-V beta family level. Overall, in this first analysis of antigen-specific TCR development in IM, a picture of polyclonal TCR stimulation is apparent. This diversity may be especially important in the establishment of an effective CTL control during acute EBV infection and in recovery from disease. PMID:8920869
S-ovalbumin, an ovalbumin conformer with properties analogous to those of loop-inserted serpins.

PubMed Central

Huntington, J. A.; Patston, P. A.; Gettins, P. G.

1995-01-01

Most serpins are inhibitors of serine proteinases and are thought to undergo a conformational change upon complex formation with proteinase that involves partial insertion of the reactive center loop into a beta-sheet of the inhibitor. Ovalbumin, although a serpin, is not an inhibitor of serine proteinases. It has been proposed that this deficiency arises from the presence of a charged residue, arginine, at a critical point (P14) in the reactive center region, which prevents loop insertion into the beta-sheet and thereby precludes inhibitory properties. To test whether loop insertion is prevented in ovalbumin we have examined the properties of two forms of ovalbumin: the native protein and S-ovalbumin, a form that forms spontaneously from native ovalbumin and has increased stability. Calorimetric measurements showed that S-ovalbumin was more stable than ovalbumin by about 3 kcal mol-1. CD spectra, which indicated that S-ovalbumin had less alpha-helix than native ovalbumin, and 1H NMR spectra, which indicated very similar overall structures, suggest limited conformational differences between the two forms. From comparison of the susceptibility of the reactive center region of each protein to proteolysis by porcine pancreatic elastase and by subtilisin Carlsberg, we concluded that the limited native-to-S conformational change specifically affected the reactive center region. These data are consistent with a structure for S-ovalbumin in which part of the reactive center loop has inserted into beta-sheet A to give a more stable structure, analogously to other serpins. However, the rate of loop insertion appears to be very much lower than for inhibitory serpins.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7613461
Oligopeptides and copeptides of homochiral sequence, via beta-sheets, from mixtures of racemic alpha-amino acids, in a one-pot reaction in water; relevance to biochirogenesis.

PubMed

Illos, Roni A; Bisogno, Fabricio R; Clodic, Gilles; Bolbach, Gerard; Weissbuch, Isabelle; Lahav, Meir

2008-07-09

As part of our studies on the biochirogenesis of peptides of homochiral sequence during early evolution, the formation of oligopeptides composed of 14-24 residues of the same handedness in the polymerization of dl-leucine (Leu), dl-phenylalanine (Phe), and dl-valine (Val) in aqueous solutions, by activation with N, N'-carbonyldiimidazole and then initiation with a primary amine, in a one-pot reaction, was demonstrated by MALDI-TOF MS using deuterium enantio-labeled alpha-amino acids. The formation of long isotactic peptides is rationalized by the following steps occurring in tandem: (i) creation of a library of short diasteroisomeric oligopeptides containing isotactic peptides in excess in comparison to a binomial kinetics, as a result of an asymmetric induction exerted by the N-terminal residue of a given handedness; (ii) precipitation of the less soluble racemic isotactic penta- and hexapeptides in the form of beta-sheets that are delineated by homochiral rims; (iii) regio-enantiospecific chain elongation occurring heterogeneously at the beta-sheets/solution interface. Polymerization of l-Leu with l-isoleucine (Ile) or l-Phe with l- (1) N-Me-histidine yielded mixtures of copeptides containing both residues. In contrast, in the polymerization of the corresponding mixtures of l- + d-alpha-amino acids, the long oligopeptides were composed mainly from oligo- l-Leu and oligo- d-Ile in the first system and oligo- d-Phe in the second. Furthermore, in the polymerization of mixtures of hydrophobic racemic alpha-amino acids dl-Leu, dl-Val, and dl-Phe and with added racemic dl-alanine and dl-tyrosine, copeptides of homochiral sequences are most dominantly represented. Possible routes for a spontaneous "mirror-symmetry breaking" process of the racemic mixtures of homochiral peptides are presented.
Usage of semantic representations in recognition memory.

PubMed

Nishiyama, Ryoji; Hirano, Tetsuji; Ukita, Jun

2017-11-01

Meanings of words facilitate false acceptance as well as correct rejection of lures in recognition memory tests, depending on the experimental context. This suggests that semantic representations are both directly and indirectly (i.e., mediated by perceptual representations) used in remembering. Studies using memory conjunction errors (MCEs) paradigms, in which the lures consist of component parts of studied words, have reported semantic facilitation of rejection of the lures. However, attending to components of the lures could potentially cause this. Therefore, we investigated whether semantic overlap of lures facilitates MCEs using Japanese Kanji words in which a whole-word image is more concerned in reading. Experiments demonstrated semantic facilitation of MCEs in a delayed recognition test (Experiment 1), and in immediate recognition tests in which participants were prevented from using phonological or orthographic representations (Experiment 2), and the salient effect on individuals with high semantic memory capacities (Experiment 3). Additionally, analysis of the receiver operating characteristic suggested that this effect is attributed to familiarity-based memory judgement and phantom recollection. These findings indicate that semantic representations can be directly used in remembering, even when perceptual representations of studied words are available.
Double-stranded helical twisted beta-sheet channels in crystals of gramicidin S grown in the presence of trifluoroacetic and hydrochloric acids.

PubMed

Llamas-Saiz, Antonio L; Grotenbreg, Gijsbert M; Overhand, Mark; van Raaij, Mark J

2007-03-01

Gramicidin S is a nonribosomally synthesized cyclic decapeptide antibiotic with twofold symmetry (Val-Orn-Leu-D-Phe-Pro)(2); a natural source is Bacillus brevis. Gramicidin S is active against Gram-positive and some Gram-negative bacteria. However, its haemolytic toxicity in humans limits its use as an antibiotic to certain topical applications. Synthetically obtained gramicidin S was crystallized from a solution containing water, methanol, trifluoroacetic acid and hydrochloric acid. The structure was solved and refined at 0.95 A resolution. The asymmetric unit contains 1.5 molecules of gramicidin S, two trifluoroacetic acid molecules and ten water molecules located and refined in 14 positions. One gramicidin S molecule has an exact twofold-symmetrical conformation; the other deviates from the molecular twofold symmetry. The cyclic peptide adopts an antiparallel beta-sheet secondary structure with two type II' beta-turns. These turns have the residues D-Phe and Pro at positions i + 1 and i + 2, respectively. In the crystals, the gramicidin S molecules line up into double-stranded helical channels that differ from those observed previously. The implications of the supramolecular structure for several models of gramicidin S conformation and assembly in the membrane are discussed.
Dynamic Instability Leading to Increased Interchange Reconnection Rates

NASA Astrophysics Data System (ADS)

Edmondson, J. K.; Antiochos, S. K.; Zurbuchen, T. H.

2008-12-01

Interchange reconnection is widely believed to play an important role in coronal magnetic field dynamics. In this investigation we investigate the 3D dynamics of interchange reconnection by extending the concept of a magnetic null-point to a null-volume, the so-called "acute-cusp field" configuration. The acute-cusp field geometry is characterized by high-beta plasma confined with favorable curvature, surrounded by a low-beta environment. First, we construct an initial translationally-symmetric potential field configuration. This configuration contains the required topological characteristics of four separate flux systems in the perpendicular plane. We then drive the system by a slow, incompressible, uniform flow at the boundary. The resulting evolution is calculated by solving numerically the MHD equations in full 3D Cartesian coordinates using the Adaptively Refined MHD Solver developed at the U.S. Naval Research Laboratory. Field shearing along the topological boundaries changes the shape of the acute-cusp field surface separating the high and low plasma beta regions. An extended, 2D current sheet is generated by the photospheric driving. We discuss the effect of 3D perturbations on the current sheet dynamics and on the rate of the resulting interchange reconnection. Finally, we discuss the implications of our simulations for coronal observations. This work has been supported, in part, by the NASA HTP and SR&T programs.
Secondary Structure Switch

ERIC Educational Resources Information Center

King, Angela G.

2006-01-01

Neurogenerative diseases like Alzheimer's disease and Parkinson's disease involve a transformation between two peptide and protein structures of alpha-helices and beta-sheets, where the peptide backbone can also participate in metal ion binding in addition to histidine residues. However, the complete absence of change in conformation of Coiled…
Biochemical and biophysical characterization of the major outer surface protein, OSP-A from North American and European isolates of Borrelia burgdorferi

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

McGrath, B.C.; Dunn, J.J.; France, L.L.

1995-12-31

Lyme borreliosis, caused by the spirochete Borrelia burgdorferi, is the most common vector-borne disease in North America and Western Europe. As the major delayed immune response in humans, a better understanding of the major outer surface lipoproteins OspA and OspB are of much interest. These proteins have been shown to exhibit three distinct phylogenetic genotypes based on their DNA sequences. This paper describes the cloning of genomic DNA for each variant and amplification of PCR. DNA sequence data was used to derive computer driven phylogenetic analysis and deduced amino acid sequences. Overproduction of variant OspAs was carried out in E.more » coli using a T7-based expression system. Circular dichroism and fluorescence studies was carried out on the recombinant B31 PspA yielding evidence supporting a B31 protein containing 11% alpha-helix, 34% antiparallel beta-sheet, 12% parallel beta sheet.« less
Functional Hydrogel Materials Inspired by Amyloid

NASA Astrophysics Data System (ADS)

Schneider, Joel

2012-02-01

Protein assembly resulting in the formation of amyloid fibrils, assemblies rich in cross beta-sheet structure, is normally thought of as a deleterious event associated with disease. However, amyloid formation is also involved in a diverse array of normal biological functions such as cell adhesion, melanin synthesis, insect defense mechanism and modulation of water surface tension by fungi and bacteria. These findings indicate that Nature has evolved to take advantage of large, proteinaceous fibrillar assemblies to elicit function. We are designing functional materials, namely hydrogels, from peptides that self-assembled into fibrillar networks, rich in cross beta-sheet structure. These gels can be used for the direct encapsulation and delivery of small molecule-, protein- and cell-based therapeutics. Loaded gels exhibit shear-thinning/self-healing mechanical properties enabling their delivery via syringe. In addition to their use for delivery, we have found that some of these gels display antibacterial activity. Although cytocompatible towards mammalian cells, the hydrogels can kill a broad spectrum of bacteria on contact.

Counterstreaming beams and flat-top electron distributions observed with Langmuir, Whistler, and compressional Alfvén waves in earth's magnetic tail.

PubMed

Teste, Alexandra; Parks, George K

2009-02-20

Relevant new clues to wave-particle interactions have been obtained in Earth's plasma sheet (PS). The plasma measurements made on Cluster spacecraft show that broadband (approximately 2-6 kHz) electrostatic emissions, in the PS boundary layer, are associated with cold counterstreaming electrons flowing at 5-12x10(3) km s(-1) through hot Maxwellian plasma. In the current sheet (CS), electromagnetic whistler mode waves (approximately 10-80 Hz) and compressional Alfvén waves (<2 Hz) are detected with flat-topped electron distributions whose cutoff speeds are approximately 15-17x10(3) km s(-1). These waves are damped in the central CS where |B|
Modeling protein homopolymeric repeats: possible polyglutamine structural motifs for Huntington's disease.

PubMed

Lathrop, R H; Casale, M; Tobias, D J; Marsh, J L; Thompson, L M

1998-01-01

We describe a prototype system (Poly-X) for assisting an expert user in modeling protein repeats. Poly-X reduces the large number of degrees of freedom required to specify a protein motif in complete atomic detail. The result is a small number of parameters that are easily understood by, and under the direct control of, a domain expert. The system was applied to the polyglutamine (poly-Q) repeat in the first exon of huntingtin, the gene implicated in Huntington's disease. We present four poly-Q structural motifs: two poly-Q beta-sheet motifs (parallel and antiparallel) that constitute plausible alternatives to a similar previously published poly-Q beta-sheet motif, and two novel poly-Q helix motifs (alpha-helix and pi-helix). To our knowledge, helical forms of polyglutamine have not been proposed before. The motifs suggest that there may be several plausible aggregation structures for the intranuclear inclusion bodies which have been found in diseased neurons, and may help in the effort to understand the structural basis for Huntington's disease.
Calmodulin-dependent gating of Ca(v)1.2 calcium channels in the absence of Ca(v)beta subunits.

PubMed

Ravindran, Arippa; Lao, Qi Zong; Harry, Jo Beth; Abrahimi, Parwiz; Kobrinsky, Evgeny; Soldatov, Nikolai M

2008-06-10

It is generally accepted that to generate calcium currents in response to depolarization, Ca(v)1.2 calcium channels require association of the pore-forming alpha(1C) subunit with accessory Ca(v)beta and alpha(2)delta subunits. A single calmodulin (CaM) molecule is tethered to the C-terminal alpha(1C)-LA/IQ region and mediates Ca2+-dependent inactivation of the channel. Ca(v)beta subunits are stably associated with the alpha(1C)-interaction domain site of the cytoplasmic linker between internal repeats I and II and also interact dynamically, in a Ca2+-dependent manner, with the alpha(1C)-IQ region. Here, we describe a surprising discovery that coexpression of exogenous CaM (CaM(ex)) with alpha(1C)/alpha(2)delta in COS1 cells in the absence of Ca(v)beta subunits stimulates the plasma membrane targeting of alpha(1C), facilitates calcium channel gating, and supports Ca2+-dependent inactivation. Neither real-time PCR with primers complementary to monkey Ca(v)beta subunits nor coimmunoprecipitation analysis with exogenous alpha(1C) revealed an induction of endogenous Ca(v)beta subunits that could be linked to the effect of CaM(ex). Coexpression of a calcium-insensitive CaM mutant CaM(1234) also facilitated gating of Ca(v)beta-free Ca(v)1.2 channels but did not support Ca2+-dependent inactivation. Our results show there is a functional matchup between CaM(ex) and Ca(v)beta subunits that, in the absence of Ca(v)beta, renders Ca2+ channel gating facilitated by CaM molecules other than the one tethered to LA/IQ to support Ca2+-dependent inactivation. Thus, coexpression of CaM(ex) creates conditions when the channel gating, voltage- and Ca2+-dependent inactivation, and plasma-membrane targeting occur in the absence of Ca(v)beta. We suggest that CaM(ex) affects specific Ca(v)beta-free conformations of the channel that are not available to endogenous CaM.
IL-1ra alleviates inflammatory hyperalgesia through preventing phosphorylation of NMDA receptor NR-1 subunit in rats.

PubMed

Zhang, Rui-Xin; Li, Aihui; Liu, Bing; Wang, Linbo; Ren, Ke; Zhang, Haiqing; Berman, Brian M; Lao, Lixing

2008-04-01

Although it has been shown that pro-inflammatory cytokines such as interleukin-1beta (IL-1beta) facilitate perception of noxious inputs at the spinal level, the mechanisms have not been understood. This study determined the cell type that produces IL-1beta, the co-localization of IL-1 receptor type I (IL-1RI) and Fos and NR1 in the spinal cord, and the effects of IL-1 receptor antagonist (IL-1ra) on NR1 phosphorylation and hyperalgesia in a rat model of inflammatory pain. Phosphorylation of NR1, an essential subunit of the NMDA receptor (NMDAR), is known to modulate NMDAR activity and facilitate pain. Hyperalgesia was induced by injecting complete Freund's adjuvant (CFA, 0.08ml, 40microg Mycobacterium tuberculosis) into one hind paw of each rat. Paw withdrawal latency (PWL) was tested before CFA (-48h) for baseline and 2 and 24h after CFA to assess hyperalgesia. IL-1ra was given (i.t.) 24h before CFA to block the action of basal IL-1beta and 2h prior to each of two PWL tests to block CFA-induced IL-1beta. Spinal cords were removed for double immunostaining of IL-1beta/neuronal marker and IL-1beta/glial cell markers, IL-1RI/Fos and IL-1RI/NR1, and for Western blot to measure NR1 phosphorylation. The data showed that: (1) astrocytes produce IL-1beta, (2) IL-1RI is localized in Fos- and NR1-immunoreactive neurons within the spinal dorsal horn, and (3) IL-1ra at 0.01mg/rat significantly increased PWL (P<0.05) and inhibited NR1 phosphorylation compared to saline control. The results suggest that spinal IL-1beta is produced by astrocytes and enhances NR1 phosphorylation to facilitate inflammatory pain.
Improving medical imaging report turnaround times: the role of technolgy.

PubMed

Marquez, Luis O; Stewart, Howard

2005-01-01

At Southern Ohio Medical Center (SOMC), the medical imaging department and the radiologists expressed a strong desire to improve workflow. The improved workflow was a major motivating factor toward implementing a new RIS and speech recognition technology. The need to monitor workflow in a real-time fashion and to evaluate productivity and resources necessitated that a new solution be found. A decision was made to roll out both the new RIS product and speech recognition to maximize the resources to interface and implement the new solution. Prior to implementation of the new RIS, the medical imaging department operated in a conventional electronic-order-entry to paper request manner. The paper request followed the study through exam completion to the radiologist. SOMC entered into a contract with its PACS vendor to participate in beta testing and clinical trials for a new RIS product for the US market. Backup plans were created in the event the product failed to function as planned--either during the beta testing period or during clinical trails. The last piece of the technology puzzle to improve report turnaround time was voice recognition technology. Speech recognition enhanced the RIS technology as soon as it was implemented. The results show that the project has been a success. The new RIS, combined with speech recognition and the PACS, makes for a very effective solution to patient, exam, and results management in the medical imaging department.
False recognition correlates with amyloid-beta (1-42) but not with total tau in cerebrospinal fluid of patients with dementia and mild cognitive impairment.

PubMed

Hildebrandt, Helmut; Haldenwanger, Andreas; Eling, Paul

2009-01-01

Severe memory impairment forms the core symptom of Alzheimer's disease (AD), which is present early in the disease course. Recent studies show that AD patients not only suffer from forgetfulness, but also differ in their response bias, when having to decide whether information has been perceived recently, or whether it is only familiar or semantically related to perceived information. Changes in total tau-protein and amyloid-beta (Abeta) (1-42) concentration in cerebrospinal fluid are also features of AD, and they predict conversion from mild cognitive impairment to dementia. In this study we correlated recognition scores with total tau and Abeta (1-42) concentrations in patients with suggested dementia. We studied 40 patients and 21 healthy controls, using an incidental recognition memory task and a neuropsychological test battery. False recognition scores correlated with delayed recall and with Abeta(1-42), and Abeta (1-42) tended to correlate with delayed recall. Total tau, however, did not correlate with memory scores or with neuropsychological performance in general. We suggest that Abeta (1-42) may indicate a reduction in the specificity of the neuronal response in the limbic cortex, due to agglomeration of plaques. This process might be more specific for AD than the increase of tau, and therefore it is stronger correlated with recognition errors.
Detecting beta-amyloid aggregation from time-resolved emission spectra

NASA Astrophysics Data System (ADS)

Alghamdi, A.; Vyshemirsky, V.; Birch, D. J. S.; Rolinski, O. J.

2018-04-01

The aggregation of beta-amyloids is one of the key processes responsible for the development of Alzheimer’s disease. Early molecular-level detection of beta-amyloid oligomers may help in early diagnosis and in the development of new intervention therapies. Our previous studies on the changes in beta-amyloid’s single tyrosine intrinsic fluorescence response during aggregation demonstrated a four-exponential fluorescence intensity decay, and the ratio of the pre-exponential factors indicated the extent of the aggregation in the early stages of the process before the beta-sheets were formed. Here we present a complementary approach based on the time-resolved emission spectra (TRES) of amyloid’s tyrosine excited at 279 nm and fluorescence in the window 240-450 nm. TRES have been used to demonstrate sturctural changes occuring on the nanosecond time scale after excitation which has significant advantages over using steady-state spectra. We demonstrate this by resolving the fluorescent species and revealing that beta-amyloid’s monomers show very fast dielectric relaxation, and its oligomers display a substantial spectral shift due to dielectric relaxation, which gradually decreases when the oligomers become larger.
Analysis of the structural organization and thermal stability of two spermadhesins. Calorimetric, circular dichroic and Fourier-transform infrared spectroscopic studies.

PubMed

Menéndez, M; Gasset, M; Laynez, J; López-Zumel, C; Usobiaga, P; Töpfer-Petersen, E; Calvete, J J

1995-12-15

The CUB domain is a widespread 110-amino-acid module found in functionally diverse, often developmentally regulated proteins, for which an antiparallel beta-barrel topology similar to that in immunoglobulin V domains has been predicted. Spermadhesins have been proposed as a subgroup of this protein family built up by a single CUB domain architecture. To test the proposed structural model, we have analyzed the structural organization of two members of the spermadhesin protein family, porcine seminal plasma proteins I/II (PSP-I/PSP-II) heterodimer and bovine acidic seminal fluid protein (aSFP) homodimer, using differential scanning calorimetry, far-ultraviolet circular dichroism and Fourier-transform infrared spectroscopy. Thermal unfolding of PSP-I/PSP-II and aSFP were irreversible and followed a one-step process with transition temperatures (Tm) of 60.5 degrees C and 78.6 degrees C, respectively. The calorimetric enthalpy changes (delta Hcat) of thermal denaturation were 439 kJ/mol for PSP-I/PSP-II and 660 kJ/mol for aSFP dimer. Analysis of the calorimetric curves of PSP-I/PSP-II showed that the entire dimer constituted the cooperative unfolding unit. Fourier-transform infrared spectroscopy and deconvolution of circular dichroic spectra using a convex constraint analysis indicated that beta-structure and turns are the major structural element of both PSP-I/PSP-II (53% of beta-sheet, 21% of turns) and aSFP (44% of beta-sheet, 36% of turns), and that the porcine and the bovine proteins contain little, if any, alpha-helical structure. Taken together, our results indicate that the porcine and the bovine spermadhesin molecules are probably all-beta-structure proteins, and would support a beta-barrel topology like that predicted for the CUB domain. Other beta-structure folds, such as the Greek-key pattern characteristic of many carbohydrate-binding protein domains cannot be eliminated. Finally, the same combination of biophysical techniques was used to characterize the residual secondary structure of thermally denatured forms of PSP-I/PSP-II and aSFP, and to emphasize the aggregation tendency of these forms.
The association of GSK3 beta with E2F1 facilitates nerve growth factor-induced neural cell differentiation.

PubMed

Zhou, Fangfang; Zhang, Long; Wang, Aijun; Song, Bo; Gong, Kai; Zhang, Lihai; Hu, Min; Zhang, Xiufang; Zhao, Nanming; Gong, Yandao

2008-05-23

It is widely acknowledged that E2F1 and GSK3beta are both involved in the process of cell differentiation. However, the relationship between E2F1 and GSK3beta in cell differentiation has yet to be discovered. Here, we provide evidence that in the differentiation of PC12 cells induced by nerve growth factor (NGF), GSK3beta was increased at both the mRNA and protein levels, whereas E2F1 at these two levels was decreased. Both wild-type GSK3beta and its kinase-defective mutant GSK3beta KM can inhibit E2F1 by promoting its ubiquitination through physical interaction. In addition, the colocalization of GSK3beta and E2F1 and their subcellular distribution, regulated by NGF, were observed in the process of PC12 differentiation. At the tissue level, GSK3beta colocalized and interacted with E2F1 in mouse hippocampus. Furthermore, GSK3beta facilitated neurite outgrowth by rescuing the promoter activities of Cdk inhibitors p21 and p15 from the inhibition caused by E2F1. To summarize, our findings suggest that GSK3beta can promote the ubiquitination of E2F1 via physical interaction and thus inhibit its transcription activity in a kinase activity independent manner, which plays an important role in the NGF-induced PC12 differentiation.
Simulation studies of substrate recognition by the exocellulase CelF from Clostridium cellulolyticum

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

Chen, Mo; Himmel, Michael E.; Wilson, David B.

Molecular dynamics (MD) simulations were used to study substrate recognition by the family 48 exocellulase CelF from Clostridium cellulolyticum. It was hypothesized that residues around the entrance of the active site tunnel of this enzyme might serve to recognize and bind the substrate through an affinity for the cellulose monomer repeat unit, ..beta..-d-glucopyranose. Simulations were conducted of the catalytic domain of this enzyme surrounded by a concentrated solution of ..beta..-d-glucopyranose, and the full three-dimensional probability distribution for finding sugar molecules adjacent to the enzyme was calculated from the trajectory. A significant probability of finding the sugar stacked against the planarmore » faces of Trp 310 and Trp 312 at the entrance of the active site tunnel was observed.« less
"Click" saccharide/beta-lactam hybrids for lectin inhibition.

PubMed

Palomo, Claudio; Aizpurua, Jesus M; Balentová, Eva; Azcune, Itxaso; Santos, J Ignacio; Jiménez-Barbero, Jesús; Cañada, Javier; Miranda, José Ignacio

2008-06-05

Hybrid glycopeptide beta-lactam mimetics designed to bind lectins or carbohydrate recognition domains in selectins have been prepared according to a "shape-modulating linker" design. This approach was implemented using the azide-alkyne "click" cycloaddition reaction, and as shown by NMR/MD experiments, binding of the resulting mimetics to Ulex Europaeus Lectin-1 (UEL-1) occurred after a "bent-to-extended" conformational change around a partially rotatable triazolylmethylene moiety.
L-selectin-carbohydrate interactions: relevant modifications of the Lewis x trisaccharide.

PubMed

Sanders, W J; Katsumoto, T R; Bertozzi, C R; Rosen, S D; Kiessling, L L

1996-11-26

Protein-carbohydrate interactions are known to mediate cell-cell recognition and adhesion events. Specifically, three carbohydrate binding proteins termed selectins (E-, P-, and L-selectin) have been shown to be essential for leukocyte rolling along the vascular endothelium, the first step in the recruitment of leukocytes from the blood into inflammatory sites or into secondary lymphoid organs. Although this phenomenon is well-established, little is known about the molecular-level interactions on which it depends. All three selectins recognize sulfated and sialylated derivatives of the Lewis x [Le(x):Gal beta 1-->4(Fuc alpha 1-->3)GlcNAc] and Lewis a [Le(a): Gal beta 1-->3(Fuc alpha 1-->4)GlcNAc] trisaccharide cores with affinities in the millimolar range, and it is believed that variants of these structures are the carbohydrate determinants of selectin recognition. Recently it was shown that the mucin GlyCAM-1, a secreted physiological ligand for L-selectin, is capped with sulfated derivatives of sialyl Lewis x [sLe(x): Sia alpha 2-->3Gal beta 1-->4(Fuc alpha 1-->3)GlcNAc] and that sulfation is required for the high-affinity interaction between GlyCAM-1 and L-selectin. To elucidate the important sites of sulfation on Le(x) with respect to L-selectin recognition, we have synthesized six sulfated Le(x) analogs and determined their abilities to block binding of a recombinant L-selectin-Ig chimera to immobilized GlyCAM-1. Our results suggest that 6-sulfo sLe(x) binds to L-selectin with higher affinity than does sLe(x) or 6'-sulfo sLe(x) and that sulfation of sLe(x) capping groups on GlyCAM-1 at the 6-position is important for L-selectin recognition.
Automatic Inspection Of Heat Seals Between Plastic Sheets

NASA Technical Reports Server (NTRS)

Rai, Kula R.; Lew, Thomas M.; Sinclair, Robert B.

1995-01-01

Automatic inspection apparatus detects flaws in heat seals between films of polyethylene or other thermoplastic material. Heat-sealed strip in multilayer plastic sheet continuously moved lengthwise over illuminators. Variations in light transmitted through sheet interpreted to find flaws in heat seal. Site of flaw marked to facilitate subsequent manual inspection. Heat sealing used to join plastic films in manufacturing of variety of products, including inflatable toys and balloons carrying scientific instruments to high altitudes.
Sequence inversion and phenylalanine surrogates at the beta-turn enhance the antibiotic activity of gramicidin S.

PubMed

Solanas, Concepción; de la Torre, Beatriz G; Fernández-Reyes, María; Santiveri, Clara M; Jiménez, M Angeles; Rivas, Luis; Jiménez, Ana I; Andreu, David; Cativiela, Carlos

2010-05-27

A series of gramicidin S (GS) analogues have been synthesized where the Phe (i + 1) and Pro (i + 2) residues of the beta-turn have been swapped while the respective chiralities (D-, L-) at each position are preserved, and Phe is replaced by surrogates with aromatic side chains of diverse size, orientation, and flexibility. Although most analogues preserve the beta-sheet structure, as assessed by NMR, their antibiotic activities turn out to be highly dependent on the bulkiness and spatial arrangement of the aromatic side chain. Significant increases in microbicidal potency against both Gram-positive and Gram-negative pathogens are observed for several analogues, resulting in improved therapeutic profiles. Data indicate that seemingly minor replacements at the GS beta-turn can have significant impact on antibiotic activity, highlighting this region as a hot spot for modulating GS plasticity and activity.
The "Decorative" Female Model: Sexual Stimuli and the Recognition of Advertisements

ERIC Educational Resources Information Center

LaChance, Charles C.; And Others

1977-01-01

Examines the impact of the decorative or functionless female models in print advertising and indicates that models facilitate recognition of model/related information but do little to increase the recognition of brand names.
A Tailward Moving Current Sheet Normal Magnetic Field Front Followed by an Earthward Moving Dipolarization Front

NASA Technical Reports Server (NTRS)

Hwang, K.-J.; Goldstein, M. L.; Moore, T. E.; Walsh, B. M.; Baishev, D. G.; Moiseyev, A. V.; Shevtsov, B. M.; Yumoto, K.

2014-01-01

A case study is presented using measurements from the Cluster spacecraft and ground-based magnetometers that show a substorm onset propagating from the inner to outer plasma sheet. On 3 October 2005, Cluster, traversing an ion-scale current sheet at the near-Earth plasma sheet, detected a sudden enhancement of Bz, which was immediately followed by a series of flux rope structures. Both the local Bz enhancement and flux ropes propagated tailward. Approximately 5 min later, another Bz enhancement, followed by a large density decrease, was observed to rapidly propagate earthward. Between the two Bz enhancements, a significant removal of magnetic flux occurred, possibly resulting from the tailward moving Bz enhancement and flux ropes. In our scenario, this flux removal caused the magnetotail to be globally stretched so that the thinnest sheet formed tailward of Cluster. The thinned current sheet facilitated magnetic reconnection that quickly evolved from plasma sheet to lobe and generated the later earthward moving dipolarization front (DF) followed by a reduction in density and entropy. Ground magnetograms located near the meridian of Cluster's magnetic foot points show two-step bay enhancements. The positive bay associated with the first Bz enhancement indicates that the substorm onset signatures propagated from the inner to the outer plasma sheet, consistent with the Cluster observation. The more intense bay features associated with the later DF are consistent with the earthward motion of the front. The event suggests that current disruption signatures that originated in the near-Earth current sheet propagated tailward, triggering or facilitating midtail reconnection, thereby preconditioning the magnetosphere for a later strong substorm enhancement.
Speaker information affects false recognition of unstudied lexical-semantic associates.

PubMed

Luthra, Sahil; Fox, Neal P; Blumstein, Sheila E

2018-05-01

Recognition of and memory for a spoken word can be facilitated by a prior presentation of that word spoken by the same talker. However, it is less clear whether this speaker congruency advantage generalizes to facilitate recognition of unheard related words. The present investigation employed a false memory paradigm to examine whether information about a speaker's identity in items heard by listeners could influence the recognition of novel items (critical intruders) phonologically or semantically related to the studied items. In Experiment 1, false recognition of semantically associated critical intruders was sensitive to speaker information, though only when subjects attended to talker identity during encoding. Results from Experiment 2 also provide some evidence that talker information affects the false recognition of critical intruders. Taken together, the present findings indicate that indexical information is able to contact the lexical-semantic network to affect the processing of unheard words.
Solution 1H NMR determination of secondary structure for the three-iron form of ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus.

PubMed

Teng, Q; Zhou, Z H; Smith, E T; Busse, S C; Howard, J B; Adams, M W; La Mar, G N

1994-05-24

Two-dimensional 1H NMR data have been used to make sequence-specific assignments and define the secondary structure of the three-iron form of the oxidized ferredoxin, Fd, from the hyperthermophilic archaeon Pyrococcus furiosus, Pf. Signals for at least some protons were located for 65 of the 66 amino acids in the sequence, in spite of the paramagnetic (S = 1/2) ground state, but not all could be assigned. Unassigned and missing signals could be qualitatively correlated with the expected proximity of the protons to the paramagnetic cluster. The secondary structure was deduced from qualitative analysis of the 2D nuclear Overhauser effect, which identified two antiparallel beta-sheets, one triple-stranded including Ala1-Ser5, Val39-Glu41, and Thr62-Ala66, and one double-stranded consisting of Glu26-Asn28 and Lys32-Glu34, as well as an alpha-helix involving Glu43-Glu54. Three tight type I turns are located at residues Asp7-Thr10, Pro22-Phe25, and Asp29-Gly31. Comparison with the crystal structure of Desulfovibrio gigas, Dg, Fd (Kissinger et al., 1991) reveals a very similar folding topology, although several secondary structural elements are extended in Pf relative to Dg Fd. Thus the beta-sheet involving the two termini is expanded to include the two terminal residues and incorporates a third strand from the internal loop that is lengthened by several insertions in Pf relative to Dg Fd. The double-stranded beta-sheet in the interior of Pf Fd is lengthened slightly due to a much tighter type I turn between the two strands. The helix near the C-terminus is three residues longer in Pf than in Dg Fd, as well as being shifted toward the N-terminus. The disulfide link between the two nonligating Cys residues (Cys21 and Cys48) is conserved in Pf Fd, but the link near the C-terminus is in the middle of the long alpha-helix in Pf Fd, instead of at the N-terminus of the helix as in Dg Fd. The extensions of the beta-sheets and alpha-helix increase the number of main-chain hydrogen bonds in Pf Fd by approximately 8 relative to those in Dg Fd and likely contribute to its remarkable thermostability (it is unaffected by anaerobic incubation at 95 degrees C for 24 h).(ABSTRACT TRUNCATED AT 400 WORDS)
Support vector machines for prediction and analysis of beta and gamma-turns in proteins.

PubMed

Pham, Tho Hoan; Satou, Kenji; Ho, Tu Bao

2005-04-01

Tight turns have long been recognized as one of the three important features of proteins, together with alpha-helix and beta-sheet. Tight turns play an important role in globular proteins from both the structural and functional points of view. More than 90% tight turns are beta-turns and most of the rest are gamma-turns. Analysis and prediction of beta-turns and gamma-turns is very useful for design of new molecules such as drugs, pesticides, and antigens. In this paper we investigated two aspects of applying support vector machine (SVM), a promising machine learning method for bioinformatics, to prediction and analysis of beta-turns and gamma-turns. First, we developed two SVM-based methods, called BTSVM and GTSVM, which predict beta-turns and gamma-turns in a protein from its sequence. When compared with other methods, BTSVM has a superior performance and GTSVM is competitive. Second, we used SVMs with a linear kernel to estimate the support of amino acids for the formation of beta-turns and gamma-turns depending on their position in a protein. Our analysis results are more comprehensive and easier to use than the previous results in designing turns in proteins.
Structure, function, and fate of the BlaR signal transducer involved in induction of beta-lactamase in Bacillus licheniformis.

PubMed Central

Zhu, Y; Englebert, S; Joris, B; Ghuysen, J M; Kobayashi, T; Lampen, J O

1992-01-01

The membrane-spanning protein BlaR is essential for the induction of beta-lactamase in Bacillus licheniformis. Its nature and location were confirmed by the use of an antiserum specific for its carboxy-terminal penicillin sensor, its function was studied by genetic dissection, and the structure of the penicillin sensor was derived from hydrophobic cluster analysis of the amino acid sequence by using, as a reference, the class A beta-lactamases with known three-dimensional structures. During the first 2 h after the addition of the beta-lactam inducer, full-size BlaR, bound to the plasma membrane, is produced, and then beta-lactamase is produced. By 2 h after induction, BlaR is present in various (membrane-bound and cytosolic) forms, and there is a gradual decrease in beta-lactamase production. The penicillin sensors of BlaR and the class D beta-lactamases show strong similarities in primary structures. They appear to have the same basic spatial disposition of secondary structures as that of the class A beta-lactamases, except that they lack several alpha helices and, therefore, have a partially uncovered five-stranded beta sheet and a more readily accessible active site. Alterations of BlaR affecting conserved secondary structures of the penicillin sensor and specific sites of the transducer annihilate beta-lactamase inducibility. Images PMID:1400165

Chest wall abscesses due to continuous application of silicone gel sheets for keloid management

PubMed Central

Tang, Hon-Lok; Lau, Keith K; Sam, Ramin; Ing, Todd S

2015-01-01

A patient with three episodes of chest wall abscesses as a result of 6 years of round-the-clock, uninterrupted (except during bathing) application of silicone gel sheets to a chest wall keloid is described. Two of the episodes occurred during hot weather. It is suggested that, in the space beneath the silicone sheet, the higher humidity and temperature, both generated as a result of prolonged sheeting, especially during hot weather, might have caused the keloid and its neighbouring skin to become soggy. This sogginess might have facilitated bacterial invasion. It is suggested that some sheeting-free time during a 24 h period might be indicated so that a keloid and its adjacent skin have the time to recover from their sheeting-induced sogginess. A sheeting-free period might especially be needed in the face of sweat accumulation beneath the silicone sheet. PMID:25920733
Chest wall abscesses due to continuous application of silicone gel sheets for keloid management.

PubMed

Tang, Hon-Lok; Lau, Keith K; Sam, Ramin; Ing, Todd S

2015-04-28

A patient with three episodes of chest wall abscesses as a result of 6 years of round-the-clock, uninterrupted (except during bathing) application of silicone gel sheets to a chest wall keloid is described. Two of the episodes occurred during hot weather. It is suggested that, in the space beneath the silicone sheet, the higher humidity and temperature, both generated as a result of prolonged sheeting, especially during hot weather, might have caused the keloid and its neighbouring skin to become soggy. This sogginess might have facilitated bacterial invasion. It is suggested that some sheeting-free time during a 24 h period might be indicated so that a keloid and its adjacent skin have the time to recover from their sheeting-induced sogginess. A sheeting-free period might especially be needed in the face of sweat accumulation beneath the silicone sheet. 2015 BMJ Publishing Group Ltd.
Type I Interferon Production Induced by Streptococcus pyogenes-Derived Nucleic Acids Is Required for Host Protection

PubMed Central

Gratz, Nina; Hartweger, Harald; Matt, Ulrich; Kratochvill, Franz; Janos, Marton; Sigel, Stefanie; Drobits, Barbara; Li, Xiao-Dong; Knapp, Sylvia; Kovarik, Pavel

2011-01-01

Streptococcus pyogenes is a Gram-positive human pathogen that is recognized by yet unknown pattern recognition receptors (PRRs). Engagement of these receptor molecules during infection with S. pyogenes, a largely extracellular bacterium with limited capacity for intracellular survival, causes innate immune cells to produce inflammatory mediators such as TNF, but also type I interferon (IFN). Here we show that signaling elicited by type I IFNs is required for successful defense of mice against lethal subcutaneous cellulitis caused by S. pyogenes. Type I IFN signaling was accompanied with reduced neutrophil recruitment to the site of infection. Mechanistic analysis revealed that macrophages and conventional dendritic cells (cDCs) employ different signaling pathways leading to IFN-beta production. Macrophages required IRF3, STING, TBK1 and partially MyD88, whereas in cDCs the IFN-beta production was fully dependent on IRF5 and MyD88. Furthermore, IFN-beta production by macrophages was dependent on the endosomal delivery of streptococcal DNA, while in cDCs streptococcal RNA was identified as the IFN-beta inducer. Despite a role of MyD88 in both cell types, the known IFN-inducing TLRs were individually not required for generation of the IFN-beta response. These results demonstrate that the innate immune system employs several strategies to efficiently recognize S. pyogenes, a pathogenic bacterium that succeeded in avoiding recognition by the standard arsenal of TLRs. PMID:21625574
How Do the Size, Charge and Shape of Nanoparticles Affect Amyloid β Aggregation on Brain Lipid Bilayer?

NASA Astrophysics Data System (ADS)

Kim, Yuna; Park, Ji-Hyun; Lee, Hyojin; Nam, Jwa-Min

2016-01-01

Here, we studied the effect of the size, shape, and surface charge of Au nanoparticles (AuNPs) on amyloid beta (Aβ) aggregation on a total brain lipid-based supported lipid bilayer (brain SLB), a fluid platform that facilitates Aβ-AuNP aggregation process. We found that larger AuNPs induce large and amorphous aggregates on the brain SLB, whereas smaller AuNPs induce protofibrillar Aβ structures. Positively charged AuNPs were more strongly attracted to Aβ than negatively charged AuNPs, and the stronger interactions between AuNPs and Aβ resulted in fewer β-sheets and more random coil structures. We also compared spherical AuNPs, gold nanorods (AuNRs), and gold nanocubes (AuNCs) to study the effect of nanoparticle shape on Aβ aggregation on the brain SLB. Aβ was preferentially bound to the long axis of AuNRs and fewer fibrils were formed whereas all the facets of AuNCs interacted with Aβ to produce the fibril networks. Finally, it was revealed that different nanostructures induce different cytotoxicity on neuroblastoma cells, and, overall, smaller Aβ aggregates induce higher cytotoxicity. The results offer insight into the roles of NPs and brain SLB in Aβ aggregation on the cell membrane and can facilitate the understanding of Aβ-nanostructure co-aggregation mechanism and tuning Aβ aggregate structures.
Copper clusters capture and convert carbon dioxide to make fuel | Argonne

Science.gov Websites

Photos Videos Fact Sheets, Brochures and Reports Summer Science Writing Internship Careers Education Photos Videos Fact Sheets, Brochures and Reports Summer Science Writing Internship Copper clusters sites, the current method of reduction creates high-pressure conditions to facilitate stronger bonds
Inflammation in Alzheimer's disease: amyloid-beta oligomers trigger innate immunity defence via pattern recognition receptors.

PubMed

Salminen, Antero; Ojala, Johanna; Kauppinen, Anu; Kaarniranta, Kai; Suuronen, Tiina

2009-02-01

The inflammatory process has a fundamental role in the pathogenesis of Alzheimer's disease (AD). Recent studies indicate that inflammation is not merely a bystander in neurodegeneration but a powerful pathogenetic force in the disease process. Increased production of amyloid-beta peptide species can activate the innate immunity system via pattern recognition receptors (PRRs) and evoke Alzheimer's pathology. We will focus on the role of innate immunity system of brain in the initiation and the propagation of inflammatory process in AD. We examine here in detail the significance of amyloid-beta oligomers and fibrils as danger-associated molecular patterns (DAMPs) in the activation of a wide array of PRRs in glial cells and neurons, such as Toll-like, NOD-like, formyl peptide, RAGE and scavenger receptors along with complement and pentraxin systems. We also characterize the signaling pathways triggered by different PRRs in evoking inflammatory responses. In addition, we will discuss whether AD pathology could be the outcome of chronic activation of the innate immunity defence in the brain of AD patients.
Identification of residue pairing in interacting β-strands from a predicted residue contact map.

PubMed

Mao, Wenzhi; Wang, Tong; Zhang, Wenxuan; Gong, Haipeng

2018-04-19

Despite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a noisy contact map, due to the presence of characteristic contact patterns in β-β interactions. This information may benefit the tertiary structure prediction of mainly β proteins. In this work, we propose a novel ridge-detection-based β-β contact predictor to identify residue pairing in β strands from any predicted residue contact map. Our algorithm RDb 2 C adopts ridge detection, a well-developed technique in computer image processing, to capture consecutive residue contacts, and then utilizes a novel multi-stage random forest framework to integrate the ridge information and additional features for prediction. Starting from the predicted contact map of CCMpred, RDb 2 C remarkably outperforms all state-of-the-art methods on two conventional test sets of β proteins (BetaSheet916 and BetaSheet1452), and achieves F1-scores of ~ 62% and ~ 76% at the residue level and strand level, respectively. Taking the prediction of the more advanced RaptorX-Contact as input, RDb 2 C achieves impressively higher performance, with F1-scores reaching ~ 76% and ~ 86% at the residue level and strand level, respectively. In a test of structural modeling using the top 1 L predicted contacts as constraints, for 61 mainly β proteins, the average TM-score achieves 0.442 when using the raw RaptorX-Contact prediction, but increases to 0.506 when using the improved prediction by RDb 2 C. Our method can significantly improve the prediction of β-β contacts from any predicted residue contact maps. Prediction results of our algorithm could be directly applied to effectively facilitate the practical structure prediction of mainly β proteins. All source data and codes are available at http://166.111.152.91/Downloads.html or the GitHub address of https://github.com/wzmao/RDb2C .
Prediction and analysis of beta-turns in proteins by support vector machine.

PubMed

Pham, Tho Hoan; Satou, Kenji; Ho, Tu Bao

2003-01-01

Tight turn has long been recognized as one of the three important features of proteins after the alpha-helix and beta-sheet. Tight turns play an important role in globular proteins from both the structural and functional points of view. More than 90% tight turns are beta-turns. Analysis and prediction of beta-turns in particular and tight turns in general are very useful for the design of new molecules such as drugs, pesticides, and antigens. In this paper, we introduce a support vector machine (SVM) approach to prediction and analysis of beta-turns. We have investigated two aspects of applying SVM to the prediction and analysis of beta-turns. First, we developed a new SVM method, called BTSVM, which predicts beta-turns of a protein from its sequence. The prediction results on the dataset of 426 non-homologous protein chains by sevenfold cross-validation technique showed that our method is superior to the other previous methods. Second, we analyzed how amino acid positions support (or prevent) the formation of beta-turns based on the "multivariable" classification model of a linear SVM. This model is more general than the other ones of previous statistical methods. Our analysis results are more comprehensive and easier to use than previously published analysis results.
A unique serpin P1' glutamate and a conserved β-sheet C arginine are key residues for activity, protease recognition and stability of serpinA12 (vaspin).

PubMed

Ulbricht, David; Pippel, Jan; Schultz, Stephan; Meier, René; Sträter, Norbert; Heiker, John T

2015-09-15

SerpinA12 (vaspin) is thought to be mainly expressed in adipose tissue and has multiple beneficial effects on metabolic, inflammatory and atherogenic processes related to obesity. KLK7 (kallikrein 7) is the only known protease target of vaspin to date and is inhibited with a moderate inhibition rate. In the crystal structure, the cleavage site (P1-P1') of the vaspin reactive centre loop is fairly rigid compared with the flexible residues before P2, possibly supported by an ionic interaction of P1' glutamate (Glu(379)) with an arginine residue (Arg(302)) of the β-sheet C. A P1' glutamate seems highly unusual and unfavourable for the protease KLK7. We characterized vaspin mutants to investigate the roles of these two residues in protease inhibition and recognition by vaspin. Reactive centre loop mutations changing the P1' residue or altering the reactive centre loop conformation significantly increased inhibition parameters, whereas removal of the positive charge within β-sheet C impeded the serpin-protease interaction. Arg(302) is a crucial contact to enable vaspin recognition by KLK7 and it supports moderate inhibition of the serpin despite the presence of the detrimental P1' Glu(379), which clearly represents a major limiting factor for vaspin-inhibitory activity. We also show that the vaspin-inhibition rate for KLK7 can be modestly increased by heparin and demonstrate that vaspin is a heparin-binding serpin. Noteworthily, we observed vaspin as a remarkably thermostable serpin and found that Glu(379) and Arg(302) influence heat-induced polymerization. These structural and functional results reveal the mechanistic basis of how reactive centre loop sequence and exosite interaction in vaspin enable KLK7 recognition and regulate protease inhibition as well as stability of this adipose tissue-derived serpin. © 2015 Authors; published by Portland Press Limited.
Solution structure for Pandinus toxin K-alpha (PiTX-K alpha), a selective blocker of A-type potassium channels.

PubMed

Tenenholz, T C; Rogowski, R S; Collins, J H; Blaustein, M P; Weber, D J

1997-03-11

PiTX-K alpha, a 35-residue peptide recently isolated from the venom of Pandinus imperator, blocks the rapidly inactivating (A-type) K+ channel(s) in rat brain synaptosomes and the cloned Kv 1.2 potassium channel at very low toxin concentrations (6 nM and 32 pM, respectively) [Rogowski, R. S., Collins, J. H., O'Neil, T. J., Gustafson, T. A., Werkman, T. A., Rogawski, M. A., Tenenholz, T. C., Weber, D. J., & Blaustein, M. P. (1996) Mol. Pharmacol. 50, 1167-1177]. The three-dimensional structure of PiTX-K alpha was determined using NMR spectroscopy in order to understand its selectivity and affinity toward K+ channels. PiTX-K alpha was found to have an alpha-helix from residues 10 to 21 and two beta-strands (betaI, 26-28; betaII, 33-35) connected by a type II beta-turn to form a small antiparallel beta-sheet. Three disulfide bonds, which are conserved in all members of the charybdotoxin family (alpha-K toxins), anchor one face of the alpha-helix to the beta-sheet. The N-terminal portion of PiTX-K alpha has three fewer residues than other alpha-K toxins such as charybdotoxin. Rather than forming a third beta-strand as found for other alpha-K toxins, the N-terminal region of PiTX-K alpha adopts an extended conformation. This structural difference in PiTX-K alpha together with differences in sequence at Pro-10, Tyr-14, and Asn-25 (versus Ser-10, Trp-14, and Arg-25 in CTX) may explain why PiTX-K alpha does not block maxi-K+ channels. Differences in three-dimensional structure between PiTX-K alpha and charybdotoxin are also observed in both the tight turn and the loop that connects the first beta-strand to the alpha-helix. As a result, side chains of two residues (Tyr-23 and Arg-31) are in regions of PiTX-K alpha that probably interact with rapidly inactivating A-type K+ channels. The analogous residues in charybdotoxin are positioned differently on the toxin surface. Thus, the locations of Tyr-23 and Arg-31 side chains in PiTX-K alpha could explain why this toxin blocks A-type channels at much lower concentrations than does charybdotoxin.
Prosody and Spoken Word Recognition in Early and Late Spanish-English Bilingual Individuals

ERIC Educational Resources Information Center

Boutsen, Frank R.; Dvorak, Justin D.; Deweber, Derick D.

2017-01-01

Purpose: This study was conducted to compare the influence of word properties on gated single-word recognition in monolingual and bilingual individuals under conditions of native and nonnative accent and to determine whether word-form prosody facilitates recognition in bilingual individuals. Method: Word recognition was assessed in monolingual and…
Positive, but Not Negative, Facial Expressions Facilitate 3-Month-Olds' Recognition of an Individual Face

ERIC Educational Resources Information Center

Brenna, Viola; Proietti, Valentina; Montirosso, Rosario; Turati, Chiara

2013-01-01

The current study examined whether and how the presence of a positive or a negative emotional expression may affect the face recognition process at 3 months of age. Using a familiarization procedure, Experiment 1 demonstrated that positive (i.e., happiness), but not negative (i.e., fear and anger) facial expressions facilitate infants' ability to…
Business and Education Transition Alliance (BETA): Opening Doors to Career Opportunities for At-Risk Youth.

ERIC Educational Resources Information Center

Stroup, Phillip

1996-01-01

The Business and Education Transition Alliance (BETA) is a model school-to-work transition program that was developed to facilitate the school-to-work transition of at-risk youth in the Boulder Valley School District in Colorado. Among the BETA program's specific goals are the following: increase students' knowledge/understanding of demands of the…
The look of fear and anger: facial maturity modulates recognition of fearful and angry expressions.

PubMed

Sacco, Donald F; Hugenberg, Kurt

2009-02-01

The current series of studies provide converging evidence that facial expressions of fear and anger may have co-evolved to mimic mature and babyish faces in order to enhance their communicative signal. In Studies 1 and 2, fearful and angry facial expressions were manipulated to have enhanced babyish features (larger eyes) or enhanced mature features (smaller eyes) and in the context of a speeded categorization task in Study 1 and a visual noise paradigm in Study 2, results indicated that larger eyes facilitated the recognition of fearful facial expressions, while smaller eyes facilitated the recognition of angry facial expressions. Study 3 manipulated facial roundness, a stable structure that does not vary systematically with expressions, and found that congruency between maturity and expression (narrow face-anger; round face-fear) facilitated expression recognition accuracy. Results are discussed as representing a broad co-evolutionary relationship between facial maturity and fearful and angry facial expressions. (c) 2009 APA, all rights reserved
Rapid response learning of brand logo priming: Evidence that brand priming is not dominated by rapid response learning.

PubMed

Boehm, Stephan G; Smith, Ciaran; Muench, Niklas; Noble, Kirsty; Atherton, Catherine

2017-08-31

Repetition priming increases the accuracy and speed of responses to repeatedly processed stimuli. Repetition priming can result from two complementary sources: rapid response learning and facilitation within perceptual and conceptual networks. In conceptual classification tasks, rapid response learning dominates priming of object recognition, but it does not dominate priming of person recognition. This suggests that the relative engagement of network facilitation and rapid response learning depends on the stimulus domain. Here, we addressed the importance of the stimulus domain for rapid response learning by investigating priming in another domain, brands. In three experiments, participants performed conceptual decisions for brand logos. Strong priming was present, but it was not dominated by rapid response learning. These findings add further support to the importance of the stimulus domain for the relative importance of network facilitation and rapid response learning, and they indicate that brand priming is more similar to person recognition priming than object recognition priming, perhaps because priming of both brands and persons requires individuation.
Preferential melting of secondary structures during protein unfolding in different solvents: Competition between hydrophobic solvation and hydrogen bonding

NASA Astrophysics Data System (ADS)

Bagchi, Biman; Roy, Susmita; Ghosh, Rikhia

2014-03-01

Aqueous binary mixtures such as water-DMSO, water-urea, and water-ethanol are known to serve as denaturants of a host of proteins, although the detailed mechanism is often not known. Here we combine studies on several proteins in multiple binary mixtures to obtain a unified understanding of the phenomenon. We compare with experiments to support the simulation findings. The proteins considered include (i) chicken villin head piece (HP-36), (ii) immunoglobulin binding protein G (GB1), (iii) myoglobin and (iv) lysozyme. We find that for amphiphilic solvents like DMSO, the hydrophobic groups and the strong hydrogen bonding ability of the >S =O oxygen atom act together to facilitate the unfolding. However, the hydrophilic solvents like urea, due to the presence of more hydrophilic ends (C =O and two NH2) has a high propensity of forming hydrogen bonds with the side-chain residues and backbone of beta-sheet than the same of alpha helix. Such diversity among the unfolding pathways of a given protein in different chemical environments is especially characterized by the preferential solvation of a particular secondary structure.
Hydrogen-bonded turns in proteins: the case for a recount.

PubMed

Panasik, Nick; Fleming, Patrick J; Rose, George D

2005-11-01

Beta-turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble beta-turns but lack the characteristic N-H(i) --> O=C(i - 3) hydrogen bond of an authentic beta-turn. Here, we identify potential hydrogen-bonded beta-turns in the coil library, a Web-accessible database utility comprised of all residues not in repetitive secondary structure, neither alpha-helix nor beta-sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four-residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference-quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen-bonded beta-turns. In particular, 33% of coil library residues were classified as beta-turns prior to minimization. After minimization, 45% of such residues could be classified as beta-turns, with another 8% in 3(10) helixes (which closely resemble type III beta-turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Amaro, Mariana; Wellbrock, Thorben; Birch, David J. S.

The fluorescence decay of beta-amyloid's (Aβ) intrinsic fluorophore tyrosine has been used for sensing the oligomer formation of dye-labelled Aβ monomers and the results compared with previously studied oligomerization of the non-labelled Aβ peptides. It has been demonstrated that two different sized, covalently bound probes 7-diethylaminocoumarin-3-carbonyl and Hilyte Fluor 488 (HLF), alter the rate and character of oligomerization to different extents. The ability of HLF to inhibit formation of highly ordered structures containing beta-sheets was also shown. The implications of our findings for using fluorescence methods in amyloidosis research are discussed and the advantages of this auto-fluorescence approach highlighted.
Genomic amplification of the human DHFR/MSH3 locus remodels mismatch recognition and repair activities.

PubMed

Drummond, J T

1999-01-01

Mismatch recognition in human cells is mediated by two heterodimers, MutS alpha and MutS beta. MutS alpha appears to shoulder primary responsibility for mismatch correction during replication, based on its relative abundance and ability to recognize a broad spectrum of base-base and base-insertion mismatches. Because MutS alpha and MutS beta share a common component, MSH2, conditions that influence the expression or degradation of MSH3 or MSH6 can redistribute the profile of mismatch recognition and repair. MSH3 is linked by a shared promoter with DHFR, connecting two pathways with key roles in DNA metabolism. In a classic example of gene amplification, the DHFR (and MSH3) locus can become amplified to several hundred copies in the presence of methotrexate. Under these conditions, MutS beta forms at the expense of MutS alpha, and the mutation rate in these tumor cells rises more than 100-fold. The implications for cancer chemotherapy include a potential increase in mutability when tumors are treated with methotrexate, which could increase the frequency of subsequent mutations that influence the tumor's drug sensitivity or aggressiveness. Because processing certain types of DNA damage by the mismatch repair pathway has also been implicated in tumor sensitivity to agents such as cisplatin, changes in expression at the DHFR/MSH3 locus may have further relevance to the outcome of multi-drug treatment regimens.
The effects of magnetic B(y) component on geomagnetic tail equilibria

NASA Technical Reports Server (NTRS)

Hilmer, Robert V.; Voigt, Gerd-Hannes

1987-01-01

A two-dimensional linear magnetohydrostatic model of the magnetotail is developed here in order to investigate the effects of a significant B(y) component on the configuration of magnetotail equilibria. It is concluded that the enhanced B(y) values must be an essential part of the quiet magnetotail and do not result from a simple intrusion of the IMF. The B(y) field consists of a constant background component plus a nonuniform field existing only in the plasma sheet, where it is dependent on the plasma paramater beta and the strength of the magnetic B(z) component. B(y) is strongest at the neutral sheet and decreases monotonically in the + or - z direction, reaching a constant tail lobe value at the plasma sheet boundaries. The presence of a significant positive B(y) component produces currents, including field-aligned currents, that flow through the equatorial plane and toward and away from earth in the northern and southern halves of the plasma sheet, respectively.

Nuclear magnetic resonance-based model of a TF1/HmU-DNA complex.

PubMed

Silva, M V; Pasternack, L B; Kearns, D R

1997-12-15

Transcription factor 1 (TF1), a type II DNA-binding protein encoded by the Bacillus subtilis bacteriophage SPO1, has the capacity for sequence-selective DNA binding and a preference for 5-hydroxymethyl-2'-deoxyuridine (HmU)-containing DNA. In NMR studies of the TF1/HmU-DNA complex, intermolecular NOEs indicate that the flexible beta-ribbon and C-terminal alpha-helix are involved in the DNA-binding site of TF1, placing it in the beta-sheet category of DNA-binding proteins proposed to bind by wrapping two beta-ribbon "arms" around the DNA. Intermolecular and intramolecular NOEs were used to generate an energy-minimized model of the protein-DNA complex in which both DNA bending and protein structure changes are evident.
External reflection FTIR of peptide monolayer films in situ at the air/water interface: experimental design, spectra-structure correlations, and effects of hydrogen-deuterium exchange.

PubMed Central

Flach, C R; Brauner, J W; Taylor, J W; Baldwin, R C; Mendelsohn, R

1994-01-01

A Fourier transform infrared spectrometer has been interfaced with a surface balance and a new external reflection infrared sampling accessory, which permits the acquisition of spectra from protein monolayers in situ at the air/water interface. The accessory, a sample shuttle that permits the collection of spectra in alternating fashion from sample and background troughs, reduces interference from water vapor rotation-vibration bands in the amide I and amide II regions of protein spectra (1520-1690 cm-1) by nearly an order of magnitude. Residual interference from water vapor absorbance ranges from 50 to 200 microabsorbance units. The performance of the device is demonstrated through spectra of synthetic peptides designed to adopt alpha-helical, antiparallel beta-sheet, mixed beta-sheet/beta-turn, and unordered conformations at the air/water interface. The extent of exchange on the surface can be monitored from the relative intensities of the amide II and amide I modes. Hydrogen-deuterium exchange may lower the amide I frequency by as much as 11-12 cm-1 for helical secondary structures. This shifts the vibrational mode into a region normally associated with unordered structures and leads to uncertainties in the application of algorithms commonly used for determination of secondary structure from amide I contours of proteins in D2O solution. PMID:7919013
Syntheses and crystal structures of two topologically related modifications of Cs(2)[(UO(2))(2)(MoO(4))(3)].

PubMed

Krivovichev, S V; Cahill, C L; Burns, P C

2002-01-14

Two polymorphs of Cs(2)(UO(2))(2)(MoO(4))(3) have been synthesized by hydrothermal (alpha-phase) and high-temperature (beta-phase) routes. Both were characterized by single-crystal X-ray diffraction: alpha-Cs(2)(UO(2))(2)(MoO(4))(3), orthorhombic, Pna2(1), a = 20.4302(15) A, b = 8.5552(7) A, c = 9.8549(7) A, Z = 4; beta-Cs(2)(UO(2))(2)(MoO(4))(3), tetragonal, P4(2)/n, a = 10.1367(8) A, c = 16.2831(17) A, Z = 4. The structures of both phases consist of linked UO(7) pentagonal bipyramids and MoO(4) tetrahedra: alpha-Cs(2)(UO(2))(2)(MoO(4))(3) is a framework compound with large channels parallel to the c axis. Two cesium sites are located in these channels and are coordinated by 8 and 10 oxygen atoms. The structure of beta-Cs(2)(UO(2))(2)(MoO(4))(3) contains corrugated [(UO(2))(2)(MoO(4))(3)] sheets that are parallel to (001). The cesium cations are located between the sheets and are coordinated by eight oxygen atoms. The structures are topologically related; both can be described in terms of chains of 5-connected UO(7) pentagonal bipyramids and 3- and 4-connected MoO(4) tetrahedra.
Template switching between PNA and RNA oligonucleotides

NASA Technical Reports Server (NTRS)

Bohler, C.; Nielsen, P. E.; Orgel, L. E.; Miller, S. L. (Principal Investigator)

1995-01-01

The origin of the RNA world is not easily understood, as effective prebiotic syntheses of the components of RNA, the beta-ribofuranoside-5'-phosphates, are hard to envisage. Recognition of this difficulty has led to the proposal that other genetic systems, the components of which are more easily formed, may have preceded RNA. This raises the question of how transitions between one genetic system and another could occur. Peptide nucleic acid (PNA) resembles RNA in its ability to form double-helical complexes stabilized by Watson-Crick hydrogen bonding between adenine and thymine and between cytosine and guanine, but has a backbone that is held together by amide rather than by phosphodiester bonds. Oligonucleotides bases on RNA are known to act as templates that catalyse the non-enzymatic synthesis of their complements from activated mononucleotides, we now show that RNA oligonucleotides facilitate the synthesis of complementary PNA strands and vice versa. This suggests that a transition between different genetic systems can occur without loss of information.
Android application for handwriting segmentation using PerTOHS theory

NASA Astrophysics Data System (ADS)

Akouaydi, Hanen; Njah, Sourour; Alimi, Adel M.

2017-03-01

The paper handles the problem of segmentation of handwriting on mobile devices. Many applications have been developed in order to facilitate the recognition of handwriting and to skip the limited numbers of keys in keyboards and try to introduce a space of drawing for writing instead of using keyboards. In this one, we will present a mobile theory for the segmentation of for handwriting uses PerTOHS theory, Perceptual Theory of On line Handwriting Segmentation, where handwriting is defined as a sequence of elementary and perceptual codes. In fact, the theory analyzes the written script and tries to learn the handwriting visual codes features in order to generate new ones via the generated perceptual sequences. To get this classification we try to apply the Beta-elliptic model, fuzzy detector and also genetic algorithms in order to get the EPCs (Elementary Perceptual Codes) and GPCs (Global Perceptual Codes) that composed the script. So, we will present our Android application M-PerTOHS for segmentation of handwriting.
Ice Sheet Model Intercomparison Project (ISMIP6) contribution to CMIP6

PubMed Central

Nowicki, Sophie M.J.; Payne, Tony; Larour, Eric; Seroussi, Helene; Goelzer, Heiko; Lipscomb, William; Gregory, Jonathan; Abe-Ouchi, Ayako; Shepherd, Andrew

2018-01-01

Reducing the uncertainty in the past, present and future contribution of ice sheets to sea-level change requires a coordinated effort between the climate and glaciology communities. The Ice Sheet Model Intercomparison Project for CMIP6 (ISMIP6) is the primary activity within the Coupled Model Intercomparison Project – phase 6 (CMIP6) focusing on the Greenland and Antarctic Ice Sheets. In this paper, we describe the framework for ISMIP6 and its relationship to other activities within CMIP6. The ISMIP6 experimental design relies on CMIP6 climate models and includes, for the first time within CMIP, coupled ice sheet – climate models as well as standalone ice sheet models. To facilitate analysis of the multi-model ensemble and to generate a set of standard climate inputs for standalone ice sheet models, ISMIP6 defines a protocol for all variables related to ice sheets. ISMIP6 will provide a basis for investigating the feedbacks, impacts, and sea-level changes associated with dynamic ice sheets and for quantifying the uncertainty in ice-sheet-sourced global sea-level change. PMID:29697697
Current trends in small vocabulary speech recognition for equipment control

NASA Astrophysics Data System (ADS)

Doukas, Nikolaos; Bardis, Nikolaos G.

2017-09-01

Speech recognition systems allow human - machine communication to acquire an intuitive nature that approaches the simplicity of inter - human communication. Small vocabulary speech recognition is a subset of the overall speech recognition problem, where only a small number of words need to be recognized. Speaker independent small vocabulary recognition can find significant applications in field equipment used by military personnel. Such equipment may typically be controlled by a small number of commands that need to be given quickly and accurately, under conditions where delicate manual operations are difficult to achieve. This type of application could hence significantly benefit by the use of robust voice operated control components, as they would facilitate the interaction with their users and render it much more reliable in times of crisis. This paper presents current challenges involved in attaining efficient and robust small vocabulary speech recognition. These challenges concern feature selection, classification techniques, speaker diversity and noise effects. A state machine approach is presented that facilitates the voice guidance of different equipment in a variety of situations.
The processing of auditory and visual recognition of self-stimuli.

PubMed

Hughes, Susan M; Nicholson, Shevon E

2010-12-01

This study examined self-recognition processing in both the auditory and visual modalities by determining how comparable hearing a recording of one's own voice was to seeing photograph of one's own face. We also investigated whether the simultaneous presentation of auditory and visual self-stimuli would either facilitate or inhibit self-identification. Ninety-one participants completed reaction-time tasks of self-recognition when presented with their own faces, own voices, and combinations of the two. Reaction time and errors made when responding with both the right and left hand were recorded to determine if there were lateralization effects on these tasks. Our findings showed that visual self-recognition for facial photographs appears to be superior to auditory self-recognition for voice recordings. Furthermore, a combined presentation of one's own face and voice appeared to inhibit rather than facilitate self-recognition and there was a left-hand advantage for reaction time on the combined-presentation tasks. Copyright © 2010 Elsevier Inc. All rights reserved.
[Rheumatologic and radiologic symptoms of dialysis-associated beta 2-microglobulin amyloidosis: long-term retrospective study of 175 chronic hemodialysis patients].

PubMed

Hermann, E; Mayet, W J; Wandel, E; Scherer, G; Schadmand, S; Klose, K J; Poralla, T; Meyer zum Büschenfelde, K H; Köhler, H

1991-01-01

beta 2-microglobulin amyloidosis is a major complication in chronic hemodialysis patients. Destructive arthropathy, spondylarthropathy, and carpal tunnel syndrome are clinical manifestations of beta 2M amyloid depositions within the joints, intervertebral discs, and tendon sheets. We have investigated the prevalence of beta 2M amyloidosis associated radiological joint lesions in a population of 175 patients on chronic hemodialysis. In 32 of 175 patients the diagnosis of amyloidosis arthropathy and spondylarthropathy was made by radiomorphological criteria. These 32 patients were asked about rheumatic symptoms (localisation and character of pain, synovitis, carpal tunnel syndrome, influence of dialysis membrane on pain) and examined clinically. Bilateral pain of the shoulders or wrists was complained by most of the patients. 24 of the 32 patients had signs of secondary hyperparathyroidism besides beta 2M-amyloidosis. 29 patients had a carpal tunnel syndrome, 23 of whom had to be operated. beta 2M-amyloid was histochemically demonstrated in all of these 23 cases. Renal transplantation led to immediate pain relief in 3 out of 3 patients, a change of the dialysis membrane (high-flux membrane) improved chronic pain in the majority of patients.
Neuropeptide S interacts with the basolateral amygdala noradrenergic system in facilitating object recognition memory consolidation.

PubMed

Han, Ren-Wen; Xu, Hong-Jiao; Zhang, Rui-San; Wang, Pei; Chang, Min; Peng, Ya-Li; Deng, Ke-Yu; Wang, Rui

2014-01-01

The noradrenergic activity in the basolateral amygdala (BLA) was reported to be involved in the regulation of object recognition memory. As the BLA expresses high density of receptors for Neuropeptide S (NPS), we investigated whether the BLA is involved in mediating NPS's effects on object recognition memory consolidation and whether such effects require noradrenergic activity. Intracerebroventricular infusion of NPS (1nmol) post training facilitated 24-h memory in a mouse novel object recognition task. The memory-enhancing effect of NPS could be blocked by the β-adrenoceptor antagonist propranolol. Furthermore, post-training intra-BLA infusions of NPS (0.5nmol/side) improved 24-h memory for objects, which was impaired by co-administration of propranolol (0.5μg/side). Taken together, these results indicate that NPS interacts with the BLA noradrenergic system in improving object recognition memory during consolidation. Copyright © 2013 Elsevier Inc. All rights reserved.
Breastfeeding experience differentially impacts recognition of happiness and anger in mothers.

PubMed

Krol, Kathleen M; Kamboj, Sunjeev K; Curran, H Valerie; Grossmann, Tobias

2014-11-12

Breastfeeding is a dynamic biological and social process based on hormonal regulation involving oxytocin. While there is much work on the role of breastfeeding in infant development and on the role of oxytocin in socio-emotional functioning in adults, little is known about how breastfeeding impacts emotion perception during motherhood. We therefore examined whether breastfeeding influences emotion recognition in mothers. Using a dynamic emotion recognition task, we found that longer durations of exclusive breastfeeding were associated with faster recognition of happiness, providing evidence for a facilitation of processing positive facial expressions. In addition, we found that greater amounts of breastfed meals per day were associated with slower recognition of anger. Our findings are in line with current views of oxytocin function and support accounts that view maternal behaviour as tuned to prosocial responsiveness, by showing that vital elements of maternal care can facilitate the rapid responding to affiliative stimuli by reducing importance of threatening stimuli.
Beta-2-microglobulin gene expression is maintained in rainbow trout and Atlantic salmon kept at low temperatures.

PubMed

Kales, Stephen; Parks-Dely, Julie; Schulte, Patricia; Dixon, Brian

2006-08-01

Finfish in the wild are regularly subjected to low temperatures, which have been shown to cause a loss of Major Histocompatibility receptor expression in common carp kept at 6 degrees C. This is similar to what was seen in a mammalian cell line cultured at 26 degrees C. Loss of expression of this critical viral recognition protein may provide one mechanism for the increased frequency of fish diseases at low temperatures. This report demonstrates that unlike carp and mammals, beta(2)m transcript levels in both rainbow trout and Atlantic salmon do not decrease after 10 days at temperatures as low as 2 degrees C. Reverse transcriptase (RT)-PCR indicated that transcript steady-state levels of trout beta(2)m were maintained in both tissues and peripheral blood leucocytes, whether freshly isolated or in primary culture. Polyclonal antibodies raised against a recombinant form of trout beta(2)m, demonstrated cross-reactivity to both rainbow trout and Atlantic salmon protein lysates. Use of these antibodies in western blot analyses indicated that cellular protein levels are also maintained at low temperatures in both species while qualitative epifluorescence analysis of freshly isolated peripheral blood leucocytes indicated persistent cell surface expression of trout beta(2)m even after 10 days at 2 degrees C. Rainbow trout and Atlantic salmon may therefore utilise an alternative mode of immune gene regulation than the common carp and mammals allowing them to maintain viral recognition machinery at low temperatures, possibly due to selection for survival in cold climates.
Expression of estrogen receptors alpha and beta in the corpus luteum and uterus from non-pregnant and pregnant llamas.

PubMed

Powell, Susan A; Smith, Bradford B; Timm, Karen I; Menino, Alfred R

2007-08-01

Because estrogen may be involved in maternal recognition of pregnancy and embryonic migration in llamas, expression of estrogen receptor subtypes alpha (ERalpha) and beta (ERbeta) was evaluated in corpus luteum (CL), endometrium, and uterus using relative RT-PCR. Tissues were recovered from sterile-mated (SM) and pregnant (PG) females during Days 7-11 and 7-13 (Day 0 = day of mating), respectively, and follicular phase and juvenile females. Luteal expression of ERalpha and beta was similar (P > 0.10) in SM and PG females and within Days 7-11, however, expression of ERalpha in ovarian tissue from follicular phase females was greater (P < 0.05) than Days 7 and 9 CL. Uterus expressed less ERalpha and beta compared to endometrium (P = 0.07 and P < 0.01, respectively). Expression of ERalpha was greater (P < 0.05) in Day 7 and follicular phase uteri than Days 9 and 11, Day 13 PG and juvenile uteri. Uterine ERbeta expression was greater (P = 0.09) in PG versus SM females and in mated compared to follicular phase females (P < 0.05). Endometrial expression of ERalpha and beta did not differ (P > 0.10) between SM and PG females or by day. The presence of luteal ER during this period may mean a role for estradiol in maternal recognition of pregnancy. Observed increases in uterine ER expression with no changes in endometrium suggest expression increased in myometrium and/or perimetrium. Upregulation of myometrial ERbeta in PG females may be involved in supporting uterine migration of the embryo.
Self-assembly of peptide-amphiphile nanofibers under physiological conditions

DOEpatents

Stupp, Samuel I [Chicago, IL; Hartgerink, Jeffrey D [Pearland, TX; Beniash, Elia [Auburndale, MA

2011-11-22

The present invention provides a method of promoting neuron growth and development by contacting cells with a peptide amphiphile molecule in an aqueous solution in the presence of a metal ion. According to the method, the peptide amphiphile forms a cylindrical micellar nanofiber composed of beta-sheets, which promote neuron growth and development.
Glycation induces formation of amyloid cross-beta structure in albumin.

PubMed

Bouma, Barend; Kroon-Batenburg, Loes M J; Wu, Ya-Ping; Brünjes, Bettina; Posthuma, George; Kranenburg, Onno; de Groot, Philip G; Voest, Emile E; Gebbink, Martijn F B G

2003-10-24

Amyloid fibrils are components of proteinaceous plaques that are associated with conformational diseases such as Alzheimer's disease, transmissible spongiform encephalopathies, and familial amyloidosis. Amyloid polypeptides share a specific quarternary structure element known as cross-beta structure. Commonly, fibrillar aggregates are modified by advanced glycation end products (AGE). In addition, AGE formation itself induces protein aggregation. Both amyloid proteins and protein-AGE adducts bind multiligand receptors, such as receptor for AGE, CD36, and scavenger receptors A and B type I, and the serine protease tissue-type plasminogen activator (tPA). Based on these observations, we hypothesized that glycation induces refolding of globular proteins, accompanied by formation of cross-beta structure. Using transmission electron microscopy, we demonstrate here that glycated albumin condensates into fibrous or amorphous aggregates. These aggregates bind to amyloid-specific dyes Congo red and thioflavin T and to tPA. In contrast to globular albumin, glycated albumin contains amino acid residues in beta-sheet conformation, as measured with circular dichroism spectropolarimetry. Moreover, it displays cross-beta structure, as determined with x-ray fiber diffraction. We conclude that glycation induces refolding of initially globular albumin into amyloid fibrils comprising cross-beta structure. This would explain how glycated ligands and amyloid ligands can bind to the same multiligand "cross-beta structure" receptors and to tPA.
Peptide adsorption to cyanine dye aggregates revealed by cryo-transmission electron microscopy.

PubMed

von Berlepsch, Hans; Brandenburg, Enrico; Koksch, Beate; Böttcher, Christoph

2010-07-06

The binding interaction between aggregates of the 5-chloro-2-[[5-chloro-3-(3-sulfopropyl)-3H-benzothiazol-2-ylidene]methyl]-3-(3-sulfopropyl)benzothiazolium hydroxide inner salt ammonium salt (CD-1) and alpha-helix, as well as beta-sheet forming de novo designed peptides, was investigated by absorption spectroscopy, circular dichroism spectroscopy, and cryogenic transmission electron microscopy. Both pure dye and pure peptides self-assembled into well-defined supramolecular assemblies in acetate buffer at pH = 4. The dye formed sheetlike and tubular H- and J-aggregates and the peptides alpha-helical coiled-coil assemblies or beta-sheet rich fibrils. After mixing dye and peptide solutions, tubular aggregates with an unusual ultrastructure were found, most likely due to the decoration of dye tubes with monolayers of peptide assemblies based on the strong electrostatic attraction between the oppositely charged species. There was neither indication of a transfer of chirality from the peptides to the dye aggregates nor the opposite effect of a structural transfer from dye aggregates onto the peptides secondary structure.
Infrared and laser-Raman spectroscopic studies of thermally-induced globular protein gels.

PubMed

Clark, A H; Saunderson, D H; Suggett, A

1981-03-01

Infrared and laser-Raman spectroscopy have been used to follow secondary structure changes during the heat-set gelation of a number of aqueous (D2O) globular protein solutions. Measurements of the infrared Amide I' absorption band around 1650 cm-1, for BSA gels of varying clarity and texture, have shown that the very considerable variations in network structure underlying these materials are not reflected in obvious differences in secondary structure. In all cases aggregation is accompanied by development of beta-sheet of a kind common in fibrous protein systems, but for BSA at least this does not appear to vary significantly in amount from one gel type to another. Infrared studies of gels formed from other protein systems have confirmed this tendency for beta-sheet to develop during aggregation, and the tendency is further substantiated by laser-Raman evidence which provides the extra information that in most of the examples studied alpha-helix content simultaneously falls. From these, and other observations, some generalisations are made about the thermally-induced sol-to-gel transformations of globular proteins.
Increasing Elasticity through Changes in the Secondary Structure of Gelatin by Gelation in a Microsized Lipid Space.

PubMed

Sakai, Atsushi; Murayama, Yoshihiro; Fujiwara, Kei; Fujisawa, Takahiro; Sasaki, Saori; Kidoaki, Satoru; Yanagisawa, Miho

2018-04-25

Even though microgels are used in a wide variety of applications, determining their mechanical properties has been elusive because of the difficulties in analysis. In this study, we investigated the surface elasticity of a spherical microgel of gelatin prepared inside a lipid droplet by using micropipet aspiration. We found that gelation inside a microdroplet covered with lipid membranes increased Young's modulus E toward a plateau value E * along with a decrease in gel size. In the case of 5.0 wt % gelatin gelled inside a microsized lipid space, the E * for small microgels with R ≤ 50 μm was 10-fold higher (35-39 kPa) than that for the bulk gel (∼3 kPa). Structural analysis using circular dichroism spectroscopy and a fluorescence indicator for ordered beta sheets demonstrated that the smaller microgels contained more beta sheets in the structure than the bulk gel. Our finding indicates that the confinement size of gelling polymers becomes a factor in the variation of elasticity of protein-based microgels via secondary structure changes.
Increasing Elasticity through Changes in the Secondary Structure of Gelatin by Gelation in a Microsized Lipid Space

PubMed Central

2018-01-01

Even though microgels are used in a wide variety of applications, determining their mechanical properties has been elusive because of the difficulties in analysis. In this study, we investigated the surface elasticity of a spherical microgel of gelatin prepared inside a lipid droplet by using micropipet aspiration. We found that gelation inside a microdroplet covered with lipid membranes increased Young’s modulus E toward a plateau value E* along with a decrease in gel size. In the case of 5.0 wt % gelatin gelled inside a microsized lipid space, the E* for small microgels with R ≤ 50 μm was 10-fold higher (35–39 kPa) than that for the bulk gel (∼3 kPa). Structural analysis using circular dichroism spectroscopy and a fluorescence indicator for ordered beta sheets demonstrated that the smaller microgels contained more beta sheets in the structure than the bulk gel. Our finding indicates that the confinement size of gelling polymers becomes a factor in the variation of elasticity of protein-based microgels via secondary structure changes. PMID:29721530
Channel specificity and secondary structure of the glucose-inducible porins of Pseudomonas spp.

PubMed

Adewoye, L O; Tschetter, L; O'Neil, J; Worobec, E A

1998-06-01

The OprB porin-mediated glucose transport system was investigated in Pseudomonas chlororaphis, Burkholderia cepacia, and Pseudomonas fluorescens. Kinetic studies of [U-14C]glucose uptake revealed an inducible system of low Km values (0.3-5 microM) and high specificity for glucose. OprB homologs were purified and reconstituted into proteoliposomes. The porin function and channel preference for glucose were demonstrated by liposome swelling assays. Examination of the periplasmic glucose-binding protein (GBP) components by Western immunoblotting using P. aeruginosa GBP-specific antiserum revealed some homology between P. aeruginosa GBP and periplasmic proteins from P. fluorescens and P. chlororaphis but not B. cepacia. Circular dichroism spectropolarimetry of purified OprB-like porins from the three species revealed beta sheet contents of 31-50% in agreement with 40% beta sheet content for the P. aeruginosa OprB porin. These findings suggest that the high-affinity glucose transport system is primarily specific for glucose and well conserved in the genus Pseudomonas although its outer membrane component may differ in channel architecture and specificity for other carbohydrates.

Dissecting the structural determinants for the difference in mechanical stability of silk and amyloid beta-sheet stacks.

PubMed

Xiao, Senbo; Xiao, Shijun; Gräter, Frauke

2013-06-14

Stacking of β-sheets results in a protein super secondary structure with remarkable mechanical properties. β-Stacks are the determinants of a silk fiber's resilience and are also the building blocks of amyloid fibrils. While both silk and amyloid-type crystals are known to feature a high resistance against rupture, their structural and mechanical similarities and particularities are yet to be fully understood. Here, we systematically compare the rupture force and stiffness of amyloid and spider silk poly-alanine β-stacks of comparable sizes using Molecular Dynamics simulations. We identify the direction of force application as the primary determinant of the rupture strength; β-sheets in silk are orientated along the fiber axis, i.e. the pulling direction, and consequently require high forces in the several nanoNewton range for shearing β-strands apart, while β-sheets in amyloid are oriented vertically to the fiber, allowing a zipper-like rupture at sub-nanoNewton forces. A secondary factor rendering amyloid β-stacks softer and weaker than their spider silk counterparts is the sub-optimal side-chain packing between β-sheets due to the sequence variations of amyloid-forming proteins as opposed to the perfectly packed poly-alanine β-sheets of silk. Taken together, amyloid fibers can reach the stiffness of silk fibers in spite of their softer and weaker β-sheet arrangement as they are missing a softening amorphous matrix.
Conformational changes of the amyloid beta-peptide (1-40) adsorbed on solid surfaces.

PubMed

Giacomelli, Carla E; Norde, Willem

2005-05-23

The conformational change of the 39-43 residues of the amyloid beta-peptide (Abeta) toward a beta-sheet enriched state promotes self-aggregation of the peptide molecules and constitutes the major peptide component of the amyloid plaques in Alzheimer patients. The crucial question behind the self-aggregation of Abeta is related to the different pathways the peptide may take after cleavage from the amyloid precursor proteins at cellular membranes. This work is aiming at determining the conformation of the Abeta (1-40) adsorbed on hydrophobic Teflon and hydrophilic silica particles, as model sorbent surfaces mimicking the apolar transmembrane environment and the polar, charged membrane surface, respectively. The mechanism by which the Abeta interacts with solid surfaces strongly depends on the hydrophobic/hydrophilic character of the particles. Hydrophobic and electrostatic interactions contribute differently in each case, causing a completely different conformational change of the adsorbed molecules on the two surfaces. When hydrophobic interactions between the peptide and the sorbent prevail, the adsorbed Abeta (1-40) mainly adopts an alpha-helix conformation due to H-bonding in the apolar part of the peptide that is oriented towards the surface. On the other hand, when the peptide adsorbs by electrostatic interactions beta-sheet formation is promoted due to intermolecular association between the apolar parts of the adsorbed peptide. Irrespective of the characteristics of the solid sorbent, crowding the surface results in intermolecular association between adsorbed molecules leading to a strong aggregation tendency of the Abeta (1-40). [Diagram: see text] CD spectra of Abeta (1-40) at pH 7: A) in solution ([Abeta]=0.2 mg.ml(-1)) freshly prepared (line) and after overnight incubation (symbols);B) on Teflon (Gamma=0.5 mg.m(-2)).
The Role of Active Exploration of 3D Face Stimuli on Recognition Memory of Facial Information

ERIC Educational Resources Information Center

Liu, Chang Hong; Ward, James; Markall, Helena

2007-01-01

Research on face recognition has mainly relied on methods in which observers are relatively passive viewers of face stimuli. This study investigated whether active exploration of three-dimensional (3D) face stimuli could facilitate recognition memory. A standard recognition task and a sequential matching task were employed in a yoked design.…
Self-Recognition in Live Videos by Young Children: Does Video Training Help?

ERIC Educational Resources Information Center

Demir, Defne; Skouteris, Helen

2010-01-01

The overall aim of the experiment reported here was to establish whether self-recognition in live video can be facilitated when live video training is provided to children aged 2-2.5 years. While the majority of children failed the test of live self-recognition prior to video training, more than half exhibited live self-recognition post video…
Orthographic Facilitation in Chinese Spoken Word Recognition: An ERP Study

ERIC Educational Resources Information Center

Zou, Lijuan; Desroches, Amy S.; Liu, Youyi; Xia, Zhichao; Shu, Hua

2012-01-01

Orthographic influences in spoken word recognition have been previously examined in alphabetic languages. However, it is unknown whether orthographic information affects spoken word recognition in Chinese, which has a clean dissociation between orthography (O) and phonology (P). The present study investigated orthographic effects using event…
CK2(beta)tes gene encodes a testis-specific isoform of the regulatory subunit of casein kinase 2 in Drosophila melanogaster.

PubMed

Kalmykova, Alla I; Shevelyov, Yuri Y; Polesskaya, Oksana O; Dobritsa, Anna A; Evstafieva, Alexandra G; Boldyreff, Brigitte; Issinger, Olaf-Georg; Gvozdev, Vladimir A

2002-03-01

An earlier described CK2(beta)tes gene of Drosophila melanogaster is shown to encode a male germline specific isoform of regulatory beta subunit of casein kinase 2. Western-analysis using anti-CK2(beta)tes Ig revealed CK2(beta)tes protein in Drosophila testes extract. Expression of a CK2(beta)tes-beta-galactosidase fusion protein driven by the CK2(beta)tes promoter was found in transgenic flies at postmitotic stages of spermatogenesis. Examination of biochemical characteristics of a recombinant CK2(beta)tes protein expressed in Escherichia coli revealed properties similar to those of CK2beta: (a) CK2(beta)tes protein stimulates CK2alpha catalytic activity toward synthetic peptide; (b) it inhibits phosphorylation of calmodulin and mediates stimulation of CK2alpha by polylysine; (c) it is able to form (CK2(beta)tes)2 dimers, as well as (CK2alpha)2(CK2(beta)tes)2 tetramers. Using the yeast two-hybrid system and coimmunoprecipitation analysis of protein extract from Drosophila testes, we demonstrated an association between CK2(beta)tes and CK2alpha. Northern-analysis has shown that another regulatory (beta') subunit found recently in D. melanogaster genome is also testis-specific. Thus, we describe the first example of two tissue-specific regulatory subunits of CK2 which might serve to provide CK2 substrate recognition during spermatogenesis.
Periodontal regeneration with multi-layered periodontal ligament-derived cell sheets in a canine model.

PubMed

Iwata, Takanori; Yamato, Masayuki; Tsuchioka, Hiroaki; Takagi, Ryo; Mukobata, Shigeki; Washio, Kaoru; Okano, Teruo; Ishikawa, Isao

2009-05-01

Periodontal regeneration has been challenged with chemical reagents and/or biological approaches, however, there is still no sufficient technique that can regenerate complete periodontium, including alveolar bone, cementum, and well-oriented collagen fibers. The purpose of this study was to examine multi-layered sheets of periodontal ligament (PDL)-derived cells for periodontal regeneration. Canine PDL cells were isolated enzymatically and expanded in vitro. The cell population contained cells capable of making single cell-derived colonies at an approximately 20% frequency. Expression of mRNA of periodontal marker genes, S100 calcium binding protein A4 and periostin, was observed. Alkaline phosphatase activity and gene expression of both osteoblastic/cementoblastic and periodontal markers were upregulated by osteoinductive medium. Then, three-layered PDL cell sheets supported with woven polyglycolic acid were transplanted to dental root surfaces having three-wall periodontal defects in an autologous manner, and bone defects were filled with porous beta-tricalcium phosphate. Cell sheet transplantation regenerated both new bone and cementum connecting with well-oriented collagen fibers, while only limited bone regeneration was observed in control group where cell sheet transplantation was eliminated. These results suggest that PDL cells have multiple differentiation properties to regenerate periodontal tissues comprising hard and soft tissues. PDL cell sheet transplantation should prove useful for periodontal regeneration in clinical settings.
Evaluation of the Transient Liquid Phase (TLP) Bonding Process for Ti3Al-Based Honeycomb Core Sandwich Structure

NASA Technical Reports Server (NTRS)

Bird, R. Keith; Hoffman, Eric K.

1998-01-01

The suitability of using transient liquid phase (TLP) bonding to fabricate honeycomb core sandwich panels with Ti-14Al-21Nb (wt%) titanium aluminide (T3Al) face sheets for high-temperature hypersonic vehicle applications was evaluated. Three titanium alloy honeycomb cores and one Ti3Al alloy honeycomb core were investigated. Edgewise compression (EWC) and flatwise tension (FWT) tests on honeycomb core sandwich specimens and tensile tests of the face sheet material were conducted at temperatures ranging from room temperature to 1500 F. EWC tests indicated that the honeycomb cores and diffusion bonded joints were able to stabilize the face sheets up to and beyond the face sheet compressive yield strength for all temperatures investigated. The specimens with the T3Al honeycomb core produced the highest FWT strengths at temperatures above 1000 F. Tensile tests indicated that TLP processing conditions resulted in decreases in ductility of the Ti-14Al-21Nb face sheets. Microstructural examination showed that the side of the face sheets to which the filler metals had been applied was transformed from equiaxed alpha2 grains to coarse plates of alpha2 with intergranular Beta. Fractographic examination of the tensile specimens showed that this transformed region was dominated by brittle fracture.
Understanding the mechanisms of ATPase beta family genes for cellular thermotolerance in crossbred bulls

NASA Astrophysics Data System (ADS)

Deb, Rajib; Sajjanar, Basavaraj; Singh, Umesh; Alex, Rani; Raja, T. V.; Alyethodi, Rafeeque R.; Kumar, Sushil; Sengar, Gyanendra; Sharma, Sheetal; Singh, Rani; Prakash, B.

2015-12-01

Na+/K+-ATPase is an integral membrane protein composed of a large catalytic subunit (alpha), a smaller glycoprotein subunit (beta), and gamma subunit. The beta subunit is essential for ion recognition as well as maintenance of the membrane integrity. Present study was aimed to analyze the expression pattern of ATPase beta subunit genes (ATPase B1, ATPase B2, and ATPase B3) among the crossbred bulls under different ambient temperatures (20-44 °C). The present study was also aimed to look into the relationship of HSP70 with the ATPase beta family genes. Our results demonstrated that among beta family genes, transcript abundance of ATPase B1 and ATPase B2 is significantly ( P < 0.05) higher during the thermal stress. Pearson correlation coefficient analysis revealed that the expression of ATPase Β1, ATPase B2, and ATPase B3 is highly correlated ( P < 0.01) with HSP70, representing that the change in the expression pattern of these genes is positive and synergistic. These may provide a foundation for understanding the mechanisms of ATPase beta family genes for cellular thermotolerance in cattle.
The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.

PubMed

Lee, Donghan; Walsh, Joseph D; Yu, Ping; Markus, Michelle A; Choli-Papadopoulou, Theodora; Schwieters, Charles D; Krueger, Susan; Draper, David E; Wang, Yun-Xing

2007-04-06

The L11 binding site is one of the most important functional sites in the ribosome. The N-terminal domain of L11 has been implicated as a "reversible switch" in facilitating the coordinated movements associated with EF-G-driven GTP hydrolysis. The reversible switch mechanism has been hypothesized to require conformational flexibility involving re-orientation and re-positioning of the two L11 domains, and warrants a close examination of the structure and dynamics of L11. Here we report the solution structure of free L11, and relaxation studies of free L11, L11 complexed to its 58 nt RNA recognition site, and L11 in a ternary complex with the RNA and thiostrepton antibiotic. The binding site of thiostrepton on L11 was also defined by analysis of structural and dynamics data and chemical shift mapping. The conclusions of this work are as follows: first, the binding of L11 to RNA leads to sizable conformation changes in the regions flanking the linker and in the hinge area that links a beta-sheet and a 3(10)-helix-turn-helix element in the N terminus. Concurrently, the change in the relative orientation may lead to re-positioning of the N terminus, as implied by a decrease of radius of gyration from 18.5 A to 16.2 A. Second, the regions, which undergo large conformation changes, exhibit motions on milliseconds-microseconds or nanoseconds-picoseconds time scales. Third, binding of thiostrepton results in more rigid conformations near the linker (Thr71) and near its putative binding site (Leu12). Lastly, conformational changes in the putative thiostrepton binding site are implicated by the re-emergence of cross-correlation peaks in the spectrum of the ternary complex, which were missing in that of the binary complex. Our combined analysis of both the chemical shift perturbation and dynamics data clearly indicates that thiostrepton binds to a pocket involving residues in the 3(10)-helix in L11.
Mechanical and biological evaluations of beta-tricalcium phosphate/silicone rubber composite as a novel soft-tissue implant.

PubMed

Zhang, Yi-ming; Wang, Shao-liang; Lei, Ze-yuan; Fan, Dong-li

2009-09-01

Although silicone rubber (SR) implants are most commonly used and effective for soft-tissue augmentation, they still have been implicated in many adverse reactions. To overcome this problem, a novel composite beta-tricalcium phosphate/silicone rubber (beta-TCP/SR) was prepared by adding beta-TCP into a SR matrix. This study was to evaluate its application potential by investigating the mechanical properties and biocompatibility of beta-TCP/SR. Mechanical properties, including Shore A hardness and tensile strength, were evaluated with 3-mm-thick samples and a universal testing machine. Cytocompatibility tests were conducted in vitro using 0.2-mm-thick beta-TCP/SR samples by seeding fibroblasts onto different samples. Soft-tissue response to beta-TCP/SR and pull-out measurements were investigated 4 weeks and 24 weeks after implantation. The main mechanical properties were all significantly changed after mixing beta-TCP into the SR matrix, except for tearing strength. The cytocompatibility test showed enhanced adhesion and proliferation of fibroblasts onto beta-TCP/SR. Fibrous tissue ingrowth after resorption of beta-TCP was observed by in vivo histologic analysis. The peri-implant capsules in the beta-TCP/SR group were thinner than in the SR group 24 weeks after implantation. In a 24-week test, the maximum force required to pull out the beta-TCP/SR sheet was about six times greater than that needed for SR. Although some mechanical properties were significantly changed, the results of the cytocompatibility test and in vivo animal study still suggest that beta-TCP/SR may be more suitable as a soft-tissue implant than SR and has the potential to be used in plastic surgery.
Preferential V beta gene usage and lack of junctional sequence conservation among human T cell receptors specific for a tetanus toxin- derived peptide: evidence for a dominant role of a germline-encoded V region in antigen/major histocompatibility complex recognition

PubMed Central

1992-01-01

To investigate the structural and genetic basis of the T cell response to defined peptide/major histocompatibility (MHC) class II complexes in humans, we established a large panel of T cell clones (61) from donors of different HLA-DR haplotypes and reactive with a tetanus toxin- derived peptide (tt830-844) recognized in association with most DR molecules (universal peptide). By using a bacterial enterotoxin-based proliferation assay and cDNA sequencing, we found preferential use of a particular V beta region gene segment, V beta 2.1, in three of the individuals studied (64%, n = 58), irrespective of whether the peptide was presented by the DR6wcI, DR4w4, or DRw11.1 and DRw11.2 alleles, demonstrating that shared MHC class II antigens are not required for shared V beta gene use by T cell receptors (TCRs) specific for this peptide. V alpha gene use was more heterogeneous, with at least seven different V alpha segments derived from five distinct families encoding alpha chains able to pair with V beta 2.1 chains to form a tt830-844/DR- specific binding site. Several cases were found of clones restricted to different DR alleles that expressed identical V beta and (or very closely related) V alpha gene segments and that differed only in their junctional sequences. Thus, changes in the putative complementary determining region 3 (CDR3) of the TCR may, in certain cases, alter MHC specificity and maintain peptide reactivity. Finally, in contrast to what has been observed in other defined peptide/MHC systems, a striking heterogeneity was found in the junctional regions of both alpha and beta chains, even for TCRs with identical V alpha and/or V beta gene segments and the same restriction. Among 14 anti-tt830-844 clones using the V beta 2.1 gene segment, 14 unique V beta-D-J beta junctions were found, with no evident conservation in length and/or amino acid composition. One interpretation for this apparent lack of coselection of specific junctional sequences in the context of a common V element, V beta 2.1, is that this V region plays a dominant role in the recognition of the tt830-844/DR complex. PMID:1371303
Development of a new family of conformationally restricted peptides as potent nucleators of beta-turns. Design, synthesis, structure, and biological evaluation of a beta-lactam peptide analogue of melanostatin.

PubMed

Palomo, Claudio; Aizpurua, Jesus M; Benito, Ana; Miranda, José Ignacio; Fratila, Raluca M; Matute, Carlos; Domercq, Maria; Gago, Federico; Martin-Santamaria, Sonsoles; Linden, Anthony

2003-12-31

Novel enantiopure (i)-(beta-lactam)-(Gly)-(i+3) peptide models, defined by the presence of a central alpha-alkyl-alpha-amino-beta-lactam ring placed as the (i+1) residue, have been synthesized in a totally stereocontrolled way by alpha-alkylation of suitable N-[bis(trimethylsilyl)methyl]-beta-lactams. The structural properties of these beta-lactam pseudopeptides have been studied by X-ray crystallography, Molecular Dynamics simulation, and NOESY-restrained NMR simulated annealing techniques, showing a strong tendency to form stable type II or type II' beta-turns either in the solid state or in highly coordinating DMSO solutions. Tetrapeptide models containing syn- or anti-alpha,beta-dialkyl-alpha-amino-beta-lactam rings have also been synthesized and their conformations analyzed, revealing that alpha-alkyl substitution is essential for beta-turn stabilization. A beta-lactam analogue of melanostatin (PLG amide) has also been prepared, characterized as a type-II beta-turn in DMSO-d6 solution, and tested by competitive binding assay as a dopaminergic D2 modulator in rat neuron cultured cells, displaying moderate agonist activity in the micromolar concentration range. On the basis of these results, a novel peptidomimetic design concept, based on the separation of constraint and recognition elements, is proposed.
Lysophospholipid presentation by CD1d and recognition by a human Natural Killer T-cell receptor

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

López-Sagaseta, Jacinto; Sibener, Leah V.; Kung, Jennifer E.

2014-10-02

Invariant Natural Killer T (iNKT) cells use highly restricted {alpha}{beta} T cell receptors (TCRs) to probe the repertoire of lipids presented by CD1d molecules. Here, we describe our studies of lysophosphatidylcholine (LPC) presentation by human CD1d and its recognition by a native, LPC-specific iNKT TCR. Human CD1d presenting LPC adopts an altered conformation from that of CD1d presenting glycolipid antigens, with a shifted {alpha}1 helix resulting in an open A pocket. Binding of the iNKT TCR requires a 7-{angstrom} displacement of the LPC headgroup but stabilizes the CD1d-LPC complex in a closed conformation. The iNKT TCR CDR loop footprint onmore » CD1d-LPC is anchored by the conserved positioning of the CDR3{alpha} loop, whereas the remaining CDR loops are shifted, due in part to amino-acid differences in the CDR3{beta} and J{beta} segment used by this iNKT TCR. These findings provide insight into how lysophospholipids are presented by human CD1d molecules and how this complex is recognized by some, but not all, human iNKT cells.« less
Effectiveness of Emotion Recognition Training for Young Children with Developmental Delays

ERIC Educational Resources Information Center

Downs, Andrew; Strand, Paul

2008-01-01

Emotion recognition is a basic skill that is thought to facilitate development of social and emotional competence. There is little research available examining whether therapeutic or instructional interventions can improve the emotion recognition skill of young children with various developmental disabilities. Sixteen preschool children with…
Environmental Identity Development through Social Interactions, Action, and Recognition

ERIC Educational Resources Information Center

Stapleton, Sarah Riggs

2015-01-01

This article uses sociocultural identity theory to explore how practice, action, and recognition can facilitate environmental identity development. Recognition, a construct not previously explored in environmental identity literature, is particularly examined. The study is based on a group of diverse teens who traveled to South Asia to participate…
Custom-shaping system for bone regeneration by seeding marrow stromal cells onto a web-like biodegradable hybrid sheet.

PubMed

Tsuchiya, Kohei; Mori, Taisuke; Chen, Guoping; Ushida, Takashi; Tateishi, Tetsuya; Matsuno, Takeo; Sakamoto, Michiie; Umezawa, Akihiro

2004-05-01

New bone for the repair or the restoration of the function of traumatized, damaged, or lost bone is a major clinical need, and bone tissue engineering has been heralded as an alternative strategy for regenerating bone. A novel web-like structured biodegradable hybrid sheet has been developed for bone tissue engineering by preparing knitted poly(DL-lactic-co-glycolic acid) sheets (PLGA sheets) with collagen microsponges in their openings. The PLGA skeleton facilitates the formation of the hybrid sheets into desired shapes, and the collagen microsponges in the pores of the PLGA sheet promote cell adhesion and uniform cell distribution throughout the sheet. A large number of osteoblasts established from marrow stroma adhere to the scaffolds and generate the desired-shaped bone in combination with these novel sheets. These results indicate that the web-like structured novel sheet shows promise for use as a tool for custom-shaped bone regeneration in basic research on osteogenesis and for the development of therapeutic applications. Copyright 2004 Springer-Verlag
Ice Sheet Model Intercomparison Project (ISMIP6) Contribution to CMIP6

NASA Technical Reports Server (NTRS)

Nowicki, Sophie M. J.; Payne, Tony; Larour, Eric; Seroussi, Helene; Goelzer, Heiko; Lipscomb, William; Gregory, Jonathan; Abe-Ouchi, Ayako; Shepherd, Andrew

2016-01-01

Reducing the uncertainty in the past, present, and future contribution of ice sheets to sea-level change requires a coordinated effort between the climate and glaciology communities. The Ice Sheet Model Intercomparison Project for CMIP6 (ISMIP6) is the primary activity within the Coupled Model Intercomparison Project phase 6 (CMIP6) focusing on the Greenland and Antarctic ice sheets. In this paper, we describe the framework for ISMIP6 and its relationship with other activities within CMIP6. The ISMIP6 experimental design relies on CMIP6 climate models and includes, for the first time within CMIP, coupled ice-sheetclimate models as well as standalone ice-sheet models. To facilitate analysis of the multi-model ensemble and to generate a set of standard climate inputs for standalone ice-sheet models, ISMIP6 defines a protocol for all variables related to ice sheets. ISMIP6 will provide a basis for investigating the feedbacks, impacts, and sea-level changes associated with dynamic ice sheets and for quantifying the uncertainty in ice-sheet-sourced global sea-level change.
Verifying visual properties in sentence verification facilitates picture recognition memory.

PubMed

Pecher, Diane; Zanolie, Kiki; Zeelenberg, René

2007-01-01

According to the perceptual symbols theory (Barsalou, 1999), sensorimotor simulations underlie the representation of concepts. We investigated whether recognition memory for pictures of concepts was facilitated by earlier representation of visual properties of those concepts. During study, concept names (e.g., apple) were presented in a property verification task with a visual property (e.g., shiny) or with a nonvisual property (e.g., tart). Delayed picture recognition memory was better if the concept name had been presented with a visual property than if it had been presented with a nonvisual property. These results indicate that modality-specific simulations are used for concept representation.
Analysis of hydrophobic interactions of antagonists with the beta2-adrenergic receptor.

PubMed

Novoseletsky, V N; Pyrkov, T V; Efremov, R G

2010-01-01

The adrenergic receptors mediate a wide variety of physiological responses, including vasodilatation and vasoconstriction, heart rate modulation, and others. Beta-adrenergic antagonists ('beta-blockers') thus constitute a widely used class of drugs in cardiovascular medicine as well as in management of anxiety, migraine, and glaucoma. The importance of the hydrophobic effect has been evidenced for a wide range of beta-blocker properties. To better understand the role of the hydrophobic effect in recognition of beta-blockers by their receptor, we carried out a molecular docking study combined with an original approach to estimate receptor-ligand hydrophobic interactions. The proposed method is based on automatic detection of molecular fragments in ligands and the analysis of their interactions with receptors separately. A series of beta-blockers, based on phenylethanolamines and phenoxypropanolamines, were docked to the beta2-adrenoceptor binding site in the crystal structure. Hydrophobic complementarity between the ligand and the receptor was calculated using the PLATINUM web-server (http://model.nmr.ru/platinum). Based on the analysis of the hydrophobic match for molecular fragments of beta-blockers, we have developed a new scoring function which efficiently predicts dissociation constant (pKd) with strong correlations (r(2) approximately 0.8) with experimental data.

[Effect of absorption enhancers on nasal ginsenoside Rg1 delivery and its nasal ciliotoxicity].

PubMed

Chen, Xin-mei; Zhu, Jia-bi; Sun, Wei-dong; Zhang, Li-jian

2006-02-01

The enhancing activity and safety of several absorption enhancers were evaluated as potential nasal absorption enhancers to increase intranasal absorption of ginsenoside Rg1. Nasal circulatory perfusion test in vivo had been employed to investigate the effect of absorption enhancers for nasal mucosa absorption of ginsenoside Rgl in rats. The safety of the absorption enhancers were evaluated by testing cilia movement of the in situ toad palate model, the hemolysis of erythrocyte membrane of the rabbit, leaching of protein and LDH from the mice nasal mucosa and the effect on cilia structural and specific cellular changes of nasal mucosa. Absorption enhancers were necessary to facilitate ginsenoside Rg1 absorption by nasal mucosa. Among the absorption enhancers 1% sodium deoxycholate had great effect to facilite ginsenoside Rgl absorption by nasal mucosa; 1% dipotassium glycyrrhizinate and 1% azone had moderate effect to facilitate ginsenoside Rg1 absorption by nasal mucosa; 1% Tween-80, 2% beta-cyclodextrin, 0.5% borneol (dissolved in paraffin liquid), 0.5% chitosan, 5% hydroxypropyl-beta-cyclodextrin and 0.1% EDTA had low effect to facilitate ginsenoside Rgl absorption by nasal mucosa. 1% sodium deoxycholate, 1% azone and 1% dipotassium glycyrrhizinate had serious nasal toxicity; 1% Tween-80, 2% beta-cyclodextrin, 5% hydroxypropyl-beta-cyclodextrin had moderate nasal toxicity; 0.5% borneol (dissolved in paraffin liquid), 0.5% chitosan and 0.1% EDTA have little nasal toxicity. 0.5% borneol and 0.5% chitosan were the promising candidates having a good balance between enhancing activity and safety for nasal ginsenoside Rg1 delivery.
49 CFR 1104.2 - Document specifications.

Code of Federal Regulations, 2014 CFR

2014-10-01

... to facilitate automated processing in document sheet feeders, original documents of more than one... textual submissions. Use of color in filings is limited to images such as graphs, maps and photographs. To facilitate automated processing of color pages, color pages may not be inserted among pages containing text...
49 CFR 1104.2 - Document specifications.

Code of Federal Regulations, 2010 CFR

2010-10-01

... to facilitate automated processing in document sheet feeders, original documents of more than one... textual submissions. Use of color in filings is limited to images such as graphs, maps and photographs. To facilitate automated processing of color pages, color pages may not be inserted among pages containing text...
49 CFR 1104.2 - Document specifications.

Code of Federal Regulations, 2012 CFR

2012-10-01

... to facilitate automated processing in document sheet feeders, original documents of more than one... textual submissions. Use of color in filings is limited to images such as graphs, maps and photographs. To facilitate automated processing of color pages, color pages may not be inserted among pages containing text...
49 CFR 1104.2 - Document specifications.

Code of Federal Regulations, 2011 CFR

2011-10-01

... to facilitate automated processing in document sheet feeders, original documents of more than one... textual submissions. Use of color in filings is limited to images such as graphs, maps and photographs. To facilitate automated processing of color pages, color pages may not be inserted among pages containing text...
49 CFR 1104.2 - Document specifications.

Code of Federal Regulations, 2013 CFR

2013-10-01

... to facilitate automated processing in document sheet feeders, original documents of more than one... textual submissions. Use of color in filings is limited to images such as graphs, maps and photographs. To facilitate automated processing of color pages, color pages may not be inserted among pages containing text...
Facilitated IEP Meetings. PACER Center ACTion Information Sheets: PHP-c90

ERIC Educational Resources Information Center

PACER Center, 2014

2014-01-01

To help special education planning teams reach agreements, the Minnesota Department of Education, Compliance and Assistance, Alternative Dispute Resolution Services provide the option of facilitated IEP (Individualized Education Program) meetings. This option is available for IEP, IIIP (Individual Interagency Intervention Plan), and IFSP…
Reconnection AND Bursty Bulk Flow Associated Turbulence IN THE Earth'S Plasma Sheet

NASA Astrophysics Data System (ADS)

Voros, Z.; Nakamura, R.; Baumjohann, W.; Runov, A.; Volwerk, M.; Jankovicova, D.; Balogh, A.; Klecker, B.

2006-12-01

Reconnection related fast flows in the Earth's plasma sheet can be associated with several accompanying phenomena, such as magnetic field dipolarization, current sheet thinning and turbulence. Statistical analysis of multi-scale properties of turbulence facilitates to understand the interaction of the plasma flow with the dipolar magnetic field and to recognize the remote or nearby temporal and spatial characteristics of reconnection. The main emphasis of this presentation is on differentiating between the specific statistical features of flow associated fluctuations at different distances from the reconnection site.
Nonlinear filtering for character recognition in low quality document images

NASA Astrophysics Data System (ADS)

Diaz-Escobar, Julia; Kober, Vitaly

2014-09-01

Optical character recognition in scanned printed documents is a well-studied task, where the captured conditions like sheet position, illumination, contrast and resolution are controlled. Nowadays, it is more practical to use mobile devices for document capture than a scanner. So as a consequence, the quality of document images is often poor owing to presence of geometric distortions, nonhomogeneous illumination, low resolution, etc. In this work we propose to use multiple adaptive nonlinear composite filters for detection and classification of characters. Computer simulation results obtained with the proposed system are presented and discussed.
Three-dimensional structure of the human immunodeficiency virus type 1 matrix protein.

PubMed

Massiah, M A; Starich, M R; Paschall, C; Summers, M F; Christensen, A M; Sundquist, W I

1994-11-25

The HIV-1 matrix protein forms an icosahedral shell associated with the inner membrane of the mature virus. Genetic analyses have indicated that the protein performs important functions throughout the viral life-cycle, including anchoring the transmembrane envelope protein on the surface of the virus, assisting in viral penetration, transporting the proviral integration complex across the nuclear envelope, and localizing the assembling virion to the cell membrane. We now report the three-dimensional structure of recombinant HIV-1 matrix protein, determined at high resolution by nuclear magnetic resonance (NMR) methods. The HIV-1 matrix protein is the first retroviral matrix protein to be characterized structurally and only the fourth HIV-1 protein of known structure. NMR signal assignments required recently developed triple-resonance (1H, 13C, 15N) NMR methodologies because signals for 91% of 132 assigned H alpha protons and 74% of the 129 assignable backbone amide protons resonate within chemical shift ranges of 0.8 p.p.m. and 1 p.p.m., respectively. A total of 636 nuclear Overhauser effect-derived distance restraints were employed for distance geometry-based structure calculations, affording an average of 13.0 NMR-derived distance restraints per residue for the experimentally constrained amino acids. An ensemble of 25 refined distance geometry structures with penalties (sum of the squares of the distance violations) of 0.32 A2 or less and individual distance violations under 0.06 A was generated; best-fit superposition of ordered backbone heavy atoms relative to mean atom positions afforded root-mean-square deviations of 0.50 (+/- 0.08) A. The folded HIV-1 matrix protein structure is composed of five alpha-helices, a short 3(10) helical stretch, and a three-strand mixed beta-sheet. Helices I to III and the 3(10) helix pack about a central helix (IV) to form a compact globular domain that is capped by the beta-sheet. The C-terminal helix (helix V) projects away from the beta-sheet to expose carboxyl-terminal residues essential for early steps in the HIV-1 infectious cycle. Basic residues implicated in membrane binding and nuclear localization functions cluster about an extruded cationic loop that connects beta-strands 1 and 2. The structure suggests that both membrane binding and nuclear localization may be mediated by complex tertiary structures rather than simple linear determinants.
Probing the Orientation of Surface-Immobilized Protein G B1 Using ToF-SIMS Sum Frequency Generation and NEXAFS Spectroscopy

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

L Baugh; T Weidner; J Baio

2011-12-31

The ability to orient active proteins on surfaces is a critical aspect of many medical technologies. An important related challenge is characterizing protein orientation in these surface films. This study uses a combination of time-of-flight secondary ion mass spectrometry (ToF-SIMS), sum frequency generation (SFG) vibrational spectroscopy, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to characterize the orientation of surface-immobilized Protein G B1, a rigid 6 kDa domain that binds the Fc fragment of IgG. Two Protein G B1 variants with a single cysteine introduced at either end were immobilized via the cysteine thiol onto maleimide-oligo(ethylene glycol)-functionalized gold and baremore » gold substrates. X-ray photoelectron spectroscopy was used to measure the amount of immobilized protein, and ToF-SIMS was used to measure the amino acid composition of the exposed surface of the protein films and to confirm covalent attachment of protein thiol to the substrate maleimide groups. SFG and NEXAFS were used to characterize the ordering and orientation of peptide or side chain bonds. On both substrates and for both cysteine positions, ToF-SIMS data showed enrichment of mass peaks from amino acids located at the end of the protein opposite to the cysteine surface position as compared with nonspecifically immobilized protein, indicating end-on protein orientations. Orientation on the maleimide substrate was enhanced by increasing pH (7.0-9.5) and salt concentration (0-1.5 M NaCl). SFG spectral peaks characteristic of ordered {alpha}-helix and {beta}-sheet elements were observed for both variants but not for cysteine-free wild type protein on the maleimide surface. The phase of the {alpha}-helix and {beta}-sheet peaks indicated a predominantly upright orientation for both variants, consistent with an end-on protein binding configuration. Polarization dependence of the NEXAFS signal from the N 1s to {pi}* transition of {beta}-sheet peptide bonds also indicated protein ordering, with an estimated tilt angle of inner {beta}-strands of 40-50{sup o} for both variants (one variant more tilted than the other), consistent with SFG results. The combined results demonstrate the power of using complementary techniques to probe protein orientation on surfaces.« less
The recognition of three different epitopes for the H-type 2 human blood group determinant by lectins of Ulex europaeus, Galactia tenuiflora and Psophocarpus tetragonolobus (winged bean).

PubMed

Du, M H; Spohr, U; Lemieux, R U

1994-10-01

The chemical mapping of the regions of H-type 2 human blood group-related trisaccharide (Fuc alpha (1-2)Gal beta (1-4)GlcNAc beta Me) that are recognized by three different lectins, the so-called epitopes, are reviewed together with an account of how and why oligosaccharides form specific complexes with proteins as presently viewed in this laboratory. The occasion is used to report the synthesis of the various mono-O-methyl derivatives of the above trisaccharide that were used in these investigations. Also, Fuc alpha (1-2)Gal beta (1-4)Xyl beta Me was synthesized in order to examine whether or not the hydroxymethyl group of the GlcNAc residue participates in the binding reaction.
Determination of the specificity of monoclonal antibodies against Schistosoma mansoni CAA glycoprotein antigen using neoglycoconjugate variants.

PubMed

Carvalho de Souza, Adriana; van Remoortere, Alexandra; Hokke, Cornelis H; Deelder, André M; Vliegenthart, Johannes F G; Kamerling, Johannis P

2005-09-01

The immunogenic O-glycan of circulating anodic antigen (CAA) is a high-molecular-mass polysaccharide with the unique -->6)-[beta-D-GlcpA-(1-->3)]-beta-D-GalpNAc-(1--> repeating unit. To obtain information at the molecular level about the specificity of monoclonal antibodies against CAA, the immunoreactivity of two series of bovine serum albumin-coupled synthetic oligosaccharides related to the CAA O-glycan was monitored using ELISA and surface plasmon resonance spectroscopy. The importance of the axial hydroxyl group of beta-D-GalpNAc for antibody binding was investigated using the following series of analogues: beta-D-GlcpA-(1-->3)-beta-D-GlcpNAc-(1-->O); beta-D-GlcpNAc-(1-->6)-[beta-D-GlcpA-(1-->3)]-beta-D-GlcpNAc-(1-->O); and beta-D-GlcpA-(1-->3)-beta-D-GlcpNAc-(1-->6)-[beta-D-GlcpA-(1-->3)]-beta-D-GlcpNAc-(1-->O). In the second series of analogues, beta-D-Glcp6S-(1-->3)-beta-D-GalpNAc-(1-->O), beta-D-GalpNAc-(1-->6)-[beta-D-Glcp6S-(1-->3)]-beta-D-GalpNAc-(1-->O), and beta-D-Glcp6S-(1-->3)-beta-D-Gal-pNAc-(1-->6)-[beta-D-Glcp6S-(1-->3)]-beta-D-GalpNAc-(1-->O), the native beta-D-GlcpA moiety was replaced by beta-D-Glcp6S to evaluate the influence of the nature of the charge on antibody recognition. Comparison of the immunoreactivity of these series with that measured for conjugates containing corresponding synthetic CAA fragments showed that the antibody binding levels can be correlated to the antibody specificity to CAA fragments. For the most reactive antibodies, the structural changes chosen (beta-D-GalpNAc replaced by beta-D-GlcpNAc, and beta-D-GlcpA replaced by beta-D-Glcp6S) completely eradicated the binding.
Usefulness of silicone elastomer sheet as another option of adhesion preventive material during craniectomies.

PubMed

Lee, Choon-Hyun; Cho, Do-Sang; Jin, Sung-Chul; Kim, Sung-Hak; Park, Dong-Been

2007-10-01

We describe the use of a silicone elastomer sheet (SILASTIC) to prevent peridural fibrosis in patients who underwent a craniectomy and a subsequent cranioplasty. We performed a decompressive craniectomy and a subsequent cranioplasty with an autologous bone flap in 50 patients (mean age, 40 years) between 1996 and 2005 at our institution. Most of the craniectomies were performed as an emergency procedure for relief of brain swelling. The standard decompressive craniectomy technique that we performed included bone removal and a duroplasty in 26 of the 50 patients, however, a SILASTIC sheet was added to the standard decompressive craniectomy in the remaining patients in an attempt to prevent dural adhesions. The development of adhesion formation between the tissue layers was evaluated during the cranioplasty in terms of operative time and the amount of blood loss. During the cranioplasty, we observed that the SILASTIC sheet succeeded in creating a controlled dissection plane, which facilitated access to the epidural space, shortened the operative time by approximately 24.8% and diminished the intraoperative blood loss by 37.9% as compared with the group of patients who underwent the standard cranioplasty. These differences were statistically significant (p<0.05). The use of a SILASTIC sheet to prevent peridural scarring and to facilitate cranioplasty in patients who have previously undergone a craniectomy is a good technique, regardless of the procedural indication.
Dynamics of the last glacial maximum Antarctic ice-sheet and its response to ocean forcing

PubMed Central

Golledge, Nicholas R.; Fogwill, Christopher J.; Mackintosh, Andrew N.; Buckley, Kevin M.

2012-01-01

Retreat of the Last Glacial Maximum (LGM) Antarctic ice sheet is thought to have been initiated by changes in ocean heat and eustatic sea level propagated from the Northern Hemisphere (NH) as northern ice sheets melted under rising atmospheric temperatures. The extent to which spatial variability in ice dynamics may have modulated the resultant pattern and timing of decay of the Antarctic ice sheet has so far received little attention, however, despite the growing recognition that dynamic effects account for a sizeable proportion of mass-balance changes observed in modern ice sheets. Here we use a 5-km resolution whole-continent numerical ice-sheet model to assess whether differences in the mechanisms governing ice sheet flow could account for discrepancies between geochronological studies in different parts of the continent. We first simulate the geometry and flow characteristics of an equilibrium LGM ice sheet, using pan-Antarctic terrestrial and marine geological data for constraint, then perturb the system with sea level and ocean heat flux increases to investigate ice-sheet vulnerability. Our results identify that fast-flowing glaciers in the eastern Weddell Sea, the Amundsen Sea, central Ross Sea, and in the Amery Trough respond most rapidly to ocean forcings, in agreement with empirical data. Most significantly, we find that although ocean warming and sea-level rise bring about mainly localized glacier acceleration, concomitant drawdown of ice from neighboring areas leads to widespread thinning of entire glacier catchments—a discovery that has important ramifications for the dynamic changes presently being observed in modern ice sheets. PMID:22988078
Dynamics of the last glacial maximum Antarctic ice-sheet and its response to ocean forcing.

PubMed

Golledge, Nicholas R; Fogwill, Christopher J; Mackintosh, Andrew N; Buckley, Kevin M

2012-10-02

Retreat of the Last Glacial Maximum (LGM) Antarctic ice sheet is thought to have been initiated by changes in ocean heat and eustatic sea level propagated from the Northern Hemisphere (NH) as northern ice sheets melted under rising atmospheric temperatures. The extent to which spatial variability in ice dynamics may have modulated the resultant pattern and timing of decay of the Antarctic ice sheet has so far received little attention, however, despite the growing recognition that dynamic effects account for a sizeable proportion of mass-balance changes observed in modern ice sheets. Here we use a 5-km resolution whole-continent numerical ice-sheet model to assess whether differences in the mechanisms governing ice sheet flow could account for discrepancies between geochronological studies in different parts of the continent. We first simulate the geometry and flow characteristics of an equilibrium LGM ice sheet, using pan-Antarctic terrestrial and marine geological data for constraint, then perturb the system with sea level and ocean heat flux increases to investigate ice-sheet vulnerability. Our results identify that fast-flowing glaciers in the eastern Weddell Sea, the Amundsen Sea, central Ross Sea, and in the Amery Trough respond most rapidly to ocean forcings, in agreement with empirical data. Most significantly, we find that although ocean warming and sea-level rise bring about mainly localized glacier acceleration, concomitant drawdown of ice from neighboring areas leads to widespread thinning of entire glacier catchments-a discovery that has important ramifications for the dynamic changes presently being observed in modern ice sheets.
Structural transition of glucagon in the concentrated solution observed by electrophoretic and spectroscopic techniques.

PubMed

Onoue, Satomi; Iwasa, Sumiko; Kojima, Takashi; Katoh, Fumie; Debari, Kazuhiro; Koh, Keitatsu; Matsuda, Yoshihisa; Yajima, Takehiko

2006-03-24

Glucagon, a polypeptide hormone consisting of 29 amino acid residues, tends to form gel-like fibrillar aggregates, and the glucagon fibril, as well as other pathologically related fibrils including prion, amylin, and beta-amyloid, have been found to be cytotoxic through the activation of apoptotic signaling pathways. To understand the aggregation properties of glucagon fibril, we have characterized and compared the physicochemical properties of glucagon, secretin, a member of the glucagon superfamily, and amylin using analytical techniques including capillary electrophoresis (CE), circular dichroism (CD), FT-IR, FT-Raman, transmission electron microscopy (TEM), and beta-sheet-imaging probe. Aging treatment of glucagon resulted in the formation of fibrillar aggregates in time- and concentration-dependent manner, and FT-IR and FT-Raman analyses showed the spectral shift of amide I band, suggesting the conformational changes from alpha-helix to beta-sheet structure. Interestingly, secretin, having high sequential and secondary structural homology with glucagon, did not generate the fibrillar aggregates at the conditions tested. In addition, we evaluated the association state of glucagon at various pHs raging from pH 2.0 to 3.5 using CE. Based on the CE data, the rate constants of glucagon aggregation were calculated to be 0.002 +/- 0.004/h and 0.080 +/- 0.011/h for aging at pH 2.0 and 3.5, respectively, suggesting the pH dependence of self-association. CE showed the potential to separate and detect the glucagon aggregates and intermediates during aging process.
Densely packed beta-structure at the protein-lipid interface of porin is revealed by high-resolution cryo-electron microscopy.

PubMed

Sass, H J; Büldt, G; Beckmann, E; Zemlin, F; van Heel, M; Zeitler, E; Rosenbusch, J P; Dorset, D L; Massalski, A

1989-09-05

Porin is an integral membrane protein that forms channels across the outer membrane of Escherichia coli. Electron microscopic studies of negatively stained two-dimensional porin crystals have shown three stain accumulations per porin trimer, revealing the locations of pores spanning the membrane. In this study, reconstituted porin lattices embedded in glucose were investigated using the low-dose technique on a cryo-electron microscope equipped with a helium-cooled superconducting objective lens. The specimen temperature was maintained at 5 K to yield an improved microscopic and specimen stability. Under these conditions, we obtained for the first time electron diffraction patterns from porin lattices to a resolution of 3.2 A and images showing optical diffraction up to a resolution of 4.9 A. Applying correlation averaging techniques to the digitized micrographs, we were able to reconstruct projected images of the porin trimer to a resolution of up to 3.5 A. In the final projection maps, amplitudes from electron diffraction and phases from these images were combined. The predominant feature is a high-density narrow band (about 6 A in thickness) that delineates the outer perimeter of the trimer. Since the molecule consists of almost exclusively beta-sheet structure, as revealed by spectroscopic data, we conclude that this band is a cylindrical beta-pleated sheet crossing the membrane nearly perpendicularly to its plane. Another intriguing finding is a low-density area (about 70 A2) situated in the centre of the trimer.
Integration of Partial Information within and across Modalities: Contributions to Spoken and Written Sentence Recognition

ERIC Educational Resources Information Center

Smith, Kimberly G.; Fogerty, Daniel

2015-01-01

Purpose: This study evaluated the extent to which partial spoken or written information facilitates sentence recognition under degraded unimodal and multimodal conditions. Method: Twenty young adults with typical hearing completed sentence recognition tasks in unimodal and multimodal conditions across 3 proportions of preservation. In the unimodal…
Characteristics of ion flow in the quiet state of the inner plasma sheet

NASA Technical Reports Server (NTRS)

Angelopoulos, V.; Kennel, C. F.; Coroniti, F. V.; Pellat, R.; Spence, H. E.; Kivelson, M. G.; Walker, R. J.; Baumjohann, W.; Feldman, W. C.; Gosling, J. T.

1993-01-01

We use AMPTE/IRM and ISEE 2 data to study the properties of the high beta plasma sheet, the inner plasma sheet (IPS). Bursty bulk flows (BBFs) are excised from the two databases, and the average flow pattern in the non-BBF (quiet) IPS is constructed. At local midnight this ensemble-average flow is predominantly duskward; closer to the flanks it is mostly earthward. The flow pattern agrees qualitatively with calculations based on the Tsyganenko (1987) model (T87), where the earthward flow is due to the ensemble-average cross tail electric field and the duskward flow is the diamagnetic drift due to an inward pressure gradient. The IPS is on the average in pressure equilibrium with the lobes. Because of its large variance the average flow does not represent the instantaneous flow field. Case studies also show that the non-BBF flow is highly irregular and inherently unsteady, a reason why earthward convection can avoid a pressure balance inconsistency with the lobes. The ensemble distribution of velocities is a fundamental observable of the quiet plasma sheet flow field.

Anisotropy influence on the failure of Ti6Al4V sheets deformed at room and elevated temperature

NASA Astrophysics Data System (ADS)

Wang, Q. L.; Ghiotti, A.; Bruschi, S.

2018-05-01

Ti6Al4V sheets are usually difficult-to-form at room temperature as a consequence of their strong basal texture and hcp crystal lattice. The heating of the alloy below the beta transus temperature is recognized to enhance its formability, reducing the flow stress and increasing the ductility. However, the influence of the sheet anisotropy on the material failure hasn't been studied yet. To this aim, the paper presents the anisotropy influence on the failure characteristics of Ti6Al4V titanium alloy sheets making use of tensile tests carried out at room temperature and 600°C on smooth, notched and shear samples in order to have various stress states. The fracture strain is measured and the effect of the sample orientation and stress state is identified. To determine the actual stress state for each sample geometry, a numerical model is set up and calibrated using elasto-plastic data from uni-axial tensile tests on smooth samples. Finally, the fracture surfaces are observed through SEM analysis to explain the failure characteristics.
Beta-catenin is required for memory consolidation.

PubMed

Maguschak, Kimberly A; Ressler, Kerry J

2008-11-01

beta-catenin has been implicated in neuronal synapse regulation and remodeling. Here we have examined beta-catenin expression in the adult mouse brain and its role in amygdala-dependent learning and memory. We found alterations in beta-catenin mRNA and protein phosphorylation during fear-memory consolidation. Such alterations correlated with a change in the association of beta-catenin with cadherin. Pharmacologically, this consolidation was enhanced by lithium-mediated facilitation of beta-catenin. Genetically, the role of beta-catenin was confirmed with site-specific deletions of loxP-flanked Ctnnb1 (encoding beta-catenin) in the amygdala. Baseline locomotion, anxiety-related behaviors and acquisition or expression of conditioned fear were normal. However, amygdala-specific deletion of Ctnnb1 prevented the normal transfer of newly formed fear learning into long-term memory. Thus, beta-catenin may be required in the amygdala for the normal consolidation, but not acquisition, of fear memory. This suggests a general role for beta-catenin in the synaptic remodeling and stabilization underlying long-term memory in adults.
Rapid effects of dorsal hippocampal G-protein coupled estrogen receptor on learning in female mice.

PubMed

Lymer, Jennifer; Robinson, Alana; Winters, Boyer D; Choleris, Elena

2017-03-01

Through rapid mechanisms of action, estrogens affect learning and memory processes. It has been shown that 17β-estradiol and an Estrogen Receptor (ER) α agonist enhances performance in social recognition, object recognition, and object placement tasks when administered systemically or infused in the dorsal hippocampus. In contrast, systemic and dorsal hippocampal ERβ activation only promote spatial learning. In addition, 17β-estradiol, the ERα and the G-protein coupled estrogen receptor (GPER) agonists increase dendritic spine density in the CA1 hippocampus. Recently, we have shown that selective systemic activation of the GPER also rapidly facilitated social recognition, object recognition, and object placement learning in female mice. Whether activation the GPER specifically in the dorsal hippocampus can also rapidly improve learning and memory prior to acquisition is unknown. Here, we investigated the rapid effects of infusion of the GPER agonist, G-1 (dose: 50nM, 100nM, 200nM), in the dorsal hippocampus on social recognition, object recognition, and object placement learning tasks in home cage. These paradigms were completed within 40min, which is within the range of rapid estrogenic effects. Dorsal hippocampal administration of G-1 improved social (doses: 50nM, 200nM G-1) and object (dose: 200nM G-1) recognition with no effect on object placement. Additionally, when spatial cues were minimized by testing in a Y-apparatus, G-1 administration promoted social (doses: 100nM, 200nM G-1) and object (doses: 50nM, 100nM, 200nM G-1) recognition. Therefore, like ERα, the GPER in the hippocampus appears to be sufficient for the rapid facilitation of social and object recognition in female mice, but not for the rapid facilitation of object placement learning. Thus, the GPER in the dorsal hippocampus is involved in estrogenic mediation of learning and memory and these effects likely occur through rapid signalling mechanisms. Copyright © 2016 Elsevier Ltd. All rights reserved.
Repetition and brain potentials when recognizing natural scenes: task and emotion differences

PubMed Central

Bradley, Margaret M.; Codispoti, Maurizio; Karlsson, Marie; Lang, Peter J.

2013-01-01

Repetition has long been known to facilitate memory performance, but its effects on event-related potentials (ERPs), measured as an index of recognition memory, are less well characterized. In Experiment 1, effects of both massed and distributed repetition on old–new ERPs were assessed during an immediate recognition test that followed incidental encoding of natural scenes that also varied in emotionality. Distributed repetition at encoding enhanced both memory performance and the amplitude of an old–new ERP difference over centro-parietal sensors. To assess whether these repetition effects reflect encoding or retrieval differences, the recognition task was replaced with passive viewing of old and new pictures in Experiment 2. In the absence of an explicit recognition task, ERPs were completely unaffected by repetition at encoding, and only emotional pictures prompted a modestly enhanced old–new difference. Taken together, the data suggest that repetition facilitates retrieval processes and that, in the absence of an explicit recognition task, differences in old–new ERPs are only apparent for affective cues. PMID:22842817
Identification and measurement of beta-lactam antibiotic residues in milk: integration of screening kits with liquid chromatography.

PubMed

Harik-Khan, R; Moats, W A

1995-01-01

A procedure for identifying and quantitating violative beta-lactams in milk is described. This procedure integrates beta-lactam residue detection kits with the multiresidue automated liquid chromatographic (LC) cleanup method developed in our laboratory. Spiked milk was deproteinized, extracted, and subjected to reversed-phase LC using a gradient program that concentrated the beta-lactams. Amoxicillin, ampicillin, cephapirin, ceftiofur, cloxacillin, and penicillin G were, thus, separated into 5 fractions that were subsequently tested for activity by using 4 kits. beta-lactams in the positive fractions were quantitated by analytical LC methods developed in our laboratory. The LC cleanup method separated beta-lactam antibiotics from each other and from interferences in the matrix and also concentrated the antibiotics, thus increasing the sensitivity of the kits to the beta-lactam antibiotics. The procedure facilitated the task of identifying and measuring the beta-lactam antibiotics that may be present in milk samples.
Structural and biological mimicry of protein surface recognition by [alpha/beta]-peptide foldamers

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

Horne, W. Seth; Johnson, Lisa M.; Ketas, Thomas J.

Unnatural oligomers that can mimic protein surfaces offer a potentially useful strategy for blocking biomedically important protein-protein interactions. Here we evaluate an approach based on combining {alpha}- and {beta}-amino acid residues in the context of a polypeptide sequence from the HIV protein gp41, which represents an excellent testbed because of the wealth of available structural and biological information. We show that {alpha}/{beta}-peptides can mimic structural and functional properties of a critical gp41 subunit. Physical studies in solution, crystallographic data, and results from cell-fusion and virus-infectivity assays collectively indicate that the gp41-mimetic {alpha}/{beta}-peptides effectively block HIV-cell fusion via a mechanism comparablemore » to that of gp41-derived {alpha}-peptides. An optimized {alpha}/{beta}-peptide is far less susceptible to proteolytic degradation than is an analogous {alpha}-peptide. Our findings show how a two-stage design approach, in which sequence-based {alpha} {yields} {beta} replacements are followed by site-specific backbone rigidification, can lead to physical and biological mimicry of a natural biorecognition process.« less
Disruption of the IS6-AID linker affects voltage-gated calcium channel inactivation and facilitation.

PubMed

Findeisen, Felix; Minor, Daniel L

2009-03-01

Two processes dominate voltage-gated calcium channel (Ca(V)) inactivation: voltage-dependent inactivation (VDI) and calcium-dependent inactivation (CDI). The Ca(V)beta/Ca(V)alpha(1)-I-II loop and Ca(2+)/calmodulin (CaM)/Ca(V)alpha(1)-C-terminal tail complexes have been shown to modulate each, respectively. Nevertheless, how each complex couples to the pore and whether each affects inactivation independently have remained unresolved. Here, we demonstrate that the IS6-alpha-interaction domain (AID) linker provides a rigid connection between the pore and Ca(V)beta/I-II loop complex by showing that IS6-AID linker polyglycine mutations accelerate Ca(V)1.2 (L-type) and Ca(V)2.1 (P/Q-type) VDI. Remarkably, mutations that either break the rigid IS6-AID linker connection or disrupt Ca(V)beta/I-II association sharply decelerate CDI and reduce a second Ca(2+)/CaM/Ca(V)alpha(1)-C-terminal-mediated process known as calcium-dependent facilitation. Collectively, the data strongly suggest that components traditionally associated solely with VDI, Ca(V)beta and the IS6-AID linker, are essential for calcium-dependent modulation, and that both Ca(V)beta-dependent and CaM-dependent components couple to the pore by a common mechanism requiring Ca(V)beta and an intact IS6-AID linker.
Graphene materials having randomly distributed two-dimensional structural defects

DOEpatents

Kung, Harold H; Zhao, Xin; Hayner, Cary M; Kung, Mayfair C

2013-10-08

Graphene-based storage materials for high-power battery applications are provided. The storage materials are composed of vertical stacks of graphene sheets and have reduced resistance for Li ion transport. This reduced resistance is achieved by incorporating a random distribution of structural defects into the stacked graphene sheets, whereby the structural defects facilitate the diffusion of Li ions into the interior of the storage materials.
Graphene materials having randomly distributed two-dimensional structural defects

DOEpatents

Kung, Harold H.; Zhao, Xin; Hayner, Cary M.; Kung, Mayfair C.

2016-05-31

Graphene-based storage materials for high-power battery applications are provided. The storage materials are composed of vertical stacks of graphene sheets and have reduced resistance for Li ion transport. This reduced resistance is achieved by incorporating a random distribution of structural defects into the stacked graphene sheets, whereby the structural defects facilitate the diffusion of Li ions into the interior of the storage materials.
Learning Partners: Escribamos! Leamos! Juguemos a las Ciencias! Juguemos a las Matematicas! (Learning Partners: Let's Write! Let's Read! Let's Play Mathematics! Let's Play Science!)

ERIC Educational Resources Information Center

Office of Educational Research and Improvement (ED), Washington, DC.

This Spanish-language document consists of four single-sheet sets of guidelines developed by the Family Involvement Partnership for Learning to assist parents in facilitating their children's elementary school success. The front part of the sheets describes general ways parents can support their children, including modeling writing, reading aloud,…
Note on tachyon actions in string theory

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

Headrick, Matthew

2009-02-15

A number of spacetime fields in string theory (notably the metric, dilaton, bosonic and type 0 bulk closed-string tachyon, and bosonic open-string tachyon) have the following property: whenever the spacetime field configuration factorizes in an appropriate sense, the matter sector of the world-sheet theory factorizes into a tensor product of two decoupled theories. Since the beta functions for such a product theory necessarily also factorize, this property strongly constrains the form of the spacetime action encoding those beta functions. We show that this constraint alone--without needing actually to compute any of the beta functions--is sufficient to fix the form ofmore » the two-derivative action for the metric-dilaton system, as well as the potential for the bosonic open-string tachyon. We also show that no action consistent with this constraint exists for the closed-string tachyon coupled to the metric and dilaton.« less
Comparative characterization of short monomeric polyglutamine peptides by replica exchange molecular dynamics simulation.

PubMed

Nakano, Miki; Watanabe, Hirofumi; Rothstein, Stuart M; Tanaka, Shigenori

2010-05-27

Polyglutamine (polyQ) diseases are caused by an abnormal expansion of CAG repeats. While their detailed structure remains unclear, polyQ peptides assume beta-sheet structures when they aggregate. To investigate the conformational ensemble of short, monomeric polyQ peptides, which consist of 15 glutamine residues (Q(15)), we performed replica exchange molecular dynamics (REMD) simulations. We found that Q(15) can assume multiple configurations due to all of the residues affecting the formation of side-chain hydrogen bonds. Analysis of the free energy landscape reveals that Q(15) has a basin for random-coil structures and another for alpha-helix or beta-turn structures. To investigate properties of aggregated polyQ peptides, we performed multiple molecular dynamics (MMD) simulations for monomeric and oligomeric Q(15). MMD revealed that the formation of oligomers stabilizes the beta-turn structure by increasing the number of hydrogen bonds between the main chains.
Collaboration in Associative Recognition Memory: Using Recalled Information to Defend "New" Judgments

ERIC Educational Resources Information Center

Clark, Steven E.; Abbe, Allison; Larson, Rakel P.

2006-01-01

S. E. Clark, A. Hori, A. Putnam, and T. J. Martin (2000) showed that collaboration on a recognition memory task produced facilitation in recognition of targets but had inconsistent and sometimes negative effects regarding distractors. They accounted for these results within the framework of a dual-process, recall-plus-familiarity model but…
Speech Recognition in Adults with Cochlear Implants: The Effects of Working Memory, Phonological Sensitivity, and Aging

ERIC Educational Resources Information Center

Moberly, Aaron C.; Harris, Michael S.; Boyce, Lauren; Nittrouer, Susan

2017-01-01

Purpose: Models of speech recognition suggest that "top-down" linguistic and cognitive functions, such as use of phonotactic constraints and working memory, facilitate recognition under conditions of degradation, such as in noise. The question addressed in this study was what happens to these functions when a listener who has experienced…
Facilitation of Learning by Social-Emotional Feedback in Humans Is Beta-Noradrenergic-Dependent

ERIC Educational Resources Information Center

Mihov, Yoan; Mayer, Simon; Musshoff, Frank; Maier, Wolfgang; Kendrick, Keith M.; Hurlemann, Rene

2010-01-01

Adaptive behavior in dynamic environments critically depends on the ability to learn rapidly and flexibly from the outcomes of prior choices. In social environments, facial expressions of emotion often serve as performance feedback and thereby guide declarative learning. Abundant evidence implicates beta-noradrenergic signaling in the modulatory…
A Simple Spreadsheet Program to Simulate and Analyze the Far-UV Circular Dichroism Spectra of Proteins

ERIC Educational Resources Information Center

Abriata, Luciano A.

2011-01-01

A simple algorithm was implemented in a spreadsheet program to simulate the circular dichroism spectra of proteins from their secondary structure content and to fit [alpha]-helix, [beta]-sheet, and random coil contents from experimental far-UV circular dichroism spectra. The physical basis of the method is briefly reviewed within the context of…
Rapid Radiochemical Method for Total Radiostrontium (Sr-90) ...

EPA Pesticide Factsheets

Technical Fact Sheet Analysis Purpose: Qualitative analysis Technique: Beta counting Method Developed for: Strontium-89 and strontium-90 in building materials Method Selected for: SAM lists this method for qualitative analysis of strontium-89 and strontium-90 in concrete or brick building materials Summary of subject analytical method which will be posted to the SAM website to allow access to the method.
Structural analysis of HLA-B40 epitopes.

PubMed

Kawaguchi, G; Kato, N; Kashiwase, K; Karaki, S; Kohsaka, T; Akaza, T; Kano, K; Takiguchi, M

1993-03-01

Two genes encoding HLA-B60 or HLA-B61 were cloned from Japanese and the exons of their genes were sequenced. One silent mutation was observed at the exon 1 between HLA-B60 (B*40012) and B*40011. Seven nucleotide substitutions were seen at the exon 3 between HLA-B61 (B*4006) and B*4002. Three substitutions at codon 95, CTC in B*4002 to TGG in B*4006, changed Leu in B*4002 to Trp in B*4006, while two substitutions at codon 97, AGC in B*4002 and ACG in B*4006, changed Ser in B*4002 to Thr in B*4006. Since B*4002 shares the epitope of alloantibodies specific for HLA-B61, two HLA-B61 subtypes are discriminated by two amino acid substitutions at residues 95 and 97. B*40012 and B*4006 differ by four amino acid substitutions on the beta sheet and five amino acid substitutions on the alpha 2 helix. Since the residues at the beta sheet seem hardly to affect the binding of alloantibody, it is suspected that the residues on the alpha 2 helix provide epitopes for alloantibodies that discriminate allospecificity between HLA-B60 and HLA-B61.
Arachidonic acid mediates the formation of abundant alpha-helical multimers of alpha-synuclein

NASA Astrophysics Data System (ADS)

Iljina, Marija; Tosatto, Laura; Choi, Minee L.; Sang, Jason C.; Ye, Yu; Hughes, Craig D.; Bryant, Clare E.; Gandhi, Sonia; Klenerman, David

2016-09-01

The protein alpha-synuclein (αS) self-assembles into toxic beta-sheet aggregates in Parkinson’s disease, while it is proposed that αS forms soluble alpha-helical multimers in healthy neurons. Here, we have made αS multimers in vitro using arachidonic acid (ARA), one of the most abundant fatty acids in the brain, and characterized them by a combination of bulk experiments and single-molecule Fӧrster resonance energy transfer (sm-FRET) measurements. The data suggest that ARA-induced oligomers are alpha-helical, resistant to fibril formation, more prone to disaggregation, enzymatic digestion and degradation by the 26S proteasome, and lead to lower neuronal damage and reduced activation of microglia compared to the oligomers formed in the absence of ARA. These multimers can be formed at physiologically-relevant concentrations, and pathological mutants of αS form less multimers than wild-type αS. Our work provides strong biophysical evidence for the formation of alpha-helical multimers of αS in the presence of a biologically relevant fatty acid, which may have a protective role with respect to the generation of beta-sheet toxic structures during αS fibrillation.
The microscopic protein structure of the lens with a theory for cataract formation as determined by Raman spectroscopy of intact bovine lenses.

PubMed

Schachar, R A; Solin, S A

1975-05-01

Intact bovine lenses have been studied using the polarized Raman spectroscopic technique. A brief theoretical and experimental review of Raman spectroscopy is presented. From the dependence of the Raman depolarization ratio on the propagation direction of the incident radiation we have determined that the uniaxial qualities of the lens result from microscopic anisotropy and have established the quantitative positional correlation of specific chemical bonds with respect to the lens optic axis. In particular, the hydrogen bonded linear CONH groups of the antiparallel beta-pleated sheet are preferentially oriented in directions orthogonal to the lens optic axis. The Raman spectra of intact lenses do not exhibit bands at positions characteristic of either the alpha-helix or the random coil protein structure. The antiparallel beta-pleated sheet protein microstructure and the lens fiber cross-sectional macrostructure exhibit a remarkable similarity. This similarity may be causal and is consistent with the protein concentration of the lens, the birefringent properties observed by both Lenhard and Brewster, the CONH bond angle distribution with respect to the optic axis, and the lens anatomy. It is suggested that cortical cataracts are caused by fluctuations in protein orientational order.

Controlling aggregation propensity in A53T mutant of alpha-synuclein causing Parkinson's disease

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

Kumar, Sonu; Sarkar, Anita; Sundar, Durai, E-mail: sundar@dbeb.iitd.ac.in

2009-09-18

Understanding {alpha}-synuclein in terms of fibrillization, aggregation, solubility and stability is fundamental in Parkinson's disease (PD). The three familial mutations, namely, A30P, E46K and A53T cause PD because the hydrophobic regions in {alpha}-synuclein acquire {beta}-sheet configuration, and have a propensity to fibrillize and form amyloids that cause cytotoxicity and neurodegeneration. On simulating the native form and mutants (A30P, E46K and A53T) of {alpha}-synuclein in water solvent, clear deviations are observed in comparison to the all-helical 1XQ8 PDB structure. We have identified two crucial residues, {sup 40}Val and {sup 74}Val, which play key roles in {beta}-sheet aggregation in the hydrophobic regionsmore » 36-41 and 68-78, respectively, leading to fibrillization and amyloidosis in familial (A53T) PD. We have also identified V40D{sub V}74D, a double mutant of A53T (the most amyloidogenic mutant). The simultaneous introduction of these two mutations in A53T nearly ends its aggregation propensity, increases its solubility and positively enhances its thermodynamic stability.« less
The protein folding network

NASA Astrophysics Data System (ADS)

Rao, Francesco; Caflisch, Amedeo

2004-03-01

Networks are everywhere. The conformation space of a 20-residue antiparallel beta-sheet peptide [1], sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. As previously found for the World-Wide Web as well as for social and biological networks , the conformation space contains highly connected hubs like the native state which is the most populated free energy basin. Furthermore, the network shows a hierarchical modularity [2] which is consistent with the funnel mechanism of folding [3] and is not observed for a random heteropolymer lacking a native state. Here we show that the conformation space network describes the free energy landscape without requiring projections into arbitrarily chosen reaction coordinates. The network analysis provides a basis for understanding the heterogeneity of the folding transition state and the existence of multiple pathways. [1] P. Ferrara and A. Caflisch, Folding simulations of a three-stranded antiparallel beta-sheet peptide, PNAS 97, 10780-10785 (2000). [2] Ravasz, E. and Barabási, A. L. Hierarchical organization in complex networks. Phys. Rev. E 67, 026112 (2003). [3] Dill, K. and Chan, H From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10-19 (1997)
Quantitative confirmation of diffusion-limited oxidation theories

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

Gillen, K.T.; Clough, R.L.

1990-01-01

Diffusion-limited (heterogeneous) oxidation effects are often important for studies of polymer degradation. Such effects are common in polymers subjected to ionizing radiation at relatively high dose rate. To better understand the underlying oxidation processes and to aid in the planning of accelerated aging studies, it would be desirable to be able to monitor and quantitatively understand these effects. In this paper, we briefly review a theoretical diffusion approach which derives model profiles for oxygen surrounded sheets of material by combining oxygen permeation rates with kinetically based oxygen consumption expressions. The theory leads to a simple governing expression involving the oxygenmore » consumption and permeation rates together with two model parameters {alpha} and {beta}. To test the theory, gamma-initiated oxidation of a sheet of commercially formulated EPDM rubber was performed under conditions which led to diffusion-limited oxidation. Profile shapes from the theoretical treatments are shown to accurately fit experimentally derived oxidation profiles. In addition, direct measurements on the same EPDM material of the oxygen consumption and permeation rates, together with values of {alpha} and {beta} derived from the fitting procedure, allow us to quantitatively confirm for the first time the governing theoretical relationship. 17 refs., 3 figs.« less
Development of self-assembling nanowires containing electronically active oligothiophenes

NASA Astrophysics Data System (ADS)

Tsai, Wei-Wen

This dissertation discusses the development of conductive one-dimensional nanowires from self-assembling oligothiophene molecules. Self-assembly has been demonstrated to be a promising alternative approach towards high performance, solution processable, and low-cost organic electronics. One of the many challenges in this field is the control of supramolecular morphologies of ordered structures containing pi-conjugated moieties. This research demonstrated several successful strategies to achieve self assembly of conductive nanowires using synergistic interactions combining pi stacking and hydrogen bonding. The first approach used was to develop a hairpin-shaped sexithiophene molecule, which features two arms of the conjugated structure. The diamidocyclohexyl headgroup of this molecule successfully directs the self-assembly from hydrogen bonding among the amides, forming high-aspect-ratio one-dimensional nanowires with well-defined diameters of 3.0 +/- 0.3 nm. The molecular orientation in the nanostructures promotes formation of sexithiophene H and J aggregates that facilitate efficient charge transport. Organic field-effect transistors were fabricated to reveal improved intrinsic hole mobility from films of the nanostructures, 3.46 x 10-6 cm2V-1s-1, which is one order of magnitude higher than films cast from unassembled molecules. Bulk heterojunction solar cells were developed from this molecule and fullerenes utilizing solution-phase fabrication methods. Intimate mix of the molecule and phenyl-C61-butyric acid methyl ester creates structured interfaces for efficient exciton splitting. The charge carrier mobilities of each material are improved by self-assembly in solution and thermal-energy assisted phase separation.The photovoltaic devices achieved the highest open-circuit voltage of 0.62 V, short-circuit current of 1.79 mA/cm2, fill factor of 35%, and power conversion efficiency of 0.48%. Another strategy to one-dimensional nanowires studied here involved the modification of a class of peptide lipids. The tripeptide segments in the molecular structure promote beta-sheet formation in nonpolar organic solvents, which is the main driving force for their self-assembly into 1D nanowires. Left-handed helical nanowires were formed with diameters of 8.9 nm and pitches between 50--150 nm. Substitutions of oligothiophenes lead to unprecedented supercoiling phenomena manifested as the transformation from helical to coiled or curved nanowires. We proposed that the curving of the nanowires is the consequence of relaxation from torsionally strained nanohelices, a process similar to supercoiling of strained DNA double helix. This process is governed by the mismatch in intermolecular distances required for peptide beta-sheets vs. pi-pi interactions of the conjugated segments decorating the periphery of the nanowires. Circular dichroism revealed helical arrangements of the conjugated moieties in these peptide lipids manifesting supercoiling phenomena. Peptide lipids without helical arrangement of the conjugated segments only exhibit helical morphologies. The self-assembly process of peptide lipids also leads to hierarchical assemblies of energetically favored single, double, and triple-helical nanostructures with well-defined dimensions. Self-assembled nanowires from oligothiophene-substituted peptide lipids revealed increased conductivity of 1.39--1.41 x 10-5 S/cm, two orders of magnitude higher than unassembled films and one order of magnitude higher than unsubstituted peptide lipids. The role of the primary beta-helix in controlling supramolecular organization was investigated by varying the chirality of the tripeptide segments, GAA. Four diastereomers of a peptide lipid substituted with p-toluene carboxylates were compared using L or D-alanines. Molecules with all L residues self-assemble into left-handed helical nanofibers with a pitch of 160 +/- 30 nm. Substitution of one or two D-alanines leads to assemblies of cylindrical nanofibers without any twisting, left-handed helices with smaller pitches (40 +/- 6 nm), or aggregates without regular shapes. We believe these effects are steric in nature that changes the beta-sheet sub-structure within the nanofibers. These principles could be utilized as strategies to optimize the morphologies and properties of nanostructures based on these amphiphilic molecules.
Transfer between pose and expression training in face recognition.

PubMed

Chen, Wenfeng; Liu, Chang Hong

2009-02-01

Prior research has shown that recognition of unfamiliar faces is susceptible to image variations due to pose and expression changes. However, little is known about how these variations on a new face are learnt and handled. We aimed to investigate whether exposures to one type of variation facilitate recognition in the untrained variation. In Experiment 1, faces were trained in multiple or single pose but were tested with a new expression. In Experiment 2, faces were trained in multiple or single expression but were tested in a new pose. We found that higher level of exposure to pose information facilitated recognition of the trained face in a new expression. However, multiple-expression training failed to transfer to a new pose. The findings suggest that generalisation of pose training may be extended to different types of variation whereas generalisation of expression training is largely confined within the trained type of variation.
Strippable grid facilitates removal of grid-surfaced conical workpiece from die

NASA Technical Reports Server (NTRS)

Ruppe, E. P.

1966-01-01

Female die facilitates the removal of a sheet metal structure from a die used for explosive forming of the metal. The female die consists of a smooth conical frustum made of fiber glass with a cured epoxy-resin surface on which a molded grid pattern made of a polyurethane resin is overlaid.
Collective behavior in two-dimensional biological systems: Receptor clustering and beta-sheet aggregation

NASA Astrophysics Data System (ADS)

Guo, Chinlin

We studied two particular biomedical systems which exhibit collective molecular behavior. One is clustering of tumor necrosis factor receptor I (TNFR1), and another is β-sheet folding and aggregation. Receptor clustering has been shown to be a crucial step in many signaling events but its biological meaning has not been adequately addressed. Here, via a simple lattice model, we show how cells use this clustering machinery to enhance sensitivity as well as robustness. On the other hand, intracellular deposition of aggregated protein rich in β-sheet is a prominent cytopathological feature of most neurodegenerative diseases. How this aggregation occurs and how it responds to therapy is not completely understood. Here, we started from a reconstruction of the H-bond potential and carry out a full investigation of β-sheet thermodynamics as well as kinetics. We show that β-sheet aggregation is most likely due to molecular stacking and found that the minimal length of an aggregate mutant polymer corresponds well with the number observed in adult Huntington's disease. We have also shown that molecular agents such as dendrimers might fail at high-dose therapy; instead, a potential therapy strategy is to block β-turn formation. Our predictions can be used for future experimental tests and clinical trials.
Alpha-helix to beta-sheet transition in long-chain poly-l-lysine: Formation of alpha-helical fibrils by poly-l-lysine.

PubMed

Cieślik-Boczula, Katarzyna

2017-06-01

The temperature-induced α-helix to β-sheet transition in long-chain poly-l-lysine (PLL), accompanied by the gauche-to-trans isomerization of CH 2 groups in the hydrocarbon side chains of Lys amino acid residues, and formation of β-sheet as well as α-helix fibrillar aggregates of PLL have been studied using Fourier-transform infrared (FT-IR) and vibrational circular dichroism (VCD) spectroscopy, and transmission electron microscopy (TEM). In a low-temperature alkaline water solution or in a methanol-rich water mixture, the secondary structure of PLL is represented by α-helical conformations with unordered and gauche-rich hydrocarbon side chains. Under these conditions, PLL molecules aggregate into α-helical fibrils. PLLs dominated by extended antiparallel β-sheet structures with highly ordered trans-rich hydrocarbon side chains are formed in a high-temperature range at alkaline pD and aggregate into fibrillar, protofibrillar, and spherical forms. Presented data support the idea that fibrillar aggregation is a varied phenomenon possible in repetitive structural elements with not only a β-sheet-rich conformation, but also an α-helical-rich conformation. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.
Selective Attention Enhances Beta-Band Cortical Oscillation to Speech under “Cocktail-Party” Listening Conditions

PubMed Central

Gao, Yayue; Wang, Qian; Ding, Yu; Wang, Changming; Li, Haifeng; Wu, Xihong; Qu, Tianshu; Li, Liang

2017-01-01

Human listeners are able to selectively attend to target speech in a noisy environment with multiple-people talking. Using recordings of scalp electroencephalogram (EEG), this study investigated how selective attention facilitates the cortical representation of target speech under a simulated “cocktail-party” listening condition with speech-on-speech masking. The result shows that the cortical representation of target-speech signals under the multiple-people talking condition was specifically improved by selective attention relative to the non-selective-attention listening condition, and the beta-band activity was most strongly modulated by selective attention. Moreover, measured with the Granger Causality value, selective attention to the single target speech in the mixed-speech complex enhanced the following four causal connectivities for the beta-band oscillation: the ones (1) from site FT7 to the right motor area, (2) from the left frontal area to the right motor area, (3) from the central frontal area to the right motor area, and (4) from the central frontal area to the right frontal area. However, the selective-attention-induced change in beta-band causal connectivity from the central frontal area to the right motor area, but not other beta-band causal connectivities, was significantly correlated with the selective-attention-induced change in the cortical beta-band representation of target speech. These findings suggest that under the “cocktail-party” listening condition, the beta-band oscillation in EEGs to target speech is specifically facilitated by selective attention to the target speech that is embedded in the mixed-speech complex. The selective attention-induced unmasking of target speech may be associated with the improved beta-band functional connectivity from the central frontal area to the right motor area, suggesting a top-down attentional modulation of the speech-motor process. PMID:28239344
Selective Attention Enhances Beta-Band Cortical Oscillation to Speech under "Cocktail-Party" Listening Conditions.

PubMed

Gao, Yayue; Wang, Qian; Ding, Yu; Wang, Changming; Li, Haifeng; Wu, Xihong; Qu, Tianshu; Li, Liang

2017-01-01

Human listeners are able to selectively attend to target speech in a noisy environment with multiple-people talking. Using recordings of scalp electroencephalogram (EEG), this study investigated how selective attention facilitates the cortical representation of target speech under a simulated "cocktail-party" listening condition with speech-on-speech masking. The result shows that the cortical representation of target-speech signals under the multiple-people talking condition was specifically improved by selective attention relative to the non-selective-attention listening condition, and the beta-band activity was most strongly modulated by selective attention. Moreover, measured with the Granger Causality value, selective attention to the single target speech in the mixed-speech complex enhanced the following four causal connectivities for the beta-band oscillation: the ones (1) from site FT7 to the right motor area, (2) from the left frontal area to the right motor area, (3) from the central frontal area to the right motor area, and (4) from the central frontal area to the right frontal area. However, the selective-attention-induced change in beta-band causal connectivity from the central frontal area to the right motor area, but not other beta-band causal connectivities, was significantly correlated with the selective-attention-induced change in the cortical beta-band representation of target speech. These findings suggest that under the "cocktail-party" listening condition, the beta-band oscillation in EEGs to target speech is specifically facilitated by selective attention to the target speech that is embedded in the mixed-speech complex. The selective attention-induced unmasking of target speech may be associated with the improved beta-band functional connectivity from the central frontal area to the right motor area, suggesting a top-down attentional modulation of the speech-motor process.
Prominent facilitation at beta and gamma frequency range revealed with physiological calcium concentration in adult mouse piriform cortex in vitro

PubMed Central

Gleizes, Marie; Perrier, Simon P.; Fonta, Caroline

2017-01-01

Neuronal activity is characterized by a diversity of oscillatory phenomena that are associated with multiple behavioral and cognitive processes, yet the functional consequences of these oscillations are not fully understood. Our aim was to determine whether and how these different oscillatory activities affect short-term synaptic plasticity (STP), using the olfactory system as a model. In response to odorant stimuli, the olfactory bulb displays a slow breathing rhythm as well as beta and gamma oscillations. Since the firing of olfactory bulb projecting neurons is phase-locked with beta and gamma oscillations, structures downstream from the olfactory bulb should be driven preferentially at these frequencies. We examined STP exhibited by olfactory bulb inputs in slices of adult mouse piriform cortex maintained in vitro in an in vivo-like ACSF (calcium concentration: 1.1 mM). We replaced the presynaptic neuronal firing rate by repeated electrical stimulation (frequency between 3.125 and 100 Hz) applied to the lateral olfactory tract. Our results revealed a considerable enhancement of postsynaptic response amplitude for stimulation frequencies in the beta and gamma range. A phenomenological model of STP fitted to the data suggests that the experimental results can be explained by the interplay between three mechanisms: a short-term facilitation mechanism (time constant ≈160 msec), and two short-term depression mechanisms (recovery time constants <20 msec and ≈140 msec). Increasing calcium concentration (2.2 mM) resulted in an increase in the time constant of facilitation and in a strengthening of the slowest depression mechanism. As a result, response enhancement was reduced and its peak shifted toward the low beta and alpha ranges while depression became predominant in the gamma band. Using environmental conditions corresponding to those that prevail in vivo, our study shows that STP in the lateral olfactory tract to layer Ia synapse allows amplification of olfactory bulb inputs at beta and gamma frequencies. PMID:28820903
Bedrock structure and the interpretation of palaeo ice stream footprints: examples from the Pleistocene British Ice Sheet

NASA Astrophysics Data System (ADS)

Krabbendam, M.; Bradwell, T.

2009-04-01

To model past and future behaviour of ice sheets, a good understanding of both modern and ancient ice streams is required. The study of present-day ice streams provides detailed data of short-term dynamic changes, whilst the study of Pleistocene palaeo-ice streams can provide crucial constraints on the longer-term evolution of ice sheets. To date, palaeo-ice streams, such as the classical Dubawnt Lake palaeo-ice stream of the former Laurentide Ice Sheet, have been recognised largely on the basis of extremely elongate drumlins and megascale glacial lineations; all soft-sediment features. Whilst it appears that topographically unconstrained ice streams (eg. within the West Antarctic Ice Sheet) are generally underlain by deformable till, topographically constrained ice streams such as Jakobshavn Isbrae do not require deformable sediment and may occur on a bedrock-dominated bed. Analysis of DEM data and geomorphology and structural geology fieldwork in Northern Scotland and Northern England has shown the occurrence of highly streamlined bedforms in bedrock of the former base of topographically controlled palaeo-ice streams, which drained parts of the British Ice Sheet. The bedforms are predominantly bedrock megagrooves with asymmetric cross-profiles. In the Ullapool tributary of the Minch palaeo ice stream, bedrock megagrooves form the dominant evidence for ice streaming. The megagrooves are typically 5-15 m deep, 10-30 m wide and 500 - 3000 m long. Spacing of megagrooves is typically 100 - 200 m. In both study areas, the bedrock is strongly anisotropic, either consisting of thin-bedded strata or strongly foliated metasedimentary rocks, with the strata or foliation having a gentle dip. Megagrooves are best developed where the strike of the anisotropy is sub-parallel (within 10 - 20°) with palaeo ice flow. The bedrock in both areas has a well-developed, relatively densely spaced (< 1m), conjugate joint system. We suggest that asymmetric megagrooves are formed by "lateral plucking", facilitated by the combination of strong bedding/foliation and the joint pattern. Glacial erosion was laterally more effective than vertically; so that stepped faces subparallel to palaeo ice flow are enhanced rather that destroyed. We propose that: a) Lateral plucking is an effective mechanism to produce streamlined bedrock bedforms by fast ice flow, providing the bedrock and bedrock structure are suitable; b) some topographically controlled palaeo-ice stream beds are dominated by bedrock rather than soft-sediment; c) the recognition of palaeo-ice streams may be dependent on the type of bedrock and the orientation of bedrock structure with respect to palaeo ice flow; d) palaeo-ice stream footprints may have been underestimated in formerly glaciated areas.
Health professionals' job satisfaction and associated factors at public health centers in West Ethiopia.

PubMed

Deriba, Beyazin Kebede; Sinke, Shimele Ololo; Ereso, Berhane Megersa; Badacho, Abebe Sorsa

2017-05-30

Human resources are vital for delivering health services, and health systems cannot function effectively without sufficient numbers of skilled, motivated, and well-supported health workers. Job satisfaction of health workers is important for motivation and efficiency, as higher job satisfaction improves both employee performance and patient satisfaction. Even though several studies have addressed job satisfaction among healthcare professionals in different part of the world, there are relatively few studies on healthcare professionals' job satisfaction in Ethiopia. A facility-based cross-sectional study was conducted among health professionals working in health centers in April 2015 using self-administered structured questionnaires. All 322 health professionals working in 23 randomly selected public health centers were included. Factor scores were computed for the identified items by varimax rotation to represent satisfaction. Multivariate linear regression analysis was performed, and the effect of independent variables on the regression factor score quantified. Three hundred eight respondents participated with a response rate of 95.56%. The overall level of job satisfaction was 41.46%. Compensation (benefits) (beta 0.448 [95% CI 0.341 to 0.554]), recognition by management (beta 0.132 [95% CI 0.035 to 0.228]), and opportunity for development (beta 0.123 [95% CI 0.020 to 0.226]) were associated with job satisfaction. A unit increase in salary and incentives and recognition by management scores resulted in 0.459 (95% CI 0.356 to 0.561) and 0.156 (95% CI 0.065 to 0.247) unit increases in job satisfaction scores, respectively. The overall level of job satisfaction in health professionals was low. Salary and incentives, recognition by management, developmental opportunities, and patient appreciation were strong predictors of job satisfaction.
The hepta-beta-glucoside elicitor-binding proteins from legumes represent a putative receptor family.

PubMed

Mithöfer, A; Fliegmann, J; Neuhaus-Url, G; Schwarz, H; Ebel, J

2000-08-01

The ability of legumes to recognize and respond to beta-glucan elicitors by synthesizing phytoalexins is consistent with the existence of a membrane-bound beta-glucan-binding site. Related proteins of approximately 75 kDa and the corresponding mRNAs were detected in various species of legumes which respond to beta-glucans. The cDNAs for the beta-glucan-binding proteins of bean and soybean were cloned. The deduced 75-kDa proteins are predominantly hydrophilic and constitute a unique class of glucan-binding proteins with no currently recognizable functional domains. Heterologous expression of the soybean beta-glucan-binding protein in tomato cells resulted in the generation of a high-affinity binding site for the elicitor-active hepta-beta-glucoside conjugate (Kd = 4.5 nM). Ligand competition experiments with the recombinant binding sites demonstrated similar ligand specificities when compared with soybean. In both soybean and transgenic tomato, membrane-bound, active forms of the glucan-binding proteins coexist with immunologically detectable, soluble but inactive forms of the proteins. Reconstitution of a soluble protein fraction into lipid vesicles regained beta-glucoside-binding activity but with lower affinity (Kd = 130 nM). We conclude that the beta-glucan elicitor receptors of legumes are composed of the 75 kDa glucan-binding proteins as the critical components for ligand-recognition, and of an as yet unknown membrane anchor constituting the plasma membrane-associated receptor complex.
Adenomatous polyposis coli protein (APC)-independent regulation of beta-catenin/Tcf-4 mediated transcription in intestinal cells.

PubMed Central

Baulida, J; Batlle, E; García De Herreros, A

1999-01-01

Alterations in the transcriptional activity of the beta-catenin-Tcf complex have been associated with the earlier stages of colonic transformation. We show here that the activation of protein kinase C by the phorbol ester PMA in several intestinal cell lines increases the levels of beta-catenin detected in the nucleus and augments the transcriptional activity mediated by beta-catenin. The response to PMA was not related to modifications in the cytosolic levels of beta-catenin and was observed not only in cells with wild-type adenomatous polyposis coli protein (APC) but also in APC-deficient cells. Binding assays in vitro revealed that PMA facilitates the interaction of the beta-catenin with the nuclear structure. Our results therefore show that beta-catenin-mediated transcription can be regulated independently of the presence of APC. PMID:10567241
Cu(II) potentiation of Alzheimer Abeta1-40 cytotoxicity and transition on its secondary structure.

PubMed

Dai, Xue-Ling; Sun, Ya-Xuan; Jiang, Zhao-Feng

2006-11-01

Mounting evidence has shown that dyshomeostasis of the redox-active biometals such as Cu and Fe can lead to oxidative stress, which plays a key role in the neuropathology of Alzheimer' disease (AD). Here we demonstrate that with the formation of Cu(II).beta1-40 complexes, copper markedly potentiates the neurotoxicity exhibited by beta-amyloid peptide (Ab). A greater amount of hydrogen peroxide was released when Cu(II).beta1-40 complexes was added to the xanthine oxidase/xanthine system detected by potassium iodide spectrophotometry. Copper bound to Abeta1-40 was observed by electron paramagnetic resonance (EPR) spectroscopy. Circular dichroism (CD) studies indicated that copper chelation could cause a structural transition of Abeta. The addition of copper to Ab introduced an increase on beta-sheet as well as alpha-helix, which may be responsible for the aggregation of Abeta. We hypothesized that Abeta aggregation induced by copper may be responsible for local injury in AD. The interaction between Cu(2+) and Ab also provides a possible mechanism for the enrichment of metal ions in amyloid plaques in the AD brain.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Driscoll, P.C.; Clore, G.M.; Beress, L.

The sequential resonance assignment of the {sup 1}H NMR spectrum of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata is presented. This is carried out with two-dimensional NMR techniques to identify through-bond and through-space (< 5{angstrom}) connectivities. Added spectral complexity arises from the fact that the sample is an approximately 1:1 mixture of two BDS-I isoproteins, (Leu-18)-BDS-I and (Phe-18)-BDS-I. Complete assignments, however, are obtained, largely due to the increased resolution and sensitivity afforded at 600 MHz. In addition, the stereospecific assignment of a large number of {beta}-methylene protons is achieved from an analysis of the patternmore » of {sup 3}J{sub {alpha}{beta}} coupling constants and the relative magnitudes of intraresidue NOEs involving the NH, C{sup {alpha}}H, and C{sup {beta}}H protons. Regular secondary structure elements are deduced from a qualitative interpretation of the nuclear Overhauser enhancement, {sup 3}J{sub HN{alpha}} coupling constant, and amide NH exchange data. A triple-stranded antiparallel {beta}-sheet is found to be related to that found in partially homologous sea anemone polypeptide toxins.« less
Speech Recognition in Adults With Cochlear Implants: The Effects of Working Memory, Phonological Sensitivity, and Aging.

PubMed

Moberly, Aaron C; Harris, Michael S; Boyce, Lauren; Nittrouer, Susan

2017-04-14

Models of speech recognition suggest that "top-down" linguistic and cognitive functions, such as use of phonotactic constraints and working memory, facilitate recognition under conditions of degradation, such as in noise. The question addressed in this study was what happens to these functions when a listener who has experienced years of hearing loss obtains a cochlear implant. Thirty adults with cochlear implants and 30 age-matched controls with age-normal hearing underwent testing of verbal working memory using digit span and serial recall of words. Phonological capacities were assessed using a lexical decision task and nonword repetition. Recognition of words in sentences in speech-shaped noise was measured. Implant users had only slightly poorer working memory accuracy than did controls and only on serial recall of words; however, phonological sensitivity was highly impaired. Working memory did not facilitate speech recognition in noise for either group. Phonological sensitivity predicted sentence recognition for implant users but not for listeners with normal hearing. Clinical speech recognition outcomes for adult implant users relate to the ability of these users to process phonological information. Results suggest that phonological capacities may serve as potential clinical targets through rehabilitative training. Such novel interventions may be particularly helpful for older adult implant users.
Speech Recognition in Adults With Cochlear Implants: The Effects of Working Memory, Phonological Sensitivity, and Aging

PubMed Central

Harris, Michael S.; Boyce, Lauren; Nittrouer, Susan

2017-01-01

Purpose Models of speech recognition suggest that “top-down” linguistic and cognitive functions, such as use of phonotactic constraints and working memory, facilitate recognition under conditions of degradation, such as in noise. The question addressed in this study was what happens to these functions when a listener who has experienced years of hearing loss obtains a cochlear implant. Method Thirty adults with cochlear implants and 30 age-matched controls with age-normal hearing underwent testing of verbal working memory using digit span and serial recall of words. Phonological capacities were assessed using a lexical decision task and nonword repetition. Recognition of words in sentences in speech-shaped noise was measured. Results Implant users had only slightly poorer working memory accuracy than did controls and only on serial recall of words; however, phonological sensitivity was highly impaired. Working memory did not facilitate speech recognition in noise for either group. Phonological sensitivity predicted sentence recognition for implant users but not for listeners with normal hearing. Conclusion Clinical speech recognition outcomes for adult implant users relate to the ability of these users to process phonological information. Results suggest that phonological capacities may serve as potential clinical targets through rehabilitative training. Such novel interventions may be particularly helpful for older adult implant users. PMID:28384805
Analysis of correlated domain motions in IgG light chain reveals possible mechanisms of immunological signal transduction.

PubMed

Król, Marcin; Roterman, Irena; Piekarska, Barbara; Konieczny, Leszek; Rybarska, Janina; Stopa, Barbara; Spólnik, Paweł

2005-05-15

It was shown experimentally that binding of a micelle composed of Congo red molecules to immunological complexes leads to the enhanced stability of the latter, and simultaneously prevents binding of a complement molecule (C1q). The dye binds in a cavity created by the removal of N-terminal polypeptide chain, as observed experimentally in a model system-immunoglobulin G (IgG) light chain dimer. Molecular Dynamics (MD) simulations of three forms of IgG light chain dimer, with and without the dye, were performed to investigate the role of N-terminal fragment and self-assembled ligand in coupling between V and C domains. Root-mean-square distance (RMSD) time profiles show that removal of N-terminal fragment leads to destabilization of V domain. A micelle composed of four self-assembled dye molecules stabilizes and fixes the domain. Analysis of root-mean-square fluctuation (RMSF) values and dynamic cross-correlation matrices (DCCM) reveals that removal of N-terminal fragment results in complete decoupling between V and C domains. Binding of self-assembled Congo red molecules improves the coupling, albeit slightly. The disruption of a small beta-sheet composed of N- and C-terminal fragments of the domain (NC sheet) is the most likely reason for the decoupling. Self-assembled ligand, bound in the place originally occupied by N-terminal fragment, is not able to take over the function of the beta-sheet. Lack of correlation of motions between residues in V and C domains denotes that light chain-Congo red complexes have hampered ability to transmit conformational changes between domains. This is a likely explanation of the lack of complement binding by immunological complexes, which bind Congo red, and supports the idea that the NC sheet is the key structural fragment taking part in immunological signal transduction. Copyright 2005 Wiley-Liss, Inc.

Improved Production Of Wrought Articles From Powders

NASA Technical Reports Server (NTRS)

Thomas, James R.; Singleton, Ogle R.

1994-01-01

Improved technique for consolidation of powders into dense articles developed. Peripheral bands used in consolidation, forging, and rolling operations. Facilitates consolidation of dispersion-hardened aluminous powders and composite mixtures for processing to such useful wrought articles as plates and sheets. Potential use in production of plates and sheets and perhaps other objects from "hard" powders, particularly from powders, objects made from which have propensity to crack when mechanically worked to other forms.
Development of visuo-haptic transfer for object recognition in typical preschool and school-aged children.

PubMed

Purpura, Giulia; Cioni, Giovanni; Tinelli, Francesca

2018-07-01

Object recognition is a long and complex adaptive process and its full maturation requires combination of many different sensory experiences as well as cognitive abilities to manipulate previous experiences in order to develop new percepts and subsequently to learn from the environment. It is well recognized that the transfer of visual and haptic information facilitates object recognition in adults, but less is known about development of this ability. In this study, we explored the developmental course of object recognition capacity in children using unimodal visual information, unimodal haptic information, and visuo-haptic information transfer in children from 4 years to 10 years and 11 months of age. Participants were tested through a clinical protocol, involving visual exploration of black-and-white photographs of common objects, haptic exploration of real objects, and visuo-haptic transfer of these two types of information. Results show an age-dependent development of object recognition abilities for visual, haptic, and visuo-haptic modalities. A significant effect of time on development of unimodal and crossmodal recognition skills was found. Moreover, our data suggest that multisensory processes for common object recognition are active at 4 years of age. They facilitate recognition of common objects, and, although not fully mature, are significant in adaptive behavior from the first years of age. The study of typical development of visuo-haptic processes in childhood is a starting point for future studies regarding object recognition in impaired populations.
Toll-like receptors participate in Naegleria fowleri recognition.

PubMed

Martínez-Castillo, Moisés; Santos-Argumedo, Leopoldo; Galván-Moroyoqui, José Manuel; Serrano-Luna, Jesús; Shibayama, Mineko

2018-01-01

Naegleria fowleri is a protozoan that invades the central nervous system and causes primary amoebic meningoencephalitis. It has been reported that N. fowleri induces an important inflammatory response during the infection. In the present study, we evaluated the roles of Toll-like receptors in the recognition of N. fowleri trophozoites by human mucoepithelial cells, analyzing the expression and production of innate immune response mediators. After amoebic interactions with NCI-H292 cells, the expression and production levels of IL-8, TNF-α, IL-1β, and human beta defensin-2 were evaluated by RT-PCR, ELISA, immunofluorescence, and dot blot assays, respectively. To determine whether the canonical signaling pathways were engaged, we used different inhibitors, namely, IMG-2005 for MyD88 and BAY 11-7085 for the nuclear factor NFkB. Our results showed that the expression and production of the pro-inflammatory cytokines and beta defensin-2 were induced by N. fowleri mainly through the canonical TLR4 pathway in a time-dependent manner.
A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey

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

Deng, Lu; Velikovsky, C. Alejandro; Xu, Gang

Adaptive immunity in jawless vertebrates is mediated by leucine-rich repeat proteins called 'variable lymphocyte receptors' (VLRs). Two types of VLR (A and B) are expressed by mutually exclusive lymphocyte populations in lamprey. VLRB lymphocytes resemble the B cells of jawed vertebrates; VLRA lymphocytes are similar to T cells. We determined the structure of a high-affinity VLRA isolated from lamprey immunized with hen egg white lysozyme (HEL) in unbound and antigen-bound forms. The VLRA-HEL complex demonstrates that certain VLRAs, like {gamma}{delta} T-cell receptors (TCRs) but unlike {alpha}{beta} TCRs, can recognize antigens directly, without a requirement for processing or antigen-presenting molecules. Thus,more » these VLRAs feature the nanomolar affinities of antibodies, the direct recognition of unprocessed antigens of both antibodies and {gamma}{delta} TCRs, and the exclusive expression on the lymphocyte surface that is unique to {alpha}{beta} and {gamma}{delta} TCRs.« less
Improving retention in alcoholic Korsakoff patients.

PubMed

Cermak, L S

1980-01-01

Use of visual images facilitated the storage and retrieval of verbal information, use of verbal cues facilitated the retention of nonverbal materials, and semantic analysis enhanced recognition of verbal material by alcoholic Korsakoff patients.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Aming; Jordan, Jacob L.; Ivanova, Magdalena I.

Understanding nonnative protein aggregation is critical not only to a number of amyloidosis disorders but also for the development of effective and safe biopharmaceuticals. In a series of previous studies [Weiss et al. (2007) Biophys. J. 93, 4392-4403; Andrews et al. (2007) Biochemistry 46, 7558-7571; Andrews et al. (2008) Biochemistry 47, 2397-2403], {alpha}-chymotrypsinogen A (aCgn) and bovine granulocyte colony stimulating factor (bG-CSF) have been shown to exhibit the kinetic and morphological features of other nonnative aggregating proteins at low pH and ionic strength. In this study, we investigated the structural mechanism of aCgn aggregation. The resultant aCgn aggregates were foundmore » to be soluble and exhibited semiflexible filamentous aggregate morphology under transmission electron microscopy. In addition, the filamentous aggregates were demonstrated to possess amyloid characteristics by both Congo red binding and X-ray diffraction. Peptide level hydrogen exchange (HX) analysis suggested that a buried native {beta}-sheet comprised of three peptide segments (39-46, 51-64, and 106-114) reorganizes into the cross-{beta} amyloid core of aCgn aggregates and that at least 50% of the sequence adopts a disordered structure in the aggregates. Furthermore, the equimolar, bimodal HX labeling distribution observed for three reported peptides (65-102, 160-180, and 229-245) suggested a heterogeneous assembly of two molecular conformations in aCgn aggregates. This demonstrates that extended {beta}-sheet interactions typical of the amyloid are sufficiently strong that a relatively small fraction of polypeptide sequence can drive formation of filamentous aggregates even under conditions favoring colloidal stability.« less
Structure of the Human Activating Natural Cytotoxicity Receptor NKp30 Bound to its Tumor Cell Ligand B7-H6

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

Y Li; Q Wang; R Mariuzza

2011-12-31

Natural killer (NK) cells are lymphocytes of the innate immune system that participate in the elimination of tumor cells. In humans, the activating natural cytotoxicity receptors (NCRs) NKp30, NKp44, and NKp46 play a major role in NK cell-mediated tumor cell lysis. NKp30 recognizes B7-H6, a member of the B7 family which is expressed on tumor, but not healthy, cells. To understand the basis for tumor surveillance by NCRs, we determined the structure of NKp30, a member of the CD28 family which includes CTLA-4 and PD-1, in complex with B7-H6. The overall organization of the NKp30-B7-H6-activating complex differs considerably from thosemore » of the CTLA-4-B7 and PD-1-PD-L T cell inhibitory complexes. Whereas CTLA-4 and PD-1 use only the front {beta}-sheet of their Ig-like domain to bind ligands, NKp30 uses both front and back {beta}-sheets, resulting in engagement of B7-H6 via the side, as well as face, of the {beta}-sandwich. Moreover, B7-H6 contacts NKp30 through the complementarity-determining region (CDR) - like loops of its V-like domain in an antibody-like interaction that is not observed for B7 or PD-L. This first structure of an NCR bound to ligand provides a template for designing molecules to stimulate NKp30-mediated cytolytic activity for tumor immunotherapy.« less
Comparative analysis of cell wall surface glycan expression in Candida albicans and Saccharomyces cerevisiae yeasts by flow cytometry.

PubMed

Martínez-Esparza, M; Sarazin, A; Jouy, N; Poulain, D; Jouault, T

2006-07-31

The yeast Candida albicans is an opportunistic pathogen, part of the normal human microbial flora that causes infections in immunocompromised individuals with a high morbidity and mortality levels. Recognition of yeasts by host cells is based on components of the yeast cell wall, which are considered part of its virulence attributes. Cell wall glycans play an important role in the continuous interchange that regulates the balance between saprophytism and parasitism, and also between resistance and infection. Some of these molecular entities are expressed both by the pathogenic yeast C. albicans and by Saccharomyces cerevisiae, a related non-pathogenic yeast, involving similar molecular mechanisms and receptors for recognition. In this work we have exploited flow cytometry methods for probing surface glycans of the yeasts. We compared glycan expression by C. albicans and by S. cerevisiae, and studied the effect of culture conditions. Our results show that the expression levels of alpha- and beta-linked mannosides as well as beta-glucans can be successfully evaluated by flow cytometry methods using different antibodies independent of agglutination reactions. We also found that the surface expression pattern of beta-mannosides detected by monoclonal or polyclonal antibodies are differently modulated during the growth course. These data indicate that the yeast beta-mannosides exposed on mannoproteins and/or phospholipomannan are increased in stationary phase, whereas those linked to mannan are not affected by the yeast growth phase. The cytometric method described here represents a useful tool to investigate to what extent C. albicans is able to regulate its glycan surface expression and therefore modify its virulence properties.
Continued effects of context reinstatement in recognition.

PubMed

Hanczakowski, Maciej; Zawadzka, Katarzyna; Macken, Bill

2015-07-01

The context reinstatement effect refers to the enhanced memory performance found when the context information paired with a target item at study is re-presented at test. Here we investigated the consequences of the way that context information is processed in such a setting that gives rise to its beneficial effect on item recognition memory. Specifically, we assessed whether reinstating context in a recognition test facilitates subsequent memory for this context, beyond the facilitation conferred by presentation of the same context with a different study item. Reinstating the study context at test led to better accuracy in two-alternative forced choice recognition for target faces than did re-pairing those faces with another context encountered during the study phase. The advantage for reinstated over re-paired conditions occurred for both within-subjects (Exp. 1) and between-subjects (Exp. 2) manipulations. Critically, in a subsequent recognition test for the contexts themselves, contexts that had previously served in the reinstated condition were recognized better than contexts that had previously served in the re-paired context condition. This constitutes the first demonstration of continuous effects of context reinstatement on memory for context.
Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition

NASA Astrophysics Data System (ADS)

Fang, Jian; Cheng, Jingdong; Wang, Jiaolong; Zhang, Qiao; Liu, Mengjie; Gong, Rui; Wang, Ping; Zhang, Xiaodan; Feng, Yangyang; Lan, Wenxian; Gong, Zhou; Tang, Chun; Wong, Jiemin; Yang, Huirong; Cao, Chunyang; Xu, Yanhui

2016-04-01

UHRF1 is an important epigenetic regulator for maintenance DNA methylation. UHRF1 recognizes hemi-methylated DNA (hm-DNA) and trimethylation of histone H3K9 (H3K9me3), but the regulatory mechanism remains unknown. Here we show that UHRF1 adopts a closed conformation, in which a C-terminal region (Spacer) binds to the tandem Tudor domain (TTD) and inhibits H3K9me3 recognition, whereas the SET-and-RING-associated (SRA) domain binds to the plant homeodomain (PHD) and inhibits H3R2 recognition. Hm-DNA impairs the intramolecular interactions and promotes H3K9me3 recognition by TTD-PHD. The Spacer also facilitates UHRF1-DNMT1 interaction and enhances hm-DNA-binding affinity of the SRA. When TTD-PHD binds to H3K9me3, SRA-Spacer may exist in a dynamic equilibrium: either recognizes hm-DNA or recruits DNMT1 to chromatin. Our study reveals the mechanism for regulation of H3K9me3 and hm-DNA recognition by URHF1.
Cooperative alpha-helix formation of beta-lactoglobulin induced by sodium n-alkyl sulfates.

PubMed

Chamani, J; Moosavi-Movahedi, A A; Rajabi, O; Gharanfoli, M; Momen-Heravi, M; Hakimelahi, G H; Neamati-Baghsiah, A; Varasteh, A R

2006-01-01

It is generally assumed that folding intermediates contain partially formed native-like secondary structures. However, if we consider the fact that the conformational stability of the intermediate state is simpler than that of the native state, it would be expected that the secondary structures in a folding intermediate would not necessarily be similar to those of the native state. beta-Lactoglobulin is a predominantly beta-sheet protein, although it has a markedly high intrinsic preference for alpha-helical structure. The formation of non-native alpha-helical intermediate of beta-lactoglobulin was induced by n-alkyl sulfates including sodium octyl sulfate, SOS; sodium decyl sulfate, SDeS; sodium dodecyl sulfate, SDS; and sodium tetradecyl sulfate, STS at special condition. The effect of n-alkyl sulfates on the structure of native beta-lactoglobulin at pH 2 was utilized to investigate the contribution of hydrophobic interactions to the stability of non-native alpha-helical intermediate. The addition of various concentrations of n-alkyl sulfates to the native state of beta-lactoglobulin (pH 2) appears to support the stabilized form of non-native alpha-helical intermediate at pH 2. The m values of the intermediate state of beta-lactoglobulin by SOS, SDeS, SDS and STS showed substantial variation. The enhancement of m values as the stability criterion of non-native alpha-helical intermediate state corresponded with increasing chain length of the cited n-alkyl sulfates. The present results suggest that the folding reaction of beta-lactoglobulin follows a non-hierarchical mechanism and hydrophobic interactions play important roles in stabilizing the non-native alpha-helical intermediate state.
Production of beta-glucan and related glucan-hydrolases by Botryosphaeria rhodina.

PubMed

Crognale, S; Bruno, M; Fidaleo, M; Moresi, M; Petruccioli, M

2007-03-01

Characterization of beta-glucan production from Botryosphaeria rhodina DABAC-P82 by detecting simultaneously glucan-hydrolytic enzymes and their localization, culture medium rheology and oxygen transfer. Mycelium growth, beta-glucan production, substrate consumption and glucan-hydrolytic enzymes were monitored both in shaken flasks and in a 3-l stirred-tank bioreactor. Glucan production (19.7 and 15.2 g l(-1), in flask and bioreactor, respectively) was accompanied by extra-cellular and cell-bound beta-glucanase and beta-glucosidase activities. In the bioreactor scale, in the time interval of 0-78 h the apparent viscosity of the culture broth exhibited a general increase; thereafter, it began to reduce, probably because of the above glucan-hydrolytic activities. Moreover, the culture media collected after 45 h behaved as solid-like materials at shear rates smaller than 0.001 s(-1), as pseudo-plastic liquids in the middle shear rate range and as Newtonian ones at shear rates greater than 1000 s(-1). The greatest beta-glucan accumulation in the bioreactor was found to be associated with nitrogen and dissolved oxygen concentrations smaller than 0.15 g l(-1) and 25%, respectively, and with the peak points of the glucan-degrading enzymes. A careful analysis of the critical factors (such as, culture broth rheology, oxygen mass transfer and glucan-hydrolytic enzymes) limiting the beta-glucan production by B. rhodina is a prerequisite to maximize beta-glucan yield and production, as well as to define the process flow sheet capable of maximizing biopolymer recovery, solvent re-utilization and glucose consumption.
Changes in the turbulent boundary layer structure associated with net drag reduction by outer layer manipulators

NASA Technical Reports Server (NTRS)

Rashidnia, N.; Falco, R. E.

1987-01-01

A specially designed wind tunnel was used to examine the effects of tandemly arranged parallel plate manipulators (TAPPMs) on a turbulent boundary-layer structure and the associated drag. Momentum balances, as well as measurements of the local shear stress from the velocity gradient near the wall, were used to obtain the net drag and local skin friction changes. Two TAPPMs, identical except for the thickness of their plates, were used in the study. Results with .003 inch plates were a maximum net drag reduction of 10 percent at 58 beta sub o (using a momentum balance). At 20 beta sub o, simultaneous laser sheet flow visualization and hot-wire anemometry data showed that the Reynolds stress in the large eddies was significantly reduced, as were the streamwise and normal velocity components. Using space-time correlations the reductions were again identified. Furthermore, quantitative flow visualization showed that the outward normal velocity of the inner region was also significantly decreased in the region around 20 beta sub o. However, throughout the first 130 beta sub o, the measured sublayer thickness with the TAPPMs in place was 15 to 20 percent greater. The data showed that the skin friction, as well as the structure of the turbulence, was strongly modified in the first 35 beta sub o, but that they both significantly relaxed toward unmanipulated boundary layer values by 50 beta sub o.
Beta Regio - Phoebe Regio on Venus: Geologic mapping with the Magellan data

NASA Technical Reports Server (NTRS)

Nikishin, A. M.; Borozdin, V. K.; Bobina, N. N.; Burba, G. A.

1993-01-01

The geologic maps of C1-15N283 and C1-00N283 sheets were produced (preliminary versions) with Magellan SAR images. This work was undertaken as a part of Russia's contribution into C1 geologic mapping efforts. The scale of the original maps is 1:8,000,000, and the maps are reproduced here at a reduced size.
Structural elucidation of the interaction between neurodegenerative disease-related tau protein with model lipid membranes

NASA Astrophysics Data System (ADS)

Jones, Emmalee M.

A protein's sequence of amino acids determines how it folds. That folded structure is linked to protein function, and misfolding to dysfunction. Protein misfolding and aggregation into beta-sheet rich fibrillar aggregates is connected with over 20 neurodegenerative diseases, including Alzheimer's disease (AD). AD is characterized in part by misfolding, aggregation and deposition of the microtubule associated tau protein into neurofibrillary tangles (NFTs). However, two questions remain: What is tau's fibrillization mechanism, and what is tau's cytotoxicity mechanism? Tau is prone to heterogeneous interactions, including with lipid membranes. Lipids have been found in NFTs, anionic lipid vesicles induced aggregation of the microtubule binding domain of tau, and other protein aggregates induced ion permeability in cells. This evidence prompted our investigation of tau's interaction with model lipid membranes to elucidate the structural perturbations those interactions induced in tau protein and in the membrane. We show that although tau is highly charged and soluble, it is highly surface active and preferentially interacts with anionic membranes. To resolve molecular-scale structural details of tau and model membranes, we utilized X-ray and neutron scattering techniques. X-ray reflectivity indicated tau aggregated at air/water and anionic lipid membrane interfaces and penetrated into membranes. More significantly, membrane interfaces induced tau protein to partially adopt a more compact conformation with density similar to folded protein and ordered structure characteristic of beta-sheet formation. This suggests possible membrane-based mechanisms of tau aggregation. Membrane morphological changes were seen using fluorescence microscopy, and X-ray scattering techniques showed tau completely disrupts anionic membranes, suggesting an aggregate-based cytotoxicity mechanism. Further investigation of protein constructs and a "hyperphosphorylation" disease mimic helped clarify the role of the microtubule binding domain in anionic lipid affinity and demonstrated even "hyperphosphorylation" did not prevent interaction with anionic membranes. Additional studies investigated more complex membrane models to increase physiological relevance. These insights revealed structural changes in tau protein and lipid membranes after interaction. We observed tau's affinity for interfaces, and aggregation and compaction once tau partitions to interfaces. We observed the beginnings of beta-sheet formation in tau at anionic lipid membranes. We also examined disruption to the membrane on a molecular scale.
The secondary structure of the ets domain of human Fli-1 resembles that of the helix-turn-helix DNA-binding motif of the Escherichia coli catabolite gene activator protein.

PubMed Central

Liang, H; Olejniczak, E T; Mao, X; Nettesheim, D G; Yu, L; Thompson, C B; Fesik, S W

1994-01-01

The ets family of eukaryotic transcription factors is characterized by a conserved DNA-binding domain of approximately 85 amino acids for which the three-dimensional structure is not known. By using multidimensional NMR spectroscopy, we have determined the secondary structure of the ets domain of one member of this gene family, human Fli-1, both in the free form and in a complex with a 16-bp cognate DNA site. The secondary structure of the Fli-1 ets domain consists of three alpha-helices and a short four-stranded antiparallel beta-sheet. This secondary structure arrangement resembles that of the DNA-binding domain of the catabolite gene activator protein of Escherichia coli, as well as those of several eukaryotic DNA-binding proteins including histone H5, HNF-3/fork head, and the heat shock transcription factor. Differences in chemical shifts of backbone resonances and amide exchange rates between the DNA-bound and free forms of the Fli-1 ets domain suggest that the third helix is the DNA recognition helix, as in the catabolite gene activator protein and other structurally related proteins. These results suggest that the ets domain is structurally similar to the catabolite gene activator protein family of helix-turn-helix DNA-binding proteins. Images PMID:7972119
[Relationships between venomous function and innate immune function].

PubMed

Goyffon, Max; Saul, Frederick; Faure, Grazyna

2015-01-01

Venomous function is investigated in relation to innate immune function in two cases selected from scorpion venom and serpent venom. In the first case, structural analysis of scorpion toxins and defensins reveals a close interrelation between both functions (toxic and innate immune system function). In the second case, structural and functional studies of natural inhibitors of toxic snake venom phospholipases A2 reveal homology with components of the innate immune system, leading to a similar conclusion. Although there is a clear functional distinction between neurotoxins, which act by targeting membrane ion channels, and the circulating defensins which protect the organism from pathogens, the scorpion short toxins and defensins share a common protein folding scaffold with a conserved cysteine-stabilized alpha-beta motif of three disulfide bridges linking a short alpha helix and an antiparallel beta sheet. Genomic analysis suggests that these proteins share a common ancestor (long venom toxins were separated from an early gene family which gave rise to separate short toxin and defensin families). Furthermore, a scorpion toxin has been experimentally synthetized from an insect defensin, and an antibacterial scorpion peptide, androctonin (whose structure is similar to that of a cone snail venom toxin), was shown to have a similar high affinity for the postsynaptic acetylcholine receptor of Torpedo sp. Natural inhibitors of phospholipase A2 found in the blood of snakes are associated with the resistance of venomous snakes to their own highly neurotoxic venom proteins. Three classes of phospholipases A2 inhibitors (PLI-α, PLI-β, PLI-γ) have been identified. These inhibitors display diverse structural motifs related to innate immune proteins including carbohydrate recognition domains (CRD), leucine rich repeat domains (found in Toll-like receptors) and three finger domains, which clearly differentiate them from components of the adaptive immune system. Thus, in structure, function and phylogeny, venomous function in both vertebrates and invertebrates are clearly interrelated with innate immune function. © Société de Biologie, 2016.
Application of optical correlation techniques to particle imaging velocimetry

NASA Technical Reports Server (NTRS)

Wernet, Mark P.; Edwards, Robert V.

1988-01-01

Pulsed laser sheet velocimetry yields nonintrusive measurements of velocity vectors across an extended 2-dimensional region of the flow field. The application of optical correlation techniques to the analysis of multiple exposure laser light sheet photographs can reduce and/or simplify the data reduction time and hardware. Here, Matched Spatial Filters (MSF) are used in a pattern recognition system. Usually MSFs are used to identify the assembly line parts. In this application, the MSFs are used to identify the iso-velocity vector contours in the flow. The patterns to be recognized are the recorded particle images in a pulsed laser light sheet photograph. Measurement of the direction of the partical image displacements between exposures yields the velocity vector. The particle image exposure sequence is designed such that the velocity vector direction is determined unambiguously. A global analysis technique is used in comparison to the more common particle tracking algorithms and Young's fringe analysis technique.
Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.

PubMed

Nakashima, T; Yao, M; Kawamura, S; Iwasaki, K; Kimura, M; Tanaka, I

2001-05-01

Ribosomal protein L5 is a 5S rRNA binding protein in the large subunit and plays an essential role in the promotion of a particular conformation of 5S rRNA. The crystal structure of the ribosomal protein L5 from Bacillus stearothermophilus has been determined at 1.8 A resolution. The molecule consists of a five-stranded antiparallel beta-sheet and four alpha-helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. The molecular shape and electrostatic representation suggest that the concave surface and loop regions are involved in 5S rRNA binding. To identify amino acid residues responsible for 5S rRNA binding, we made use of Ala-scanning mutagenesis of evolutionarily conserved amino acids occurring in the beta-strands and loop regions. The mutations of Asn37 at the beta1-strand and Gln63 at the loop between helix 2 and beta3-strand as well as that of Phe77 at the tip of the loop structure between the beta2- and beta3-strands caused a significant reduction in 5S rRNA binding. In addition, the mutations of Thr90 on the beta3-strand and Ile141 and Asp144 at the loop between beta4- and beta5-strands moderately reduced the 5S rRNA-binding affinity. Comparison of these results with the more recently analyzed structure of the 50S subunit from Haloarcula marismortui suggests that there are significant differences in the structure at N- and C-terminal regions and probably in the 5S rRNA binding.
Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.

PubMed Central

Nakashima, T; Yao, M; Kawamura, S; Iwasaki, K; Kimura, M; Tanaka, I

2001-01-01

Ribosomal protein L5 is a 5S rRNA binding protein in the large subunit and plays an essential role in the promotion of a particular conformation of 5S rRNA. The crystal structure of the ribosomal protein L5 from Bacillus stearothermophilus has been determined at 1.8 A resolution. The molecule consists of a five-stranded antiparallel beta-sheet and four alpha-helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. The molecular shape and electrostatic representation suggest that the concave surface and loop regions are involved in 5S rRNA binding. To identify amino acid residues responsible for 5S rRNA binding, we made use of Ala-scanning mutagenesis of evolutionarily conserved amino acids occurring in the beta-strands and loop regions. The mutations of Asn37 at the beta1-strand and Gln63 at the loop between helix 2 and beta3-strand as well as that of Phe77 at the tip of the loop structure between the beta2- and beta3-strands caused a significant reduction in 5S rRNA binding. In addition, the mutations of Thr90 on the beta3-strand and Ile141 and Asp144 at the loop between beta4- and beta5-strands moderately reduced the 5S rRNA-binding affinity. Comparison of these results with the more recently analyzed structure of the 50S subunit from Haloarcula marismortui suggests that there are significant differences in the structure at N- and C-terminal regions and probably in the 5S rRNA binding. PMID:11350033

Differential effects of Phe19 and Phe20 on fibril formation by amyloidogenic peptide A beta 16-22 (Ac-KLVFFAE-NH2).

PubMed

Inouye, Hideyo; Gleason, Katherine A; Zhang, Dong; Decatur, Sean M; Kirschner, Daniel A

2010-08-01

The sequence KLVFFAE (A beta 16-22) in Alzheimer's beta-amyloid is thought to be a core beta-structure that could act as a template for folding other parts of the polypeptide or molecules into fibrillar assemblies rich in beta-sheet. To elucidate the mechanism of the initial folding process, we undertook combined X-ray fiber/powder diffraction and infrared (IR) spectroscopy to analyze lyophilized A beta 16-22 and solubilized/dried peptide containing nitrile probes at F19 and/or F20. Solubilized/dried wild-type (WT) A beta 16-22 and the peptide containing cyanophenylalanine at F19 (19CN) or at F20 (20CN) gave fiber patterns consistent with slab-like beta-crystallites that were cylindrically averaged around the axis parallel to the polypeptide chain direction. The WT and 19CN assemblies showed 30-A period arrays arising from the stacking of the slabs along the peptide chain direction, whereas the 20CN assemblies lacked any such stacking. The electron density projection along the peptide chain direction indicated similar side-chain dispositions for WT and 20CN, but not for 19CN. These X-ray results and modeling imply that in the assembly of WT A beta 16-22 the F19 side chain is localized within the intersheet space and is involved in hydrophobic contact with amino acids across the intersheet space, whereas the F20 side chain localized near the slab surface is less important for the intersheet interaction, but involved in slab stacking. IR observations for the same peptides in dilute solution showed a greater degree of hydrogen bonding for the nitrile groups in 20CN than in 19CN, supporting this interpretation. (c) 2010 Wiley-Liss, Inc.
NNvPDB: Neural Network based Protein Secondary Structure Prediction with PDB Validation.

PubMed

Sakthivel, Seethalakshmi; S K M, Habeeb

2015-01-01

The predicted secondary structural states are not cross validated by any of the existing servers. Hence, information on the level of accuracy for every sequence is not reported by the existing servers. This was overcome by NNvPDB, which not only reported greater Q3 but also validates every prediction with the homologous PDB entries. NNvPDB is based on the concept of Neural Network, with a new and different approach of training the network every time with five PDB structures that are similar to query sequence. The average accuracy for helix is 76%, beta sheet is 71% and overall (helix, sheet and coil) is 66%. http://bit.srmuniv.ac.in/cgi-bin/bit/cfpdb/nnsecstruct.pl.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Wemmer, D.E.; Kumar, N.V.; Metrione, R.M.

Toxin II from Radianthus paumotensis (Rp/sub II/) has been investigated by high-resolution NMR and chemical sequencing methods. Resonance assignments have been obtained for this protein by the sequential approach. NMR assignments could not be made consistent with the previously reported primary sequence for this protein, and chemical methods have been used to determine a sequence with which the NMR data are consistent. Analysis of the 2D NOE spectra shows that the protein secondary structure is comprised of two sequences of ..beta..-sheet, probably joined into a distorted continuous sheet, connected by turns and extended loops, without any regular ..cap alpha..-helical segments.more » The residues previously implicated in activity in this class of proteins, D8 and R13, occur in a loop region.« less
Effect of Curcumin on the metal ion induced fibrillization of Amyloid-β peptide

NASA Astrophysics Data System (ADS)

Banerjee, Rona

2014-01-01

The effect of Curcumin on Cu(II) and Zn(II) induced oligomerization and protofibrillization of the amyloid-beta (Aβ) peptide has been studied by spectroscopic and microscopic methods. Curcumin could significantly reduce the β-sheet content of the peptide in a time dependent manner. It also plays an antagonistic role in β-sheet formation that is promoted by metal ions like Cu(II) and Zn(II) as observed by Circular Dichroism (CD) spectroscopy. Atomic force microscopic (AFM) images show that spontaneous fibrillization of the peptide occurs in presence of Cu(II) and Zn(II) but is inhibited on incubation of the peptide with Curcumin indicating the beneficial role of Curcumin in preventing the aggregation of Aβ peptide.
Crystallographic Studies of Prion Protein (PrP) Segments Suggest How Structural Changes Encoded by Polymorphism at Residue 129 Modulate Susceptibility to Human Prion Disease

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

Apostol, Marcin I.; Sawaya, Michael R.; Cascio, Duilio

2010-09-23

A single nucleotide polymorphism (SNP) in codon 129 of the human prion gene, leading to a change from methionine to valine at residue 129 of prion protein (PrP), has been shown to be a determinant in the susceptibility to prion disease. However, the molecular basis of this effect remains unexplained. In the current study, we determined crystal structures of prion segments having either Met or Val at residue 129. These 6-residue segments of PrP centered on residue 129 are 'steric zippers,' pairs of interacting {beta}-sheets. Both structures of these 'homozygous steric zippers' reveal direct intermolecular interactions between Met or Valmore » in one sheet and the identical residue in the mating sheet. These two structures, plus a structure-based model of the heterozygous Met-Val steric zipper, suggest an explanation for the previously observed effects of this locus on prion disease susceptibility and progression.« less
The Structural Basis of Substrate Recognition in an exo-beta-d-Glucosaminidase Involved in Chitosan Hydrolysis

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

Lammerts van Bueren, A.; Ghinet, M; Gregg, K

2009-01-01

Family 2 of the glycoside hydrolase classification is one of the largest families. Structurally characterized members of this family include enzymes with beta-galactosidase activity (Escherichia coli LacZ), beta-glucuronidase activity (Homo sapiens GusB), and beta-mannosidase activity (Bacteroides thetaiotaomicron BtMan2A). Here, we describe the structure of a family 2 glycoside hydrolase, CsxA, from Amycolatopsis orientalis that has exo-beta-D-glucosaminidase (exo-chitosanase) activity. Analysis of a product complex (1.85 A resolution) reveals a unique negatively charged pocket that specifically accommodates the nitrogen of nonreducing end glucosamine residues, allowing this enzyme to discriminate between glucose and glucosamine. This also provides structural evidence for the role ofmore » E541 as the catalytic nucleophile and D469 as the catalytic acid/base. The structures of an E541A mutant in complex with a natural beta-1,4-D-glucosamine tetrasaccharide substrate and both E541A and D469A mutants in complex with a pNP-beta-D-glucosaminide synthetic substrate provide insight into interactions in the +1 subsite of this enzyme. Overall, a comparison with the active sites of other GH2 enzymes highlights the unique architecture of the CsxA active site, which imparts specificity for its cationic substrate.« less
Water-Floating Giant Nanosheets from Helical Peptide Pentamers

NASA Astrophysics Data System (ADS)

Lee, Jaehun; Nam, Ki Tae

One of the important challenges in the development of protein-mimetic materials is to understand the sequence specific assembly behavior and the dynamic folding change. Conventional strategies to construct two dimensional nanostructures from the peptides have been limited to beta-sheet forming sequences in use of basic building blocks because of their natural tendency to form sheet like aggregations. Here we identified a new peptide sequence, YFCFY that can form dimers by the disulfide bridge, fold into helix and assemble into macroscopic flat sheet at the air/water interface. Because of large driving force for two dimensional assembly and high elastic modulus of the resulting sheet, the peptide assembly induces the flattening of initially round water droplet. Additionally, we found that stabilization of helix by the dimerization is a key determinant for maintaining macroscopic flatness over a few tens centimeter even with a uniform thickness below 10 nm. Furthermore, the capability to transfer 2D film from water droplet to other substrates allows for the multiple stacking of 2D peptide nanostructure, suggesting possible applications in the biomimetic catalysts, biosensor and 2D related electronic devices. This work was supported by Samsung Research Funding Center of Samsung Electronics under Project Number SRFC-MA1401-01.
Patient-Centered Medical Home Undergraduate Internship, Benefits to a Practice Manager: Case Study.

PubMed

Sasnett, Bonita; Harris, Susie T; White, Shelly

Health services management interns become practice facilitators for primary care clinics interested in pursuing patient-centered recognition for their practice. This experience establishes a collaborative relationship between the university and clinic practices where students apply their academic training to a system of documentation to improve the quality of patient care delivery. The case study presents the process undertaken, benefits, challenges, lessons learned, and recommendations for intern, practice mangers, and educators. The practice manager benefits as interns become Patient-Centered Medical Home facilitators and assist practice managers in the recognition process.
Differential mode of interaction of ThioflavinT with native β structural motif in human α 1-acid glycoprotein and cross beta sheet of its amyloid: Biophysical and molecular docking approach

NASA Astrophysics Data System (ADS)

Ajmal, Mohammad Rehan; Nusrat, Saima; Alam, Parvez; Zaidi, Nida; Badr, Gamal; Mahmoud, Mohamed H.; Rajpoot, Ravi Kant; Khan, Rizwan Hasan

2016-08-01

The present study details the interaction mechanism of Thioflavin T (ThT) to Human α1-acid glycoprotein (AAG) applying various spectroscopic and molecular docking methods. Fluorescence quenching data revealed the binding constant in the order of 104 M-1 and the standard Gibbs free energy change value, ΔG = -6.78 kcal mol-1 for the interaction between ThT and AAG indicating process is spontaneous. There is increase in absorbance of AAG upon the interaction of ThT that may be due to ground state complex formation between ThT and AAG. ThT impelled rise in β-sheet structure in AAG as observed from far-UV CD spectra while there are minimal changes in tertiary structure of the protein. DLS results suggested the reduction in AAG molecular size, ligand entry into the central binding pocket of AAG may have persuaded the molecular compaction in AAG. Isothermal titration calorimetric (ITC) results showed the interaction process to be endothermic with the values of standard enthalpy change ΔH0 = 4.11 kcal mol-1 and entropy change TΔS0 = 10.82 kcal.mol- 1. Moreover, docking results suggested hydrophobic interactions and hydrogen bonding played the important role in the binding process of ThT with F1S and A forms of AAG. ThT fluorescence emission at 485 nm was measured for properly folded native form and for thermally induced amyloid state of AAG. ThT fluorescence with native AAG was very low, while on the other hand with amyloid induced state of the protein AAG showed a positive emission peak at 485 nm upon the excitation at 440 nm, although it binds to native state as well. These results confirmed that ThT binding alone is not responsible for enhancement of ThT fluorescence but it also required beta stacked sheet structure found in protein amyloid to give proper signature signal for amyloid. This study gives the mechanistic insight into the differential interaction of ThT with beta structures found in native state of the proteins and amyloid forms, this study reinforce the notion that ThT is amyloid specific dye and interacts differently with the beta structures in native protein and that of the structures found in aggregated form of the same protein.
Isolation and functional characterization of a lycopene beta-cyclase gene that controls fruit colour of papaya (Carica papaya L.).

PubMed

Devitt, Luke C; Fanning, Kent; Dietzgen, Ralf G; Holton, Timothy A

2010-01-01

The colour of papaya fruit flesh is determined largely by the presence of carotenoid pigments. Red-fleshed papaya fruit contain lycopene, whilst this pigment is absent from yellow-fleshed fruit. The conversion of lycopene (red) to beta-carotene (yellow) is catalysed by lycopene beta-cyclase. This present study describes the cloning and functional characterization of two different genes encoding lycopene beta-cyclases (lcy-beta1 and lcy-beta2) from red (Tainung) and yellow (Hybrid 1B) papaya cultivars. A mutation in the lcy-beta2 gene, which inactivates enzyme activity, controls lycopene production in fruit and is responsible for the difference in carotenoid production between red and yellow-fleshed papaya fruit. The expression level of both lcy-beta1 and lcy-beta2 genes is similar and low in leaves, but lcy-beta2 expression increases markedly in ripe fruit. Isolation of the lcy-beta2 gene from papaya, that is preferentially expressed in fruit and is correlated with fruit colour, will facilitate marker-assisted breeding for fruit colour in papaya and should create possibilities for metabolic engineering of carotenoid production in papaya fruit to alter both colour and nutritional properties.
Separation of drug stereoisomers by the formation of. beta. -cyclodextrin inclusion complexes

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

Armstrong, D.W.; Ward, T.J.; Armstrong, R.D.

For many drugs, only racemic mixtures are available for clinical use. Because different stereoisomers of drugs often cause different physiological responses, the use of pure isomers could elicit more exact therapeutic effects. Differential complexation of a variety of drug stereoisomers by immobilized ..beta..-cyclodextrin was investigated. Chiral recognition and racemic resolution were observed with a number of compounds from such clinically useful classes as ..beta..-blockers, calcium-channel blockers, sedative hypnotics, antihistamines, anticonvulsants, diuretics, and synthetic opiates. Separation of the diastereomers of the cardioactive and antimalarial cinchona alkaloids and of two antiestrogens was demonstrated as well. Three dimensional projections of ..beta..-cyclodextrin complexes ofmore » propanol, which is resolved by this technique, and warfarin, which is not, are compared. These studies have improved the understanding and application of the chiral interactions of ..beta..-cyclodextrin, and they have demonstrated a means to measure optical purity and to isolate or produce pure enantiomers of drugs. In addition, this highly specific technique could also be used in the pharmacological evaluation of enantiometric drugs. 27 references, 3 figures, 2 tables.« less
Dietary sterol preference in the silkworm, Bombyx mori.

PubMed

Nagata, Shinji; Omori, Yukie; Nagasawa, Hiromichi

2006-12-01

Since insects are unable to biosynthesize sterols de novo, sterols must be obtained from dietary sources. Although it has been reported that beta-sitosterol is crucial for larval growth in the silkworm, Bombyx mori, little has been investigated concerning the dietary selection of sterols by Bombyx larvae. Here, we demonstrate that Bombyx larvae have the following sterol preference: beta-sitosterol > ergosterol > cholesterol = stigmasterol. Interestingly, Bombyx larvae preferred ergosterol, an inhibitory sterol on larval growth, indicating that sterol selection following first contact of the diet with the mouth part might be different from the sterol recognition mechanism present in sterol metabolism.
What's she doing in the kitchen? Context helps when actions are hard to recognize.

PubMed

Wurm, Moritz F; Schubotz, Ricarda I

2017-04-01

Specific spatial environments are often indicative of where certain actions may take place: In kitchens we prepare food, and in bathrooms we engage in personal hygiene, but not vice versa. In action recognition, contextual cues may constrain an observer's expectations toward actions that are more strongly associated with a particular context than others. Such cues should become particularly helpful when the action itself is difficult to recognize. However, to date only easily identifiable actions were investigated, and the effects of context on recognition were rather interfering than facilitatory. To test whether context also facilitates action recognition, we measured recognition performance of hardly identifiable actions that took place in compatible, incompatible, and neutral contextual settings. Action information was degraded by pixelizing the area of the object manipulation while the room in which the action took place remained fully visible. We found significantly higher accuracy for actions that took place in compatible compared to incompatible and neutral settings, indicating facilitation. Additionally, action recognition was slower in incompatible settings than in compatible and neutral settings, indicating interference. Together, our findings demonstrate that contextual information is effectively exploited during action observation, in particular when visual information about the action itself is sparse. Differential effects on speed and accuracy suggest that contexts modulate action recognition at different levels of processing. Our findings emphasize the importance of contextual information in comprehensive, ecologically valid models of action recognition.
Conversion of human choriogonadotropin into a follitropin by protein engineering

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

Campbell, R.K.; Dean-Emig, D.M.; Moyle, W.R.

1991-02-01

Human reproduction is dependent upon the action of follicle-stimulating hormone (hFSH), luteinizing hormone (hLH), and chorionic gonadotropin (hCG). While the {alpha} subunits of these heterodimeric proteins can be interchanged without effect on receptor-binding specificity, their {beta} subunits differ and direct hormone binding to either LH/CG or FSH receptors. Previous studies employing chemical modifications of the hormones, monoclonal antibodies, or synthetic peptides have implicated hCG {beta}-subunit residues between Cys-38 and Cys-57 and corresponding regions of hLH{beta} and hFSH{beta} in receptor recognition and activation. Since the {beta} subunits of hCG or hLH and hFSH exhibit very little sequence similarity in this region,more » the authors postulated that these residues might contribute to hormone specificity. To test this hypothesis the authors constructed chimeric hCG/hFSH {beta} subunits, coexpressed them with the human {alpha} subunit, and examined their ability to interact with LH and FSH receptors and hormone-specific monoclonal antibodies. Surprisingly, substitution of hFSH{beta} residues 33-52 for hCG{beta} residues 39-58 had no effect on receptor binding or stimulation. However, substitution of hFSH{beta} residues 88-108 in place of the carboxyl terminus of hCG{beta} (residues 94-145) resulted in a hormone analog identical to hFSH in its ability to bind and stimulate FSH receptors. The altered binding specificity displayed by this analog is not attributable solely to the replacement of hCG{beta} residues 108-145 or substitution of residues in the determinant loop located between hCD{beta} residues 93 and 100.« less
Alcohol acutely enhances decoding of positive emotions and emotional concern for positive stimuli and facilitates the viewing of sexual images.

PubMed

Dolder, Patrick C; Holze, Friederike; Liakoni, Evangelia; Harder, Samuel; Schmid, Yasmin; Liechti, Matthias E

2017-01-01

Social cognition influences social interactions. Alcohol reportedly facilitates social interactions. However, the acute effects of alcohol on social cognition are relatively poorly studied. We investigated the effects of alcoholic or non-alcoholic beer on emotion recognition, empathy, and sexual arousal using the dynamic face emotion recognition task (FERT), Multifaceted Empathy Test (MET), and Sexual Arousal Task (SAT) in a double-blind, random-order, cross-over study in 60 healthy social drinkers. We also assessed subjective effects using visual analog scales (VASs), blood alcohol concentrations, and plasma oxytocin levels. Alcohol increased VAS ratings of stimulated, happy, talkative, open, and want to be with others. The subjective effects of alcohol were greater in participants with higher trait inhibitedness. Alcohol facilitated the recognition of happy faces on the FERT and enhanced emotional empathy for positive stimuli on the MET, particularly in participants with low trait empathy. Pictures of explicit sexual content were rated as less pleasant than neutral pictures after non-alcoholic beer but not after alcoholic beer. Explicit sexual pictures were rated as more pleasant after alcoholic beer compared with non-alcoholic beer, particularly in women. Alcohol did not alter the levels of circulating oxytocin. Alcohol biased emotion recognition toward better decoding of positive emotions and increased emotional concern for positive stimuli. No support was found for a modulatory role of oxytocin. Alcohol also facilitated the viewing of sexual images, consistent with disinhibition, but it did not actually enhance sexual arousal. These effects of alcohol on social cognition likely enhance sociability. www.clinicaltrials.gov/ct2/show/NCT02318823.
CSC Tip Sheets: Community-Based Social Marketing

EPA Pesticide Factsheets

Use community-based social marketing (CBSM) to facilitate direct neighbor-to-neighbor communication and influence to promote behavior change. In-person communications are often complemented by electronic social media tools.
Self-recognition in corals facilitates deep-sea habitat engineering

USGS Publications Warehouse

Hennige, Sebastian J; Morrison, Cheryl L.; Form, Armin U.; Buscher, Janina; Kamenos, Nicholas A.; Roberts, J. Murray

2014-01-01

The ability of coral reefs to engineer complex three-dimensional habitats is central to their success and the rich biodiversity they support. In tropical reefs, encrusting coralline algae bind together substrates and dead coral framework to make continuous reef structures, but beyond the photic zone, the cold-water coral Lophelia pertusa also forms large biogenic reefs, facilitated by skeletal fusion. Skeletal fusion in tropical corals can occur in closely related or juvenile individuals as a result of non-aggressive skeletal overgrowth or allogeneic tissue fusion, but contact reactions in many species result in mortality if there is no ‘self-recognition’ on a broad species level. This study reveals areas of ‘flawless’ skeletal fusion in Lophelia pertusa, potentially facilitated by allogeneic tissue fusion, are identified as having small aragonitic crystals or low levels of crystal organisation, and strong molecular bonding. Regardless of the mechanism, the recognition of ‘self’ between adjacent L. pertusa colonies leads to no observable mortality, facilitates ecosystem engineering and reduces aggression-related energetic expenditure in an environment where energy conservation is crucial. The potential for self-recognition at a species level, and subsequent skeletal fusion in framework-forming cold-water corals is an important first step in understanding their significance as ecological engineers in deep-seas worldwide.
A novel role for integrin-linked kinase in epithelial sheet morphogenesis.

PubMed

Vespa, Alisa; D'Souza, Sudhir J A; Dagnino, Lina

2005-09-01

Integrin-linked kinase (ILK) is a multidomain protein involved in cell motility and cell-extracellular matrix interactions. ILK is found in integrin-containing focal adhesions in undifferentiated primary epidermal keratinocytes. Induction of keratinocyte differentiation by treatment with Ca(2+) triggers formation of cell-cell junctions, loss of focal adhesions, and ILK distribution to cell borders. We now show that Ca(2+) treatment of keratinocytes induces rapid (6 h) localization of tight junction (TJ) proteins. The kinetics of ILK movement toward the cell periphery mimics that of AJ components, suggesting that ILK plays a role in the early formation of cell-cell contacts. Whereas the N terminus in ILK mediates localization to cell borders, expression of an ILK deletion mutant incapable of localizing to the cell membrane (ILK 191-452) interferes with translocation of E-cadherin/beta-catenin to cell borders, precluding Ca(2+)-induced AJ formation. Cells expressing ILK 191-452 also fail to form TJ and sealed cell-cell borders and do not form epithelial sheets. Thus, we have uncovered a novel role for ILK in epithelial cell-cell adhesion, independent of its well-established role in integrin-mediated adhesion and migration.
Toward structural dynamics: protein motions viewed by chemical shift modulations and direct detection of C'N multiple-quantum relaxation.

PubMed

Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel

2010-03-17

Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.
Rapid amyloid fiber formation from the fast-folding WW domain FBP28.

PubMed

Ferguson, Neil; Berriman, John; Petrovich, Miriana; Sharpe, Timothy D; Finch, John T; Fersht, Alan R

2003-08-19

The WW domains are small proteins that contain a three-stranded, antiparallel beta-sheet. The 40-residue murine FBP28 WW domain rapidly formed twirling ribbon-like fibrils at physiological temperature and pH, with morphology typical of amyloid fibrils. These ribbons were unusually wide and well ordered, making them highly suitable for structural studies. Their x-ray and electron-diffraction patterns displayed the characteristic amyloid fiber 0.47-nm reflection of the cross-beta diffraction signature. Both conventional and electron cryomicroscopy showed clearly that the ribbons were composed of many 2.5-nm-wide subfilaments that ran parallel to the long axis of the fiber. There was a region of lower density along the center of each filament. Lateral association of these filaments generated twisted, often interlinked, sheets up to 40 nm wide and many microns in length. The pitch of the helix varied from 60 to 320 nm, depending on the width of the ribbon. The wild-type FBP28 fibers were formed under conditions in which multiexponential folding kinetics is observed in other studies and which was attributed to a change in the mechanism of folding. It is more likely that those phases result from initial events in the off-pathway aggregation observed here.

Hemin as a generic and potent protein misfolding inhibitor

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

Liu, Yanqin; Carver, John A.; Ho, Lam H.

2014-11-14

Highlights: • Hemin prevents Aβ42, α-synuclein and RCM-κ-casein forming amyloid fibrils. • Hemin inhibits the β-sheet structure formation of Aβ42. • Hemin reduces the cell toxicity caused by fibrillar Aβ42. • Hemin dissociates partially formed Aβ42 fibrils. • Hemin prevents amorphous aggregation by ADH, catalase and γs-crystallin. - Abstract: Protein misfolding causes serious biological malfunction, resulting in diseases including Alzheimer’s disease, Parkinson’s disease and cataract. Molecules which inhibit protein misfolding are a promising avenue to explore as therapeutics for the treatment of these diseases. In the present study, thioflavin T fluorescence and transmission electron microscopy experiments demonstrated that hemin preventsmore » amyloid fibril formation of kappa-casein, amyloid beta peptide and α-synuclein by blocking β-sheet structure assembly which is essential in fibril aggregation. Further, inhibition of fibril formation by hemin significantly reduces the cytotoxicity caused by fibrillar amyloid beta peptide in vitro. Interestingly, hemin degrades partially formed amyloid fibrils and prevents further aggregation to mature fibrils. Light scattering assay results revealed that hemin also prevents protein amorphous aggregation of alcohol dehydrogenase, catalase and γs-crystallin. In summary, hemin is a potent agent which generically stabilises proteins against aggregation, and has potential as a key molecule for the development of therapeutics for protein misfolding diseases.« less
Mechanical characteristics of beta sheet-forming peptide hydrogels are dependent on peptide sequence, concentration and buffer composition

PubMed Central

Müller, Michael; König, Finja; Meyer, Nina; Gattlen, Jasmin; Pieles, Uwe; Peters, Kirsten; Kreikemeyer, Bernd; Mathes, Stephanie; Saxer, Sina

2018-01-01

Self-assembling peptide hydrogels can be modified regarding their biodegradability, their chemical and mechanical properties and their nanofibrillar structure. Thus, self-assembling peptide hydrogels might be suitable scaffolds for regenerative therapies and tissue engineering. Owing to the use of various peptide concentrations and buffer compositions, the self-assembling peptide hydrogels might be influenced regarding their mechanical characteristics. Therefore, the mechanical properties and stability of a set of self-assembling peptide hydrogels, consisting of 11 amino acids, made from four beta sheet self-assembling peptides in various peptide concentrations and buffer compositions were studied. The formed self-assembling peptide hydrogels exhibited stiffnesses ranging from 0.6 to 205 kPa. The hydrogel stiffness was mostly affected by peptide sequence followed by peptide concentration and buffer composition. All self-assembling peptide hydrogels examined provided a nanofibrillar network formation. A maximum self-assembling peptide hydrogel dissolution of 20% was observed for different buffer solutions after 7 days. The stability regarding enzymatic and bacterial digestion showed less degradation in comparison to the self-assembling peptide hydrogel dissolution rate in buffer. The tested set of self-assembling peptide hydrogels were able to form stable scaffolds and provided a broad spectrum of tissue-specific stiffnesses that are suitable for a regenerative therapy. PMID:29657766
Coding SNP in tenascin-C Fn-III-D domain associates with adult asthma.

PubMed

Matsuda, Akira; Hirota, Tomomitsu; Akahoshi, Mitsuteru; Shimizu, Makiko; Tamari, Mayumi; Miyatake, Akihiko; Takahashi, Atsushi; Nakashima, Kazuko; Takahashi, Naomi; Obara, Kazuhiko; Yuyama, Noriko; Doi, Satoru; Kamogawa, Yumiko; Enomoto, Tadao; Ohshima, Koichi; Tsunoda, Tatsuhiko; Miyatake, Shoichiro; Fujita, Kimie; Kusakabe, Moriaki; Izuhara, Kenji; Nakamura, Yusuke; Hopkin, Julian; Shirakawa, Taro

2005-10-01

The extracellular matrix glycoprotein tenascin-C (TNC) has been accepted as a valuable histopathological subepithelial marker for evaluating the severity of asthmatic disease and the therapeutic response to drugs. We found an association between an adult asthma and an SNP encoding TNC fibronectin type III-D (Fn-III-D) domain in a case-control study between a Japanese population including 446 adult asthmatic patients and 658 normal healthy controls. The SNP (44513A/T in exon 17) strongly associates with adult bronchial asthma (chi2 test, P=0.00019, Odds ratio=1.76, 95% confidence interval=1.31-2.36). This coding SNP induces an amino acid substitution (Leu1677Ile) within the Fn-III-D domain of the alternative splicing region. Computer-assisted protein structure modeling suggests that the substituted amino acid locates at the outer edge of the beta-sheet in Fn-III-D domain and causes instability of this beta-sheet. As the TNC fibronectin-III domain has molecular elasticity, the structural change may affect the integrity and stiffness of asthmatic airways. In addition, TNC expression in lung fibroblasts increases with Th2 immune cytokine stimulation. Thus, Leu1677Ile may be valuable marker for evaluating the risk for developing asthma and plays a role in its pathogenesis.
Aβ1-16 conformational changes induced by heavy metals, antioxidants, and corn zeins: CD, AFM, SEM, and FT-IR studies

NASA Astrophysics Data System (ADS)

Murariu, Manuela; Mihai, Marcela; Zaharia, Marius; Drochioiu, Gabi

2014-10-01

Amyloid-beta (known also as Aβ or A-beta or beta-amyloid) is a peptide of 36-43 amino acids that appears to be the main constituent of amyloid plaques in the brains of Alzheimer's disease (AD) patients. The transformation process from α-helix to β-sheet structures appears to be one of the major factors in the genesis and evolution of a variety of neurodegenerative diseases such as AD, Parkinson's disease (PD), and several prion diseases [1,2]. Metal-based reactions of some polypeptides and proteins are considered as a common denominator for neurodegenerative diseases (Figure 1) [3,4]. Amyloid-β (Aβ) aggregates are associated with Alzheimer's disease (AD), and may be promoted by the trace amounts of metal ions like aluminium, iron, zinc or copper [5-11]. For example, copper ions cause the peptide aggregation to a great extent and highly increase the neurotoxicity exhibited by Aβ1-40 in cell culture [11].
Structural Characterization of the Boca/Mesd Maturation Factors for LDL-Receptor-Type beta Propeller Domains

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

M Collins; W Hendrickson

2011-12-31

Folding and trafficking of low-density lipoprotein receptor (LDLR) family members, which play essential roles in development and homeostasis, are mediated by specific chaperones. The Boca/Mesd chaperone family specifically promotes folding and trafficking of the YWTD {beta} propeller-EGF domain pair found in the ectodomain of all LDLR members. Limited proteolysis, NMR spectroscopy, analytical ultracentrifugation, and X-ray crystallography were used to define a conserved core composed of a structured domain that is preceded by a disordered N-terminal region. High-resolution structures of the ordered domain were determined for homologous proteins from three metazoans. Seven independent protomers reveal a novel ferrodoxin-like superfamily fold withmore » two distinct {beta} sheet topologies. A conserved hydrophobic surface forms a dimer interface in each crystal, but these differ substantially at the atomic level, indicative of nonspecific hydrophobic interactions that may play a role in the chaperone activity of the Boca/Mesd family.« less
The predicted secondary structures of class I fructose-bisphosphate aldolases.

PubMed Central

Sawyer, L; Fothergill-Gilmore, L A; Freemont, P S

1988-01-01

The results of several secondary-structure prediction programs were combined to produce an estimate of the regions of alpha-helix, beta-sheet and reverse turns for fructose-bisphosphate aldolases from human and rat muscle and liver, from Trypanosoma brucei and from Drosophila melanogaster. All the aldolase sequences gave essentially the same pattern of secondary-structure predictions despite having sequences up to 50% different. One exception to this pattern was an additional strongly predicted helix in the rat liver and Drosophila enzymes. Regions of relatively high sequence variation generally were predicted as reverse turns, and probably occur as surface loops. Most of the positions corresponding to exon boundaries are located between regions predicted to have secondary-structural elements consistent with a compact structure. The predominantly alternating alpha/beta structure predicted is consistent with the alpha/beta-barrel structure indicated by preliminary high-resolution X-ray diffraction studies on rabbit muscle aldolase [Sygusch, Beaudry & Allaire (1986) Biophys. J. 49, 287a]. Images Fig. 1. (cont.) Fig. 1. PMID:3128269
Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida.

PubMed

Sander, C; Vriend, G; Bazan, F; Horovitz, A; Nakamura, H; Ribas, L; Finkelstein, A V; Lockhart, A; Merkl, R; Perry, L J

1992-02-01

What is the current state of the art in protein design? This question was approached in a recent two-week protein design workshop sponsored by EMBO and held at the EMBL in Heidelberg. The goals were to test available design tools and to explore new design strategies. Five novel proteins were designed: Shpilka, a sandwich of two four-stranded beta-sheets, a scaffold on which to explore variations in loop topology; Grendel, a four-helical membrane anchor, ready for fusion to water-soluble functional domains; Finger-clasp, a dimer of interdigitating beta-beta-alpha units, the simplest variant of the "handshake" structural class; Aida, an antibody binding surface intended to be specific for flavodoxin; Leather--a minimal NAD binding domain, extracted from a larger protein. Each design is available as a set of three-dimensional coordinates, the corresponding amino acid sequence and a set of analytical results. The designs are placed in the public domain for scrutiny, improvement, and possible experimental verification.
Imaging multicellular specimens with real-time optimized tiling light-sheet selective plane illumination microscopy

PubMed Central

Fu, Qinyi; Martin, Benjamin L.; Matus, David Q.; Gao, Liang

2016-01-01

Despite the progress made in selective plane illumination microscopy, high-resolution 3D live imaging of multicellular specimens remains challenging. Tiling light-sheet selective plane illumination microscopy (TLS-SPIM) with real-time light-sheet optimization was developed to respond to the challenge. It improves the 3D imaging ability of SPIM in resolving complex structures and optimizes SPIM live imaging performance by using a real-time adjustable tiling light sheet and creating a flexible compromise between spatial and temporal resolution. We demonstrate the 3D live imaging ability of TLS-SPIM by imaging cellular and subcellular behaviours in live C. elegans and zebrafish embryos, and show how TLS-SPIM can facilitate cell biology research in multicellular specimens by studying left-right symmetry breaking behaviour of C. elegans embryos. PMID:27004937
Development of a tunable femtosecond stimulated raman apparatus and its application to beta-carotene.

PubMed

Shim, Sangdeok; Mathies, Richard A

2008-04-17

We have developed a tunable femtosecond stimulated Raman spectroscopy (FSRS) apparatus and used it to perform time-resolved resonance Raman experiments with <100 fs temporal and <35 cm(-1) spectral resolution. The key technical change that facilitates this advance is the use of a tunable narrow-bandwidth optical parametric amplifier (NB-OPA) presented recently by Shim et al. (Shim, S.; Mathies, R. A. Appl. Phys. Lett. 2006, 89, 121124). The practicality of tunable FSRS is demonstrated by examining the photophysical dynamics of beta-carotene. Using 560 nm Raman excitation, the resonant S1 state modes are enhanced by a factor of approximately 200 compared with 800 nm FSRS experiments. The improved signal-to-noise ratios facilitate the measurement of definitive time constants for beta-carotene dynamics including the 180 fs appearance of the S1 vibrational features due to direct internal conversion from S2 and their characteristic 9 ps decay to S0. By tuning the FSRS system to 590 nm Raman excitation, we are able to selectively enhance vibrational features of the hot ground state S hot 0 and monitor its approximately 5 ps cooling dynamics. This tunable FSRS system is valuable because it facilitates the direct observation of structural changes of selected resonantly enhanced states and intermediates during photochemical and photobiological reactions.
Nomenclature of Vertebral Laminae in Lizards, with Comments on Ontogenetic and Serial Variation in Lacertini (Squamata, Lacertidae)

PubMed Central

Tschopp, Emanuel

2016-01-01

Vertebral laminae are bony ridges or sheets that connect important morphological landmarks on the vertebrae, like diapophyses or zygapophyses. They usually exhibit some serial variation throughout the column. A consistent terminology facilitates the morphological description of this variation, and the recognition of patterns that could be taxonomically significant and could serve as phylogenetic characters. Such a terminology was designed for saurischian dinosaurs, and has also been applied to other members of Archosauriformes. Herein, this terminology is applied for the first time to lizards (Squamata). Probably due to their generally smaller size compared to saurischian dinosaurs, lizards have less developed vertebral laminae. Some laminae could not be recognized in this group and others require new names to account for differences in basic vertebral morphology. For instance, the fusion of diapophysis and parapophysis in lacertids into a structure called synapophysis necessitates the creation of the new term synapophyseal laminae for both diapophyseal and parapophyseal laminae. An assessment of occurrence and serial variation in a number of lacertid species shows that some laminae develop throughout ontogeny or only occur in large-sized species, whereas the distribution of other laminae might prove to be taxonomically significant in future. PMID:26907769
Nomenclature of Vertebral Laminae in Lizards, with Comments on Ontogenetic and Serial Variation in Lacertini (Squamata, Lacertidae).

PubMed

Tschopp, Emanuel

2016-01-01

Vertebral laminae are bony ridges or sheets that connect important morphological landmarks on the vertebrae, like diapophyses or zygapophyses. They usually exhibit some serial variation throughout the column. A consistent terminology facilitates the morphological description of this variation, and the recognition of patterns that could be taxonomically significant and could serve as phylogenetic characters. Such a terminology was designed for saurischian dinosaurs, and has also been applied to other members of Archosauriformes. Herein, this terminology is applied for the first time to lizards (Squamata). Probably due to their generally smaller size compared to saurischian dinosaurs, lizards have less developed vertebral laminae. Some laminae could not be recognized in this group and others require new names to account for differences in basic vertebral morphology. For instance, the fusion of diapophysis and parapophysis in lacertids into a structure called synapophysis necessitates the creation of the new term synapophyseal laminae for both diapophyseal and parapophyseal laminae. An assessment of occurrence and serial variation in a number of lacertid species shows that some laminae develop throughout ontogeny or only occur in large-sized species, whereas the distribution of other laminae might prove to be taxonomically significant in future.
The 3-D description of vertical current sheets with application to solar flares

NASA Technical Reports Server (NTRS)

Fontenla, Juan M.; Davis, J. M.

1991-01-01

Following a brief review of the processes which have been suggested for explaining the occurrence of solar flares we suggest a new scenario which builds on the achievements of the previous suggestion that the current sheets, which develop naturally in 3-D cases with gravity from impacting independent magnetic structures (i.e., approaching current systems), do not consist of horizontal currents but are instead predominantly vertical current systems. This suggestion is based on the fact that as the subphotospheric sources of the magnetic field displace the upper photosphere and lower chromosphere regions, where plasma beta is near unity, will experience predominantly horizontal mass motions which will lead to a distorted 3-D configurations of the magnetic field having stored free energy. In our scenario, a vertically flowing current sheet separates the plasma regions associated with either of the subphotospheric sources. This reflects the balanced tension of the two stressed fields which twist around each other. This leads naturally to a metastable or unstable situation as the twisted field emerges into a low beta region where vertical motions are not inhibited by gravity. In our flare scenario the impulsive energy release occurs, initially, not by reconnection but mainly by the rapid change of the magnetic field which has become unstable. During the impulsive phase the field lines contort in such way as to realign the electric current sheet into a minimum energy horizontal flow. This contortion produces very large electric fields which will accelerate particles. As the current evolves to a horizontal configuration the magnetic field expands vertically, which can be accompanied by eruptions of material. The instability of a horizontal current is well known and causes the magnetic field to undergo a rapid outward expansion. In our scenario, fast reconnection is not necessary to trigger the flare, however, slow reconnection would occur continuously in the current layer at the locations of potential flaring. During the initial rearrangement of the field strong plasma turbulence develops. Following the impulsive phase, the final current sheet will experience faster reconnection which we believe responsible for the gradual phase of the flare. The reconnection will dissipate part of the current and will produce sustained and extended heating in the flare region and in the postflare loops.
Collisionless current sheet equilibria

NASA Astrophysics Data System (ADS)

Neukirch, T.; Wilson, F.; Allanson, O.

2018-01-01

Current sheets are important for the structure and dynamics of many plasma systems. In space and astrophysical plasmas they play a crucial role in activity processes, for example by facilitating the release of magnetic energy via processes such as magnetic reconnection. In this contribution we will focus on collisionless plasma systems. A sensible first step in any investigation of physical processes involving current sheets is to find appropriate equilibrium solutions. The theory of collisionless plasma equilibria is well established, but over the past few years there has been a renewed interest in finding equilibrium distribution functions for collisionless current sheets with particular properties, for example for cases where the current density is parallel to the magnetic field (force-free current sheets). This interest is due to a combination of scientific curiosity and potential applications to space and astrophysical plasmas. In this paper we will give an overview of some of the recent developments, discuss their potential applications and address a number of open questions.
Isolation and characterization of cDNA clones for human erythrocyte beta-spectrin.

PubMed Central

Prchal, J T; Morley, B J; Yoon, S H; Coetzer, T L; Palek, J; Conboy, J G; Kan, Y W

1987-01-01

Spectrin is an important structural component of the membrane skeleton that underlies and supports the erythrocyte plasma membrane. It is composed of nonidentical alpha (Mr 240,000) and beta (Mr 220,000) subunits, each of which contains multiple homologous 106-amino acid segments. We report here the isolation and characterization of a human erythroid-specific beta-spectrin cDNA clone that encodes parts of the beta-9 through beta-12 repeat segments. This cDNA was used as a hybridization probe to assign the beta-spectrin gene to human chromosome 14 and to begin molecular analysis of the gene and its mRNA transcripts. RNA transfer blot analysis showed that the reticulocyte beta-spectrin mRNA is 7.8 kilobases in length. Southern blot analysis of genomic DNA revealed the presence of restriction fragment length polymorphisms (RFLPs) within the beta-spectrin gene locus. The isolation of human spectrin cDNA probes and the identification of closely linked RFLPs will facilitate analysis of mutant spectrin genes causing congenital hemolytic anemias associated with quantitative and qualitative spectrin abnormalities. Images PMID:3478706
Control of yeast mating signal transduction by a mammalian. beta. sub 2 -adrenergic receptor and G sub s. alpha. subunit

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

King, K.; Caron, M.G.; Lefkowitz, R.J.

1990-10-05

To facilitate functional and mechanistic studies of receptor-G protein interactions by expression of the human {beta}{sub 2}-adrenergic receptor (h{beta}-AR) has been expressed in Saccharomyces cerevisiae. This was achieved by placing a modified h{beta}-AR gene under control of the galactose-inducible GAL1 promoter. After induction by galactose, functional h{beta}-AR was expressed at a concentration several hundred times as great as that found in any human tissue. As determined from competitive ligand binding experiments, h{beta}-AR expressed in yeast displayed characteristic affinities, specificity, and stereoselectivity. Partial activation of the yeast pheromone response pathway by {beta}-adrenergic receptor agonists was achieved in cells coexpressing h{beta}-AR andmore » a mammalian G protein (G{sub s}) {alpha} subunit - demonstrating that these components can couple to each other and to downstream effectors when expressed in yeast. This in vivo reconstitution system provides a new approach for examining ligand binding and G protein coupling to cell surface receptors.« less
Biosynthesis of ketomycin. (II) biomimetic model for beta-lactamase catalysis: host-guest interactions in cyclodextrin-penicillin inclusion complex

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

Mak, H.W.

The antibiotic ketomycin is formed from shikimic acid via chorismic acid and prephenic acid. Phenylalanine and 2',5'-dihydrophenylalanine derived from shikimic acid are not intermediates in the biosynthesis. Degradation of ketomycin derived from (1,6-/sup 14/C)shikimic acid showed that prephenic acid is converted into ketomycin with stereospecific discrimination between the two enantiotopic edges of the ring, the pro-S-R edge giving rise to the C-2', C-3' side of the cyclohexane ring of ketomycin. The resistance of pathogenic bacteria to the action of ..beta..-lactam antibiotics is mainly ascribed to their ability to produce ..beta..-lactamase to cleave the ..beta..-lactam ring. It is essential to understandmore » the molecular nature of ..beta..-lactamase-penicillin recognition for designing and formulating more effective ..beta..-lactam antibiotics. A biomimetic study of ..beta..-lactamase is therefore initiated. To meet the requirements of hydrophobic and serine protease characteristics of ..beta..-lactamase, ..cap alpha..-cyclodextrin is chosen as a biomimetic model for ..beta..-lactamase. The structural specificity and the chemical dynamics of ..cap alpha..-cyclodextrin-phenoxymethyl penicillin inclusion complex in solid state and in solution have been determined by IR and NMR spectroscopy. The spectral results strongly indicate that the phenyl portion of the phenoxymethyl penicillin forms a stable inclusion complex with the hydrophobic cavity of ..cap alpha..-cyclodextrin in solution as well as in the solid state. Kinetic studies followed by /sup 1/HNMR and HPLC analyses under alkaline condition have shown that the ..cap alpha..-cyclodextrin mimics the catalytic function of serine of ..beta..-lactamase in the stereospecific hydrolysis of the ..beta..-lactam ring of phenoxymethyl penicillin.« less
Helix formation in arrestin accompanies recognition of photoactivated rhodopsin.

PubMed

Feuerstein, Sophie E; Pulvermüller, Alexander; Hartmann, Rudolf; Granzin, Joachim; Stoldt, Matthias; Henklein, Peter; Ernst, Oliver P; Heck, Martin; Willbold, Dieter; Koenig, Bernd W

2009-11-17

Binding of arrestin to photoactivated phosphorylated rhodopsin terminates the amplification of visual signals in photoreceptor cells. Currently, there is no crystal structure of a rhodopsin-arrestin complex available, although structures of unbound rhodopsin and arrestin have been determined. High-affinity receptor binding is dependent on distinct arrestin sites responsible for recognition of rhodopsin activation and phosphorylation. The loop connecting beta-strands V and VI in rod arrestin has been implicated in the recognition of active rhodopsin. We report the structure of receptor-bound arrestin peptide Arr(67-77) mimicking this loop based on solution NMR data. The peptide binds photoactivated rhodopsin in the unphosphorylated and phosphorylated form with similar affinities and stabilizes the metarhodopsin II photointermediate. A largely alpha-helical conformation of the receptor-bound peptide is observed.
Relationship between listeners' nonnative speech recognition and categorization abilities

PubMed Central

Atagi, Eriko; Bent, Tessa

2015-01-01

Enhancement of the perceptual encoding of talker characteristics (indexical information) in speech can facilitate listeners' recognition of linguistic content. The present study explored this indexical-linguistic relationship in nonnative speech processing by examining listeners' performance on two tasks: nonnative accent categorization and nonnative speech-in-noise recognition. Results indicated substantial variability across listeners in their performance on both the accent categorization and nonnative speech recognition tasks. Moreover, listeners' accent categorization performance correlated with their nonnative speech-in-noise recognition performance. These results suggest that having more robust indexical representations for nonnative accents may allow listeners to more accurately recognize the linguistic content of nonnative speech. PMID:25618098
Optically transparent microwave screens based on engineered graphene layers.

PubMed

Grande, M; Bianco, G V; Vincenti, M A; de Ceglia, D; Capezzuto, P; Petruzzelli, V; Scalora, M; Bruno, G; D'Orazio, A

2016-10-03

We propose an innovative approach for the realization of a microwave absorber fully transparent in the optical regime. This device is based on the Salisbury screen configuration, which consists of a lossless spacer, sandwiched between two graphene sheets whose sheet resistances are different and properly engineered. Experimental results show that it is possible to achieve near-perfect electromagnetic absorption in the microwave X-band. These findings are fully supported by an analytical approach based on an equivalent circuital model. Engineering and integration of graphene sheets could facilitate the realization of innovative microwave absorbers with additional electromagnetic and optical functionalities that could circumvent some of the major limitations of opaque microwave absorbers.
A Single Mutation at the Sheet Switch Region Results in Conformational Changes Favoring 6 Light-Chain Fibrillogenesis

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

Hernández-Santoyo, A.; Del Pozo Yauner, L; Fuentes-Silva, D

Systemic amyloid light-chain (LC) amyloidosis is a disease process characterized by the pathological deposition of monoclonal LCs in tissue. All LC subtypes are capable of fibril formation although {lambda} chains, particularly those belonging to the {lambda}6 type, are overrepresented. Here, we report the thermodynamic and in vitro fibrillogenic properties of several mutants of the {lambda}6 protein 6aJL2 in which Pro7 and/or His8 was substituted by Ser or Pro. The H8P and H8S mutants were almost as stable as the wild-type protein and were poorly fibrillogenic. In contrast, the P7S mutation decreased the thermodynamic stability of 6aJL2 and greatly enhanced itsmore » capacity to form amyloid-like fibrils in vitro. The crystal structure of the P7S mutant showed that the substitution induced both local and long-distance effects, such as the rearrangement of the VL (variable region of the light chain)-VL interface. This mutant crystallized in two orthorhombic polymorphs, P2{sub 1}2{sub 1}2{sub 1} and C222{sub 1}. In the latter, a monomer that was not arranged in the typical Bence-Jones dimer was observed for the first time. Crystal-packing analysis of the C222{sub 1} lattice showed the establishment of intermolecular {beta}-{beta} interactions that involved the N-terminus and {beta}-strand B and that these could be relevant in the mechanism of LC fibril formation. Our results strongly suggest that Pro7 is a key residue in the conformation of the N-terminal sheet switch motif and, through long-distance interactions, is also critically involved in the contacts that stabilized the VL interface in {lambda}6 LCs.« less

Male tawny dragons use throat patterns to recognize rivals.

PubMed

Osborne, Louise; Umbers, Kate D L; Backwell, Patricia R Y; Keogh, J Scott

2012-10-01

The ability to distinguish between familiar and unfamiliar conspecifics is important for many animals, especially territorial species since it allows them to avoid unnecessary interactions with individuals that pose little threat. There are very few studies, however, that identify the proximate cues that facilitate such recognition in visual systems. Here, we show that in tawny dragons (Ctenophorus decresii), males can recognize familiar and unfamiliar conspecific males based on morphological features alone, without the aid of chemical or behavioural cues. We further show that it is the colour pattern of the throat patches (gular) that facilitates this recognition.
Effect of colour pop-out on the recognition of letters in crowding conditions.

PubMed

Põder, Endel

2007-11-01

The crowding effect of adjacent objects on the recognition of a target can be reduced when target and flankers differ in some feature, that is irrelevant to the recognition task. In this study, the mechanisms of this effect were explored using targets and flankers of the same and different colours. It was found that facilitation nearly equal to that of differently coloured targets and flankers can be observed with a differently coloured background blob in the location of the target. The different-colour effect does not require advance knowledge of the target and flanker colours, but the effect increases in the course of three trials with constant mapping of colours. The results are consistent with the notion of exogenous attention that facilitates the processing at the most salient locations in the visual field.
Development of a mobile application for amphibian species recognition

NASA Astrophysics Data System (ADS)

Parveen, B.; H, Chew T.; Shamsir, M. S.; Ahmad, N.

2014-02-01

The smartphones mobility and its pervasiveness are beginning to transform practices in biodiversity conservation. The integrated functionalities of a smartphone have created for the public and biodiversity specialists means to identify, gather and record biodiversity data while simultaneously creating knowledge portability in the digital forms of mobile guides. Smartphones enable beginners to recreate the delight of species identification usually reserved for specialist with years of experience. Currently, the advent of Android platform has enabled stakeholders in biodiversity to harness the ubiquity of this platform and create various types of mobile application or "apps" for use in biodiversity research and conservation. However, there is an apparent lack of application devoted to the identification in herpetofauna or amphibian science. Amphibians are a large class of animals with many different species still unidentified under this category. Here we describe the development of an app called Amphibian Recognition Android Application (ARAA) to identify frog amphibian species as well as an accompanying field guide. The app has the amphibian taxonomic key which assists the users in easy and rapid species identification, thus facilitating the process of identification and recording of species occurrences in conservation work. We will also present an overview of the application work flow and how it is designed to meet the needs a conservationist. As this application is still in its beta phase, further research is required to improve the application to include tools such automatic geolocation and geotagging, participative sensing via crowdsourcing and automated identification via image capture. We believe that the introduction of this app will create an impetus to the awareness of nature via species identification.
Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution: an extended phase space sampling by molecular dynamics simulations in explicit water.

PubMed

Daidone, Isabella; Amadei, Andrea; Di Nola, Alfredo

2005-05-15

The folding of the amyloidogenic H1 peptide MKHMAGAAAAGAVV taken from the syrian hamster prion protein is explored in explicit aqueous solution at 300 K using long time scale all-atom molecular dynamics simulations for a total simulation time of 1.1 mus. The system, initially modeled as an alpha-helix, preferentially adopts a beta-hairpin structure and several unfolding/refolding events are observed, yielding a very short average beta-hairpin folding time of approximately 200 ns. The long time scale accessed by our simulations and the reversibility of the folding allow to properly explore the configurational space of the peptide in solution. The free energy profile, as a function of the principal components (essential eigenvectors) of motion, describing the main conformational transitions, shows the characteristic features of a funneled landscape, with a downhill surface toward the beta-hairpin folded basin. However, the analysis of the peptide thermodynamic stability, reveals that the beta-hairpin in solution is rather unstable. These results are in good agreement with several experimental evidences, according to which the isolated H1 peptide adopts very rapidly in water beta-sheet structure, leading to amyloid fibril precipitates [Nguyen et al., Biochemistry 1995;34:4186-4192; Inouye et al., J Struct Biol 1998;122:247-255]. Moreover, in this article we also characterize the diffusion behavior in conformational space, investigating its relations with folding/unfolding conditions. Copyright 2005 Wiley-Liss, Inc.
Systematic review of genuine versus spurious side-effects of beta-blockers in heart failure using placebo control: Recommendations for patient information☆☆☆

PubMed Central

Barron, Anthony J.; Zaman, Nabeela; Cole, Graham D.; Wensel, Roland; Okonko, Darlington O.; Francis, Darrel P.

2013-01-01

Background Patients trying life-preserving agents such as beta-blockers may be discouraged by listings of harmful effects provided in good faith by doctors, drug information sheets, and media. We systematically review the world experience of side-effect information in blinded, placebo-controlled beta-blockade in heart failure. We present information for a physician advising a patient experiencing an unwanted symptom and suspecting the drug. Methods We searched Medline for double-blinded randomized trials of beta-blocker versus placebo in heart failure reporting side-effects. We calculated, per 100 patients reporting the symptom on beta-blockade, how many would have experienced it on placebo: the “proportion of symptoms non-pharmacological”. Results 28 of the 33 classically-described side-effects are not significantly more common on beta-blockers than placebo. Of the 100 patients developing dizziness on beta-blockers, 81 (95% CI 73–89) would have developed it on placebo. For diarrhoea this proportion is 82/100 (70–95), and hyperglycaemia 83/100 (68–98). For only two side-effects is this under half (i.e. predominantly due to beta-blocker): bradycardia (33/100, CI 21–44) and intermittent claudication (41/100, 2–81). At least 6 so-called side-effects are less common on beta-blocker than placebo, including depression (reduced by 35%, p < 0.01) and insomnia (by 27%, p = 0.01). Conclusions Clinicians might reconsider whether it is scientifically and ethically correct to warn a patient that a drug might cause them a certain side-effect, when randomized controlled trials show no significant increase, or indeed a significant reduction. A better informed consultation could, in patients taking beta-blockers, alleviate suffering. In patients who might otherwise not take the drug, it might prevent deaths. PMID:23796325
The Psychophysics of Algebra Expertise: Mathematics Perceptual Learning Interventions Produce Durable Encoding Changes

ERIC Educational Resources Information Center

Bufford, Carolyn A.; Mettler, Everett; Geller, Emma H.; Kellman, Philip J.

2014-01-01

Mathematics requires thinking but also pattern recognition. Recent research indicates that perceptual learning (PL) interventions facilitate discovery of structure and recognition of patterns in mathematical domains, as assessed by tests of mathematical competence. Here we sought direct evidence that a brief perceptual learning module (PLM)…
Visual Speech Primes Open-Set Recognition of Spoken Words

ERIC Educational Resources Information Center

Buchwald, Adam B.; Winters, Stephen J.; Pisoni, David B.

2009-01-01

Visual speech perception has become a topic of considerable interest to speech researchers. Previous research has demonstrated that perceivers neurally encode and use speech information from the visual modality, and this information has been found to facilitate spoken word recognition in tasks such as lexical decision (Kim, Davis, & Krins,…
Thermal crystallization mechanism of silk fibroin protein

NASA Astrophysics Data System (ADS)

Hu, Xiao

In this thesis, the thermal crystallization mechanism of silk fibroin protein from Bombyx mori silkworm, was treated as a model for the general study of protein based materials, combining theories from both biophysics and polymer physics fields. A systematic and scientific path way to model the dynamic beta-sheet crystallization process of silk fibroin protein was presented in the following sequence: (1) The crystallinity, fractions of secondary structures, and phase compositions in silk fibroin proteins at any transition stage were determined. Two experimental methods, Fourier transform infrared spectroscopy (FTIR) with Fourier self-deconvolution, and specific reversing heat capacity, were used together for the first time for modeling the static structures and phases in the silk fibroin proteins. The protein secondary structure fractions during the crystallization were quantitatively determined. The possibility of existence of a "rigid amorphous phase" in silk protein was also discussed. (2) The function of bound water during the crystallization process of silk fibroin was studied using heat capacity, and used to build a silk-water dynamic crystallization model. The fundamental concepts and thermal properties of silk fibroin with/without bound water were discussed. Results show that intermolecular bound water molecules, acting as a plasticizer, will cause silk to display a water-induced glass transition around 80°C. During heating, water is lost, and the change of the microenvironment in the silk fibroin chains induces a mesophase prior to thermal crystallization. Real time FTIR during heating and isothermal holding above Tg show the tyrosine side chain changes only during the former process, while beta sheet crystallization occurs only during the latter process. Analogy is made between the crystallization of synthetic polymers according to the four-state scheme of Strobl, and the crystallization process of silk fibroin, which includes an intermediate precursor stage before crystallization. (3) The beta-sheet crystallization kinetics in silk fibroin protein were measured using X-ray, FTIR and heat flow, and the structure reveals the formation mechanism of the silk crystal network. Avrami kinetics theories, which were established for studies of synthetic polymer crystal growth, were for the first time extended to investigate protein self-assembly in multiblock silk fibroin samples. The Avrami exponent, n, was close to two for all methods, indicating formation of beta sheet crystals in silk proteins is different from the 3-D spherulitic crystal growth found in most synthetic homopolymers. A microphase separation pattern after chymotrypsin enzyme biodegradation was shown in the protein structures using scanning electron microscopy. A model was then used to explain the crystallization of silk fibroin protein by analogy to block copolymers. (4) The effects of metal ions during the crystallization of silk fibroin was investigated using thermal analysis. Advanced thermal analysis methods were used to analyze the thermal protein-metallic ion interactions in silk fibroin proteins. Results show that K+ and Ca2+ metallic salts play different roles in silk fibroin proteins, which either reduce (K+) or increase (Ca2+ ) the glass transition (Tg) of pure silk protein and affect the thermal stability of this structure.
Assessing and Improving Student Organizations: Resources for Facilitators CD-ROM. The Assessing and Improving Student Organization (AISO) Program

ERIC Educational Resources Information Center

Nolfi, Tricia; Ruben, Brent D.

2010-01-01

This companion to the "Guide for Students" and "Student Workbook" includes the complete set of PowerPoint slides, a PDF of the Facilitator's Guide in PPT (PowerPoint) slide show format, and PDFs of all scoring sheets, handouts and project planning guides needed for the AISO (Assessing and Improving Student Organization) process. The Assessing and…
U.S. Army Reserve 88th Readiness Division Finds Big Savings

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

None

Fact sheet features lighting work done for the U.S. Army Reserve 88th Readiness Division, which was recognized in two 2017 Interior Lighting Campaign exemplary recognition categories. The troffer lighting upgrade projects at the two recognized sites are expected to save more than 246,000 kWh annually or roughly enough electricity to run 23 homes for a year.
Constitutive Smad signaling and Smad-dependent collagen gene expression in mouse embryonic fibroblasts lacking peroxisome proliferator-activated receptor-{gamma}

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

Ghosh, Asish K; Wei, Jun; Wu, Minghua

2008-09-19

Transforming growth factor-{beta} (TGF-{beta}), a potent inducer of collagen synthesis, is implicated in pathological fibrosis. Peroxisome proliferator-activated receptor-{gamma} (PPAR-{gamma}) is a nuclear hormone receptor that regulates adipogenesis and numerous other biological processes. Here, we demonstrate that collagen gene expression was markedly elevated in mouse embryonic fibroblasts (MEFs) lacking PPAR-{gamma} compared to heterozygous control MEFs. Treatment with the PPAR-{gamma} ligand 15d-PGJ{sub 2} failed to down-regulate collagen gene expression in PPAR-{gamma} null MEFs, whereas reconstitution of these cells with ectopic PPAR-{gamma} resulted in their normalization. Compared to control MEFs, PPAR-{gamma} null MEFs displayed elevated levels of the Type I TGF-{beta} receptor (T{beta}RI),more » and secreted more TGF-{beta}1 into the media. Furthermore, PPAR-{gamma} null MEFs showed constitutive phosphorylation of cellular Smad2 and Smad3, even in the absence of exogenous TGF-{beta}, which was abrogated by the ALK5 inhibitor SB431542. Constitutive Smad2/3 phosphorylation in PPAR-{gamma} null MEFs was associated with Smad3 binding to its cognate DNA recognition sequences, and interaction with coactivator p300 previously implicated in TGF-{beta} responses. Taken together, these results indicate that loss of PPAR-{gamma} in MEFs is associated with upregulation of collagen synthesis, and activation of intracellular Smad signal transduction, due, at least in part, to autocrine TGF-{beta} stimulation.« less
Current sheet in plasma as a system with a controlling parameter

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

Fridman, Yu. A., E-mail: yulya-fridman@yandex.ru; Chukbar, K. V., E-mail: Chukbar-KV@nrcki.ru

2015-08-15

A simple kinetic model describing stationary solutions with bifurcated and single-peaked current density profiles of a plane electron beam or current sheet in plasma is presented. A connection is established between the two-dimensional constructions arising in terms of the model and the one-dimensional considerations by Bernstein−Greene−Kruskal facilitating the reconstruction of the distribution function of trapped particles when both the profile of the electric potential and the free particles distribution function are known.
Stereoselective determination of amino acids in beta-amyloid peptides and senile plaques.

PubMed

Thorsén, G; Bergquist, J; Westlind-Danielsson, A; Josefsson, B

2001-06-01

A novel method for the determination of the enantiomeric composition of peptides is presented. In this paper, the focus has been on beta-amyloid peptides from deceased Alzheimer's disease patients. The peptides are hydrolyzed using mineral acid. The free amino acids are derivatized with the chiral reagent (+)- or (-)-1-(9-anthryl)-2-propyl chloroformate and subsequently separated using micellar electrokinetic chromatography (MEKC) and detected using laser-induced fluorescence (LIF) detection. The high separation efficiency of the MEKC-LIF system, yielding approximately 1 million theoretical plates/m for most amino acids, facilitates the simultaneous chiral determination of nine amino acids. The samples that have been analyzed were standard 1-40 beta-amyloid peptides, in vitro precipitated beta-amyloid fibrils, and human senile plaque samples.
Functional Implications of the Subcellular Localization of Ethylene-Induced Chitinase and [beta]-1,3-Glucanase in Bean Leaves.

PubMed Central

Mauch, F.; Staehelin, L. A.

1989-01-01

Plants respond to an attack by potentially pathogenic organisms and to the plant stress hormone ethylene with an increased synthesis of hydrolases such as chitinase and [beta]-1,3-glucanase. We have studied the subcellular localization of these two enzymes in ethylene-treated bean leaves by immunogold cytochemistry and by biochemical fractionation techniques. Our micrographs indicate that chitinase and [beta]-1,3-glucanase accumulate in the vacuole of ethylene-treated leaf cells. Within the vacuole label was found predominantly over ethylene-induced electron dense protein aggregates. A second, minor site of accumulation of [beta]-1,3-glucanase was the cell wall, where label was present nearly exclusively over the middle lamella surrounding intercellular air spaces. Both kinds of antibodies labeled Golgi cisternae of ethylene-treated tissue, suggesting that the newly synthesized chitinase and [beta]-1,3-glucanase are processed in the Golgi apparatus. Biochemical fractionation studies confirmed the accumulation in high concentrations of both chitinase and [beta]-1,3-glucanase in isolated vacuoles, and demonstrated that only [beta]-1,3-glucanase, but not chitinase, was present in intercellular washing fluids collected from ethylene-treated leaves. Based on these results and earlier studies, we propose a model in which the vacuole-localized chitinase and [beta]-1,3-glucanase are used as a last line of defense to be released when the attacked host cells lyse. The cell wall-localized [beta]-1,3-glucanase, on the other hand, would be involved in recognition processes, releasing defense activating signaling molecules from the walls of invading pathogens. PMID:12359894
Hydrogels constructed via self-assembly of beta-hairpin molecules

NASA Astrophysics Data System (ADS)

Ozbas, Bulent

There is a recent and growing interest in hydrogel materials that are formed via peptide self-assembly for tissue engineering applications. Peptide based materials are excellent candidates for diverse applications in biomedical field due to their responsive behavior and complex self-assembled structures. However, there is very limited information on the self-assembly and resultant network and mechanical properties of these types of hydrogels. The main goal of this dissertation is to investigate the self-assembly mechanism and viscoelastic properties of hydrogels that can be altered by changing solution conditions as well as the primary structure of the peptide. These hydrogels are formed via intramolecular folding and consequent self-assembly of 20 amino acid long beta-hairpin peptide molecules (Max1). The peptide molecules are locally amphiphilic with two linear strands of alternating hydrophobic valine and hydrophilic lysine amino acids connected with a Dproline-LProline turn sequence. Circular dichroism and FTIR spectroscopy show that at physiological conditions peptides are unfolded in the absence of salt. By raising the ionic strength of the solution electrostatic interactions between charged lysines are screened and the peptide arms are forced into a beta-sheet secondary structure stabilized by the turn sequence. These folded molecules intermolecularly assemble via hydrophobic collapse and hydrogen bonding into a three dimensional network. Folding and self-assembly of these molecules can also be triggered by increasing temperature and/or pH of the peptide solution. In addition, the random-coil to beta-sheet transition of the beta-hairpin peptides is pH and, with proper changes in the peptide sequence, thermally reversible. Rheological measurements demonstrate that the resultant supramolecular structure forms an elastic material, whose structure, and thus modulus, can be tuned by magnitude of the stimulus. Hydrogels recover their initial viscoelastic properties after cessation of high magnitude of strain due to the physically crosslinked network structure and strong inter-fibrillar interactions. These interactions can be turned off by either condensing anions or covalently attaching PEG chains on lysine-decorated fibrillar surfaces. TEM, SANS, and rheological data reveal that the elasticity arises from a network consisting of semiflexible fibrillar assemblies that are monodisperse in width. The experimental results are compared with scaling relationships developed for permanently crosslinked semiflexible biopolymer networks. (Abstract shortened by UMI.)
Molecular dynamics studies of protein folding and aggregation

NASA Astrophysics Data System (ADS)

Ding, Feng

This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism that globular proteins under a denaturing environment partially unfold and aggregate by forming stabilizing hydrogen bonds between the backbones of the partial folded substructures. Proteins or peptides rich in alpha-helices also aggregate into beta-rich amyloid fibrils. Upon aggregation, the protein or peptide undergoes a conformational transition from alpha-helices to beta-sheets. The transition of alpha-helix to beta-hairpin (two-stranded beta-sheet) is studied in an all-heavy-atom discrete molecular dynamics model of a polyalanine chain. An entropical driving scenario for the alpha-helix to beta-hairpin transition is discovered.
Biochemical basis of type IB (E1beta ) mutations in maple syrup urine disease. A prevalent allele in patients from the Druze kindred in Israel.

PubMed

Wynn, R M; Chuang, J L; Sansaricq, C; Mandel, H; Chuang, D T

2001-09-28

Maple syrup urine disease (MSUD) is a metabolic disorder associated with often-fatal ketoacidosis, neurological derangement, and mental retardation. In this study, we identify and characterize two novel type IB MSUD mutations in Israeli patients, which affect the E1beta subunit in the decarboxylase (E1) component of the branched-chain alpha-ketoacid dehydrogenase complex. The recombinant mutant E1 carrying the prevalent S289L-beta (TCG --> TTG) mutation in the Druze kindred exists as a stable inactive alphabeta heterodimer. Based on the human E1 structure, the S289L-beta mutation disrupts the interactions between Ser-289-beta and Glu-290-beta', and between Arg-309-beta and Glu-290-beta', which are essential for native alpha(2)beta(2) heterotetrameric assembly. The R133P-beta (CGG --> CCG) mutation, on the other hand, is inefficiently expressed in Escherichia coli as heterotetramers in a temperature-dependent manner. The R133P-beta mutant E1 exhibits significant residual activity but is markedly less stable than the wild-type, as measured by thermal inactivation and free energy change of denaturation. The R133P-beta substitution abrogates the coordination of Arg-133-beta to Ala-95-beta, Glu-96-beta, and Ile-97-beta, which is important for strand-strand interactions and K(+) ion binding in the beta subunit. These findings provide new insights into folding and assembly of human E1 and will facilitate DNA-based diagnosis for MSUD in the Israeli population.
Oxytocin, vasopressin and estrogen receptor gene expression in relation to social recognition in female mice

PubMed Central

Clipperton-Allen, Amy E.; Lee, Anna W.; Reyes, Anny; Devidze, Nino; Phan, Anna; Pfaff, Donald W.; Choleris, Elena

2012-01-01

Inter- and intra-species differences in social behavior and recognition-related hormones and receptors suggest that different distribution and/or expression patterns may relate to social recognition. We used qRT-PCR to investigate naturally occurring differences in expression of estrogen receptor-alpha (ERα), ER-beta (ERβ), progesterone receptor (PR), oxytocin (OT) and receptor, and vasopressin (AVP) and receptors in proestrous female mice. Following four 5 min exposures to the same two conspecifics, one was replaced with a novel mouse in the final trial (T5). Gene expression was examined in mice showing high (85–100%) and low (40–60%) social recognition scores (i.e., preferential novel mouse investigation in T5) in eight socially-relevant brain regions. Results supported OT and AVP involvement in social recognition, and suggest that in the medial preoptic area, increased OT and AVP mRNA, together with ERα and ERβ gene activation, relate to improved social recognition. Initial social investigation correlated with ERs, PR and OTR in the dorsolateral septum, suggesting that these receptors may modulate social interest without affecting social recognition. Finally, increased lateral amygdala gene activation in the LR mice may be associated with general learning impairments, while decreased lateral amygdala activity may indicate more efficient cognitive mechanisms in the HR mice. PMID:22079582
Stabilizing Protein Effects on the Pressure Sensitivity of Fluorescent Gold Nanoclusters

DTIC Science & Technology

2016-01-13

excess Au salt. The purified sample was lyophilized and resuspended at a concentration of 10 mg/mL in ultrapure water . BSA ( PDB :3v03) 100 % α...effect of scaffold protein secondary structure on the pressure response of protein-stabilized gold nanoclusters (P:NCs). These studies were...demonstrate that the pressure response of P:NCs is indeed dependent on the secondary structure of the protein. Proteins with high beta sheet content
Surfactant-free electrodeposition of reduced graphene oxide/copper composite coatings with enhanced wear resistance

NASA Astrophysics Data System (ADS)

Mai, Y. J.; Zhou, M. P.; Ling, H. J.; Chen, F. X.; Lian, W. Q.; Jie, X. H.

2018-03-01

How to uniformly disperse graphene sheets into the electrolyte is one of the main challenges to synthesize graphene enhanced nanocomposites by electrodeposition. A surfactant-free colloidal solution comprised of copper (II)-ethylene diamine tetra acetic acid ([CuIIEDTA]2-) complexes and graphene oxide (GO) sheets is proposed to electrodeposit reduced graphene oxide/copper (RGO/Cu) composite coatings. Anionic [CuIIEDTA]2- complexes stably coexist with negatively charged GO sheets due to the electrostatic repulsion between them, facilitating the electrochemical reduction and uniform dispersion of GO sheets into the copper matrix. The RGO/Cu composite coatings are well characterized by XRD, Raman, SEM and XPS. Their tribological behavior as a function of RGO content in composite coatings and normal loads are investigated. Also the chemical composition and topography of the wear tracks for the composite coatings are analyzed to deduce the lubricating and anti-wear mechanism of RGO/Cu composite coatings.

High Resistivity Transparent/Conductive Coatings for Space Applications: Problems and Possible Improvements

NASA Technical Reports Server (NTRS)

Cashman, Thomas; Demko, Rikako; Uppala, Nischala; Vemulapalli, Jyothi; Welch, Bryan; Hambourger, Paul D.

2003-01-01

We have prepared transparent films with a sheet relativity of 10(exp 1) to 10(exp 12) ohm/square by co-depositing a transparent conducting oxide (TCO) with magnesium fluoride, using two independently controlled RF magnetron sputter guns to facilitate adjustment of the film composition, Co-deposited indium tin oxide (ITO) and MgF2 on quartz and flexible polymeric substrate exhibited reasonably stable sheet resistivity over several months' time, with substantially lower optical reflectance than that of pure ITO. However, exposure to low-intensity blue light reduces sheet resistivity by as much as two orders of magnitude. Our results suggest this photoconductivity effect may be present in all InO(x)-based materials. We find that sheet resistivity can by "tuned" by admitting a small amount of high-purity air during deposition offering the possibility of closed loop process control.
Conformational study of 13C-enriched fibroin in the solid state, using the cross polarization nuclear magnetic resonance method.

PubMed

Fujiwara, T; Kobayashi, Y; Kyogoku, Y; Kataoka, K

1986-01-05

Silk fibroin with the alanyl carboxyl carbon enriched with 13C was obtained by giving a diet containing 13C-enriched alanine to the larvae of Bombyx mori and Antheraea pernyi at the fifth instar. Sericin-free fibroin fibers were prepared from cocoons, and gut was made from the liquid silk in the gland. The final 13C content was about 13%. Cross polarization/magic angle sample spinning spectra at 25 MHz and 75 MHz were measured for each sample at different orientations. Spectra were simulated using the principal values and orientations of the shielding tensor in the alanine crystal. The results indicate that the beta-structure of the fibroin may be a little more flattened than the typical pleated sheet beta-structure.
Frontal theta and beta synchronizations for monetary reward increase visual working memory capacity

PubMed Central

Yamaguchi, Yoko

2013-01-01

Visual working memory (VWM) capacity is affected by motivational influences; however, little is known about how reward-related brain activities facilitate the VWM systems. To investigate the dynamic relationship between VWM- and reward-related brain activities, we conducted time–frequency analyses using electroencephalograph (EEG) data obtained during a monetary-incentive delayed-response task that required participants to memorize the position of colored disks. In case of a correct answer, participants received a monetary reward (0, 10 or 50 Japanese yen) announced at the beginning of each trial. Behavioral results showed that VWM capacity under high-reward condition significantly increased compared with that under low- or no-reward condition. EEG results showed that frontal theta (6 Hz) amplitudes enhanced during delay periods and positively correlated with VWM capacity, indicating involvement of theta local synchronizations in VWM. Moreover, frontal beta activities (24 Hz) were identified as reward-related activities, because delay-period amplitudes correlated with increases in VWM capacity between high-reward and no-reward conditions. Interestingly, cross-frequency couplings between frontal theta and beta phases were observed only under high-reward conditions. These findings suggest that the functional dynamic linking between VWM-related theta and reward-related beta activities on the frontal regions plays an integral role in facilitating increases in VWM capacity. PMID:22349800
Frontal theta and beta synchronizations for monetary reward increase visual working memory capacity.

PubMed

Kawasaki, Masahiro; Yamaguchi, Yoko

2013-06-01

Visual working memory (VWM) capacity is affected by motivational influences; however, little is known about how reward-related brain activities facilitate the VWM systems. To investigate the dynamic relationship between VWM- and reward-related brain activities, we conducted time-frequency analyses using electroencephalograph (EEG) data obtained during a monetary-incentive delayed-response task that required participants to memorize the position of colored disks. In case of a correct answer, participants received a monetary reward (0, 10 or 50 Japanese yen) announced at the beginning of each trial. Behavioral results showed that VWM capacity under high-reward condition significantly increased compared with that under low- or no-reward condition. EEG results showed that frontal theta (6 Hz) amplitudes enhanced during delay periods and positively correlated with VWM capacity, indicating involvement of theta local synchronizations in VWM. Moreover, frontal beta activities (24 Hz) were identified as reward-related activities, because delay-period amplitudes correlated with increases in VWM capacity between high-reward and no-reward conditions. Interestingly, cross-frequency couplings between frontal theta and beta phases were observed only under high-reward conditions. These findings suggest that the functional dynamic linking between VWM-related theta and reward-related beta activities on the frontal regions plays an integral role in facilitating increases in VWM capacity.
Structural changes induced by acidic pH in human apolipoprotein B-100

PubMed Central

Fernández-Higuero, José A.; Benito-Vicente, Asier; Etxebarria, Aitor; Milicua, José Carlos G.; Ostolaza, Helena; Arrondo, José L. R.; Martín, Cesar

2016-01-01

Acidification in the endosome causes lipoprotein release by promoting a conformational change in the LDLR allowing its recycling and degradation of LDL. Notwithstanding conformational changes occurring in the LDLR have expanded considerably, structural changes occurring in LDL particles have not been fully explored yet. The objectives of the present work were to study structural changes occurring in apoB100 by infrared spectroscopy (IR) and also LDL size and morphology by dynamic light scattering (DLS) and electron microscopy (EM) at both pH 7.4 and 5.0. We determined by IR that pH acidification from 7.4 to 5.0, resembling that occurring within endosomal environment, induces a huge reversible structural rearrangement of apoB100 that is characterized by a reduction of beta-sheet content in favor of alpha-helix structures. Data obtained from DLS and EM showed no appreciable differences in size and morphology of LDL. These structural changes observed in apoB100, which are likely implied in particle release from lipoprotein receptor, also compromise the apoprotein stability what would facilitate LDL degradation. In conclusion, the obtained results reveal a more dynamic picture of the LDL/LDLR dissociation process than previously perceived and provide new structural insights into LDL/LDLR interactions than can occur at endosomal low-pH milieu. PMID:27824107
Reversible Hydrogel–Solution System of Silk with High Beta-Sheet Content

PubMed Central

2015-01-01

Silkworm silk has been widely used as a textile fiber, as biomaterials and in optically functional materials due to its extraordinary properties. The β-sheet-rich natural nanofiber units of about 10–50 nm in diameter are often considered the origin of these properties, yet it remains unclear how silk self-assembles into these hierarchical structures. A new system composed of β-sheet-rich silk nanofibers about 10–20 nm in diameter is reported here, where these nanofibers formed into “flowing hydrogels” at 0.5–2% solutions and could be transformed back into the solution state at lower concentrations, even with a high β-sheet content. This is in contrast with other silk processed materials, where significant β-sheet content negates reversibility between solution and solid states. These fibers are formed by regulating the self-assembly process of silk in aqueous solution, which changes the distribution of negative charges while still supporting β-sheet formation in the structures. Mechanistically, there appears to be a shift toward negative charges along the outside of the silk nanofibers in our present study, resulting in a higher zeta potential (above −50 mV) than previous silk materials which tend to be below −30 mV. The higher negative charge on silk nanofibers resulted in electrostatic repulsion strong enough to negate further assembly of the nanofibers. Changing silk concentration changed the balance between hydrophobic interactions and electrostatic repulsion of β-sheet-rich silk nanofibers, resulting in reversible hydrogel–solution transitions. Furthermore, the silk nanofibers could be disassembled into shorter fibers and even nanoparticles upon ultrasonic treatment following the transition from hydrogel to solution due to the increased dispersion of hydrophobic smaller particles, without the loss of β-sheet content, and with retention of the ability to transition between hydrogel and solution states through reversion to longer nanofibers during self-assembly. These reversible solution-hydrogel transitions were tunable with ultrasonic intensity, time, or temperature. PMID:25056606
Reversible hydrogel-solution system of silk with high beta-sheet content.

PubMed

Bai, Shumeng; Zhang, Xiuli; Lu, Qiang; Sheng, Weiqin; Liu, Lijie; Dong, Boju; Kaplan, David L; Zhu, Hesun

2014-08-11

Silkworm silk has been widely used as a textile fiber, as biomaterials and in optically functional materials due to its extraordinary properties. The β-sheet-rich natural nanofiber units of about 10-50 nm in diameter are often considered the origin of these properties, yet it remains unclear how silk self-assembles into these hierarchical structures. A new system composed of β-sheet-rich silk nanofibers about 10-20 nm in diameter is reported here, where these nanofibers formed into "flowing hydrogels" at 0.5-2% solutions and could be transformed back into the solution state at lower concentrations, even with a high β-sheet content. This is in contrast with other silk processed materials, where significant β-sheet content negates reversibility between solution and solid states. These fibers are formed by regulating the self-assembly process of silk in aqueous solution, which changes the distribution of negative charges while still supporting β-sheet formation in the structures. Mechanistically, there appears to be a shift toward negative charges along the outside of the silk nanofibers in our present study, resulting in a higher zeta potential (above -50 mV) than previous silk materials which tend to be below -30 mV. The higher negative charge on silk nanofibers resulted in electrostatic repulsion strong enough to negate further assembly of the nanofibers. Changing silk concentration changed the balance between hydrophobic interactions and electrostatic repulsion of β-sheet-rich silk nanofibers, resulting in reversible hydrogel-solution transitions. Furthermore, the silk nanofibers could be disassembled into shorter fibers and even nanoparticles upon ultrasonic treatment following the transition from hydrogel to solution due to the increased dispersion of hydrophobic smaller particles, without the loss of β-sheet content, and with retention of the ability to transition between hydrogel and solution states through reversion to longer nanofibers during self-assembly. These reversible solution-hydrogel transitions were tunable with ultrasonic intensity, time, or temperature.
Iris Recognition Using Feature Extraction of Box Counting Fractal Dimension

NASA Astrophysics Data System (ADS)

Khotimah, C.; Juniati, D.

2018-01-01

Biometrics is a science that is now growing rapidly. Iris recognition is a biometric modality which captures a photo of the eye pattern. The markings of the iris are distinctive that it has been proposed to use as a means of identification, instead of fingerprints. Iris recognition was chosen for identification in this research because every human has a special feature that each individual is different and the iris is protected by the cornea so that it will have a fixed shape. This iris recognition consists of three step: pre-processing of data, feature extraction, and feature matching. Hough transformation is used in the process of pre-processing to locate the iris area and Daugman’s rubber sheet model to normalize the iris data set into rectangular blocks. To find the characteristics of the iris, it was used box counting method to get the fractal dimension value of the iris. Tests carried out by used k-fold cross method with k = 5. In each test used 10 different grade K of K-Nearest Neighbor (KNN). The result of iris recognition was obtained with the best accuracy was 92,63 % for K = 3 value on K-Nearest Neighbor (KNN) method.
Persistent suppression of subthalamic beta-band activity during rhythmic finger tapping in Parkinson's disease.

PubMed

Joundi, Raed A; Brittain, John-Stuart; Green, Alex L; Aziz, Tipu Z; Brown, Peter; Jenkinson, Ned

2013-03-01

The function of synchronous oscillatory activity at beta band (15-30Hz) frequencies within the basal ganglia is unclear. Here we sought support for the hypothesis that beta activity has a global function within the basal ganglia and is not directly involved in the coding of specific biomechanical parameters of movement. We recorded local field potential activity from the subthalamic nuclei of 11 patients with Parkinson's disease during a synchronized tapping task at three different externally cued rates. Beta activity was suppressed during tapping, reaching a minimum that differed little across the different tapping rates despite an increase in velocity of finger movements. Thus beta power suppression was independent of specific motor parameters. Moreover, although beta oscillations remained suppressed during all tapping rates, periods of resynchronization between taps were markedly attenuated during high rate tapping. As such, a beta rebound above baseline between taps at the lower rates was absent at the high rate. Our results demonstrate that beta desynchronization in the region of the subthalamic nucleus is independent of motor parameters and that the beta resynchronization is differentially modulated by rate of finger tapping, These findings implicate consistent beta suppression in the facilitation of continuous movement sequences. Copyright © 2012 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.
Facilitating Sound, Cost-Effective Federal Energy Management

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

FEMP

2016-07-01

Fact sheet offers an overview of the Federal Energy Management Program (FEMP), which provides agencies and organizations with the information, tools, and assistance they need to achieve their energy-related requirements and goals through specialized initiatives.
Superfund and Technology Liaison Program Fact Sheet

EPA Pesticide Factsheets

The Superfund and Technology Liaison (STL) Program was established to facilitate regional access to ORD laboratories, provide technical support, and assist with the integration of science and technology into decision-making for hazardous waste programs.
Study on adsorption of rhodamine B onto Beta zeolites by tuning SiO2/Al2O3 ratio.

PubMed

Cheng, Zhi-Lin; Li, Yan-Xiang; Liu, Zan

2018-02-01

The exploration of the relationship between zeolite composition and adsorption performance favored to facilitate its better application in removal of the hazardous substances from water. The adsorption capacity of rhodamine B (RB) onto Beta zeolite from aqueous solution was reported. The relationship between SiO 2 /Al 2 O 3 ratio and adsorption capacity of Beta zeolite for RB was explored. The structure and physical properties of Beta zeolites with various SiO 2 /Al 2 O 3 ratios were determined by XRD, FTIR, TEM, BET, UV-vis and so on characterizations. The adsorption behavior of rhodamine B onto Beta zeolite matched to Langmuir adsorption isotherm and more suitable description for the adsorption kinetics was a pseudo-second-order reaction model. The maximum adsorption capacity of the as-prepared Beta zeolite with SiO 2 /Al 2 O 3 = 18.4 was up to 27.97mg/g. Copyright © 2017 Elsevier Inc. All rights reserved.
Professional Mobility and the Mutual Recognition of Qualifications in the European Union: Two Institutional Approaches.

ERIC Educational Resources Information Center

Blitz, Brad K.

1999-01-01

Examines the role of transnational institutions (particularly the European Commission and committees of the European Parliament) in facilitating the mutual recognition of professional qualifications among members of the European Economic Community (EEC). Discusses relevant EEC directives, varying compliance among nations, and six cases of citizen…
Priming Contour-Deleted Images: Evidence for Immediate Representations in Visual Object Recognition.

ERIC Educational Resources Information Center

Biederman, Irving; Cooper, Eric E.

1991-01-01

Speed and accuracy of identification of pictures of objects are facilitated by prior viewing. Contributions of image features, convex or concave components, and object models in a repetition priming task were explored in 2 studies involving 96 college students. Results provide evidence of intermediate representations in visual object recognition.…
Fungal Beta-Glucosidases: A Bottleneck in Industrial Use of Lignocellulosic Materials

PubMed Central

Sørensen, Annette; Lübeck, Mette; Lübeck, Peter S.; Ahring, Birgitte K.

2013-01-01

Profitable biomass conversion processes are highly dependent on the use of efficient enzymes for lignocellulose degradation. Among the cellulose degrading enzymes, beta-glucosidases are essential for efficient hydrolysis of cellulosic biomass as they relieve the inhibition of the cellobiohydrolases and endoglucanases by reducing cellobiose accumulation. In this review, we discuss the important role beta-glucosidases play in complex biomass hydrolysis and how they create a bottleneck in industrial use of lignocellulosic materials. An efficient beta-glucosidase facilitates hydrolysis at specified process conditions, and key points to consider in this respect are hydrolysis rate, inhibitors, and stability. Product inhibition impairing yields, thermal inactivation of enzymes, and the high cost of enzyme production are the main obstacles to commercial cellulose hydrolysis. Therefore, this sets the stage in the search for better alternatives to the currently available enzyme preparations either by improving known or screening for new beta-glucosidases. PMID:24970184
Deterioration of Speech Recognition Ability Over a Period of 5 Years in Adults Ages 18 to 70 Years: Results of the Dutch Online Speech-in-Noise Test.

PubMed

Stam, Mariska; Smits, Cas; Twisk, Jos W R; Lemke, Ulrike; Festen, Joost M; Kramer, Sophia E

2015-01-01

The first aim of the present study was to determine the change in speech recognition in noise over a period of 5 years in participants ages 18 to 70 years at baseline. The second aim was to investigate whether age, gender, educational level, the level of initial speech recognition in noise, and reported chronic conditions were associated with a change in speech recognition in noise. The baseline and 5-year follow-up data of 427 participants with and without hearing impairment participating in the National Longitudinal Study on Hearing (NL-SH) were analyzed. The ability to recognize speech in noise was measured twice with the online National Hearing Test, a digit-triplet speech-in-noise test. Speech-reception-threshold in noise (SRTn) scores were calculated, corresponding to 50% speech intelligibility. Unaided SRTn scores obtained with the same transducer (headphones or loudspeakers) at both test moments were included. Changes in SRTn were calculated as a raw shift (T1 - T0) and an adjusted shift for regression towards the mean. Paired t tests and multivariable linear regression analyses were applied. The mean increase (i.e., deterioration) in SRTn was 0.38-dB signal-to-noise ratio (SNR) over 5 years (p < 0.001). Results of the multivariable regression analyses showed that the age group of 50 to 59 years had a significantly larger deterioration in SRTn compared with the age group of 18 to 39 years (raw shift: beta: 0.64-dB SNR; 95% confidence interval: 0.07-1.22; p = 0.028, adjusted for initial speech recognition level - adjusted shift: beta: 0.82-dB SNR; 95% confidence interval: 0.27-1.34; p = 0.004). Gender, educational level, and the number of chronic conditions were not associated with a change in SRTn over time. No significant differences in increase of SRTn were found between the initial levels of speech recognition (i.e., good, insufficient, or poor) when taking into account the phenomenon regression towards the mean. The study results indicate that hearing deterioration of speech recognition in noise over 5 years can also be detected in adults ages 18 to 70 years. This rather small numeric change might represent a relevant impact on an individual's ability to understand speech in everyday life.
Sleep facilitates consolidation of emotional declarative memory.

PubMed

Hu, Peter; Stylos-Allan, Melinda; Walker, Matthew P

2006-10-01

Both sleep and emotion are known to modulate processes of memory consolidation, yet their interaction is poorly understood. We examined the influence of sleep on consolidation of emotionally arousing and neutral declarative memory. Subjects completed an initial study session involving arousing and neutral pictures, either in the evening or in the morning. Twelve hours later, after sleeping or staying awake, subjects performed a recognition test requiring them to discriminate between these original pictures and novel pictures by responding "remember,"know" (familiar), or "new." Selective sleep effects were observed for consolidation of emotional memory: Recognition accuracy for know judgments of arousing stimuli improved by 42% after sleep relative to wake, and recognition bias for remember judgments of these stimuli increased by 58% after sleep relative to wake (resulting in more conservative responding). These findings hold important implications for understanding of human memory processing, suggesting that the facilitation of memory for emotionally salient information may preferentially develop during sleep.
Preliminary in vivo efficacy studies of a recombinant rhesus anti-alpha(4)beta(7) monoclonal antibody.

PubMed

Pereira, L E; Onlamoon, N; Wang, X; Wang, R; Li, J; Reimann, K A; Villinger, F; Pattanapanyasat, K; Mori, K; Ansari, A A

2009-01-01

Recent findings established that primary targets of HIV/SIV are lymphoid cells within the gastrointestinal (GI) tract. Focus has therefore shifted to T-cells expressing alpha(4)beta(7) integrin which facilitates trafficking to the GI tract via binding to MAdCAM-1. Approaches to better understand the role of alpha(4)beta(7)+ T-cells in HIV/SIV pathogenesis include their depletion or blockade of their synthesis, binding and/or homing capabilities in vivo. Such studies can ideally be conducted in rhesus macaques (RM), the non-human primate model of AIDS. Characterization of alpha(4)beta(7) expression on cell lineages in RM blood and GI tissues reveal low densities of expression by NK cells, B-cells, naïve and TEM (effector memory) T-cells. High densities were observed on TCM (central memory) T-cells. Intravenous administration of a single 50mg/kg dose of recombinant rhesus alpha(4)beta(7) antibody resulted in significant initial decline of alpha(4)beta(7)+ lymphocytes and sustained coating of the alpha(4)beta(7) receptor in both the periphery and GI tissues.
Full-Thickness Skin Wound Healing Using Human Placenta-Derived Extracellular Matrix Containing Bioactive Molecules

PubMed Central

Choi, Ji Suk; Kim, Jae Dong; Yoon, Hyun Soo

2013-01-01

The human placenta, a complex organ, which facilitates exchange between the fetus and the mother, contains abundant extracellular matrix (ECM) components and well-preserved endogenous growth factors. In this study, we designed a new dermal substitute from human placentas for full-thickness wound healing. Highly porous, decellularized ECM sheets were fabricated from human placentas via homogenization, centrifugation, chemical and enzymatic treatments, molding, and freeze-drying. The physical structure and biological composition of human placenta-derived ECM sheets dramatically supported the regeneration of full-thickness wound in vivo. At the early stage, the ECM sheet efficiently absorbed wound exudates and tightly attached to the wound surface. Four weeks after implantation, the wound was completely closed, epidermic cells were well arranged and the bilayer structure of the epidermis and dermis was restored. Moreover, hair follicles and microvessels were newly formed in the ECM sheet-implanted wounds. Overall, the ECM sheet produced a dermal substitute with similar cellular organization to that of normal skin. These results suggest that human placenta-derived ECM sheets provide a microenvironment favorable to the growth and differentiation of cells, and positive modulate the healing of full-thickness wounds. PMID:22891853
Embedded Heaters for Joining or Separating Plastic Parts

NASA Technical Reports Server (NTRS)

Bryant, Melvin A., III

2004-01-01

A proposed thermal-bonding technique would make it possible to join or separate thermoplastic parts quickly and efficiently. The technique would eliminate the need for conventional welding or for such conventional fastening components as bolted flanges or interlocking hooks. The technique could be particularly useful in the sign industry (in which large quantities of thermoplastics are used) or could be used to join plastic pipes. A thin sheet of a suitable electrically conductive material would be formed to fit between two thermoplastic parts to be joined (see figure). The electrically conductive sheet and the two parts would be put together tightly, then an electrical current would be sent through the conductor to heat the thermoplastic locally. The magnitude of the current and the heating time would be chosen to generate just enough heat to cause the thermoplastic to adhere to both sides of the electrically conductive sheet. Optionally, the electrically conductive sheet could contain many small holes to provide purchase or to increase electrical resistance to facilitate the generation of heat. After thermal bonding, the electrically conductive sheet remains as an integral part of the structure. If necessary, the electrically conductive sheet can be reheated later to separate the joined thermoplastic parts.

Structural modifications of human beta 2 microglobulin treated with oxygen-derived radicals.

PubMed Central

Capeillere-Blandin, C; Delaveau, T; Descamps-Latscha, B

1991-01-01

Treatment of human beta 2 microglobulin (beta 2m) with defined oxygen-derived species generated by treatment with gamma-radiation was studied. As assessed by SDS/PAGE, the hydroxyl radicals (.OH) caused the disappearance of the protein band at 12 kDa that represents beta 2m, and cross-linked the protein into protein bands stable to both SDS and reducing conditions. However, when .OH was generated under oxygen in equimolar combination with the superoxide anion radical (O2.-), the high-molecular-mass protein products were less represented, and fragmented derivatives were not obviously detectable. Exposure to .OH alone, or to .OH + O2.- in the presence of O2, induced the formation of beta 2m protein derivatives with a more acidic net electrical charge than the parent molecule. In contrast, O2.- alone had virtually no effect on molecular mass or pI. Changes in u.v. fluorescence during .OH attack indicated changes in conformation, as confirmed by c.d. spectrometry. A high concentration of radicals caused the disappearance of the beta-pleated sheet structure and the formation of a random coil structure. Loss of tryptophan and significant production of dityrosine (2,2'-biphenol type) were noted, exhibiting a clear dose-dependence with .OH alone or with .OH + O2.-. The combination of .OH + O2.- induced a pattern of changes similar to that with .OH alone, but more extensive for c.d. and tryptophan oxidation (2 Trp/beta 2m molecule), and more limited for dityrosine formation. Lower levels of these oxidative agents caused the reproducible formation of species at 18 and 25 kDa which were recognized by antibodies against native beta 2m. These findings provide a model for the protein pattern observed in beta 2m amyloidosis described in the literature. Images Fig. 4. Fig. 5. PMID:1649598
Axin and GSK3- control Smad3 protein stability and modulate TGF- signaling.

PubMed

Guo, Xing; Ramirez, Alejandro; Waddell, David S; Li, Zhizhong; Liu, Xuedong; Wang, Xiao-Fan

2008-01-01

The broad range of biological responses elicited by transforming growth factor-beta (TGF-beta) in various types of tissues and cells is mainly determined by the expression level and activity of the effector proteins Smad2 and Smad3. It is not fully understood how the baseline properties of Smad3 are regulated, although this molecule is in complex with many other proteins at the steady state. Here we show that nonactivated Smad3, but not Smad2, undergoes proteasome-dependent degradation due to the concerted action of the scaffolding protein Axin and its associated kinase, glycogen synthase kinase 3-beta (GSK3-beta). Smad3 physically interacts with Axin and GSK3-beta only in the absence of TGF-beta. Reduction in the expression or activity of Axin/GSK3-beta leads to increased Smad3 stability and transcriptional activity without affecting TGF-beta receptors or Smad2, whereas overexpression of these proteins promotes Smad3 basal degradation and desensitizes cells to TGF-beta. Mechanistically, Axin facilitates GSK3-beta-mediated phosphorylation of Smad3 at Thr66, which triggers Smad3 ubiquitination and degradation. Thr66 mutants of Smad3 show altered protein stability and hence transcriptional activity. These results indicate that the steady-state stability of Smad3 is an important determinant of cellular sensitivity to TGF-beta, and suggest a new function of the Axin/GSK3-beta complex in modulating critical TGF-beta/Smad3-regulated processes during development and tumor progression.
Insulin release: the receptor hypothesis.

PubMed

Malaisse, Willy J

2014-07-01

It is currently believed that the stimulation of insulin release by nutrient secretagogues reflects their capacity to act as fuel in pancreatic islet beta cells. In this review, it is proposed that such a fuel concept is not incompatible with a receptor hypothesis postulating the participation of cell-surface receptors in the recognition of selected nutrients as insulinotropic agents. Pursuant to this, attention is drawn to such matters as the anomeric specificity of the beta cell secretory response to D-glucose and its perturbation in diabetes mellitus, the insulinotropic action of artificial sweeteners, the possible role of bitter taste receptors in the stimulation of insulin secretion by L-glucose pentaacetate, the recently documented presence of cell-surface sweet taste receptors in insulin-producing cells, the multimodal signalling process resulting from the activation of these latter receptors, and the presence in beta cells of a sweet taste receptor mediating the fructose-induced potentiation of glucose-stimulated insulin secretion.
Nuclear Magnetic Resonance (NMR) Spectroscopic Characterization of Nanomaterials and Biopolymers

NASA Astrophysics Data System (ADS)

Guo, Chengchen

Nanomaterials have attracted considerable attention in recent research due to their wide applications in various fields such as material science, physical science, electrical engineering, and biomedical engineering. Researchers have developed many methods for synthesizing different types of nanostructures and have further applied them in various applications. However, in many cases, a molecular level understanding of nanoparticles and their associated surface chemistry is lacking investigation. Understanding the surface chemistry of nanomaterials is of great significance for obtaining a better understanding of the properties and functions of the nanomaterials. Nuclear magnetic resonance (NMR) spectroscopy can provide a familiar means of looking at the molecular structure of molecules bound to surfaces of nanomaterials as well as a method to determine the size of nanoparticles in solution. Here, a combination of NMR spectroscopic techniques including one- and two-dimensional NMR spectroscopies was used to investigate the surface chemistry and physical properties of some common nanomaterials, including for example, thiol-protected gold nanostructures and biomolecule-capped silica nanoparticles. Silk is a natural protein fiber that features unique properties such as excellent mechanical properties, biocompatibility, and non-linear optical properties. These appealing physical properties originate from the silk structure, and therefore, the structural analysis of silk is of great importance for revealing the mystery of these impressive properties and developing novel silk-based biomaterials as well. Here, solid-state NMR spectroscopy was used to elucidate the secondary structure of silk proteins in N. clavipes spider dragline silk and B. mori silkworm silk. It is found that the Gly-Gly-X (X=Leu, Tyr, Gln) motif in spider dragline silk is not in a beta-sheet or alpha-helix structure and is very likely to be present in a disordered structure with evidence for 31-helix confirmation. In addition, the conformations of the Ala, Ser, and Tyr residues in silk fibroin of B. mori were investigated and it indicates that the Ala, Ser, and Tyr residues are all present in disordered structures in silk I (before spinning), while show different conformations in silk II (after spinning). Specifically, in silk II, the Ala and Tyr residues are present in both disordered structures and beta-sheet structures, and the Ser residues are present primarily in beta-sheet structures.
Detection of defects in formed sheet metal using medial axis transformation

NASA Astrophysics Data System (ADS)

Murmu, Naresh C.; Velgan, Roman

2003-05-01

In the metal forming processes, the sheet metals are often prone to various defects such as thinning, dents, wrinkles etc. In the present manufacturing environments with ever increasing demand of higher quality, detecting the defects of formed sheet metal using an effective and objective inspection system is the foremost norm to remain competitive in market. The defect detection using optical techniques aspire to satisfy its needs to be non-contact and fast. However, the main difficulties to achieve this goal remain essentially on the development of efficient evaluation technique and accurate interpretation of extracted data. The defect like thinning is detected by evaluating the deviations of the thickness in the formed sheet metal against its nominal value. The present evaluation procedure for determination of thickness applied on the measurements data is not without deficiency. To improve this procedure, a new evaluation approach based on medial axis transformation is proposed here. The formed sheet metals are digitized using fringe projection systems in different orientations, and afterwards registered into one coordinate frame. The medial axis transformation (MAT) is applied on the point clouds, generating the point clouds of MAT. This data is further processed and medial surface is determined. The thinning defect is detected by evaluating local wall thickness and other defects like wrinkles are determined using the shape recognition on the medial surface. The applied algorithm is simple, fast and robust.
Isolation and bacterial expression of a sesquiterpene synthase CDNA clone from peppermint(mentha .chi. piperita, L.) that produces the aphid alarm pheromone (E)-.beta.-farnesene

DOEpatents

Croteau, Rodney Bruce; Wildung, Mark Raymond; Crock, John E.

1999-01-01

A cDNA encoding (E)-.beta.-farnesene synthase from peppermint (Mentha piperita) has been isolated and sequenced, and the corresponding amino acid sequence has been determined. Accordingly, an isolated DNA sequence (SEQ ID NO:1) is provided which codes for the expression of (E)-.beta.-farnesene synthase (SEQ ID NO:2), from peppermint (Mentha piperita). In other aspects, replicable recombinant cloning vehicles are provided which code for (E)-.beta.-farnesene synthase, or for a base sequence sufficiently complementary to at least a portion of (E)-.beta.-farnesene synthase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding (E)-.beta.-farnesene synthase. Thus, systems and methods are provided for the recombinant expression of the aforementioned recombinant (E)-.beta.-farnesene synthase that may be used to facilitate its production, isolation and purification in significant amounts. Recombinant (E)-.beta.-farnesene synthase may be used to obtain expression or enhanced expression of (E)-.beta.-farnesene synthase in plants in order to enhance the production of (E)-.beta.-farnesene, or may be otherwise employed for the regulation or expression of (E)-.beta.-farnesene synthase, or the production of its product.
Isolation and bacterial expression of a sesquiterpene synthase cDNA clone from peppermint (Mentha x piperita, L.) that produces the aphid alarm pheromone (E)-.beta.-farnesene

DOEpatents

Croteau, Rodney Bruce; Crock, John E.

2005-01-25

A cDNA encoding (E)-.beta.-farnesene synthase from peppermint (Mentha piperita) has been isolated and sequenced, and the corresponding amino acid sequence has been determined. Accordingly, an isolated DNA sequence (SEQ ID NO:1) is provided which codes for the expression of (E)-.beta.-farnesene synthase (SEQ ID NO:2), from peppermint (Mentha piperita). In other aspects, replicable recombinant cloning vehicles are provided which code for (E)-.beta.-farnesene synthase, or for a base sequence sufficiently complementary to at least a portion of (E)-.beta.-farnesene synthase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding (E)-.beta.-farnesene synthase. Thus, systems and methods are provided for the recombinant expression of the aforementioned recombinant (E)-.beta.-famesene synthase that may be used to facilitate its production, isolation and purification in significant amounts. Recombinant (E)-.beta.-farnesene synthase may be used to obtain expression or enhanced expression of (E)-.beta.-famesene synthase in plants in order to enhance the production of (E)-.beta.-farnesene, or may be otherwise employed for the regulation or expression of (E)-.beta.-farnesene synthase, or the production of its product.
Home Energy Professional Certifications (Fact Sheet)

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

Not Available

2012-11-01

As the weatherization and home energy upgrade industries expand and gain recognition, the need for a qualified workforce becomes more apparent. The certification component of the Guidelines project was designed to create meaningful and lasting careers for weatherization workers. Intended for experienced home energy professionals, the four new certifications focus on the most common jobs in the industry: energy auditor, retrofit installer technician, crew leader, and quality control inspector.
The role of novel chitin-like polysaccharides in Alzheimer disease.

PubMed

Castellani, Rudy J; Perry, George; Smith, Mark A

2007-12-01

While controversy over the role of carbohydrates in amyloidosis has existed since the initial recognition of amyloid, current understanding of the role of polysaccharides in the pathogenesis of amyloid deposition of Alzheimer disease and other amyloidoses is limited to studies of glyco-conjugates such as heparin sulfate proteoglycan. We hypothesized that polysaccharides may play a broader role in light of 1) the impaired glucose utilization in Alzheimer disease; 2) the demonstration of amylose in the Alzheimer disease brain; 3) the role of amyloid in Alzheimer disease pathogenesis. Specifically, as with glucose polymers (amyloid), we wanted to explore whether glucosamine polymers such as chitin were being synthesized and deposited as a result of impaired glucose utilization and aberrant hexosamine pathway activation. To this end, using calcofluor histochemistry, we recently demonstrated that amyloid plaques and blood vessels affected by amyloid angiopathy in subjects with sporadic and familial Alzheimer disease elicit chitin-type characteristics. Since chitin is a highly insoluble molecule and a substrate for glycan-protein interactions, chitin-like polysaccharides within the Alzheimer disease brain could provide a scaffolding for amyloid-beta deposition. As such, glucosamine may facilitate the process of amyloidosis, and /or provide neuroprotection in the Alzheimer disease brain.
Ligand-free method to produce the anti-angiogenic recombinant Galectin-3 carbohydrate recognition domain.

PubMed

Wiecikowski, Adalgisa; Cabral, Katia Maria Dos Santos; Almeida, Marcius da Silva; Carvalho, Renato Sampaio

2018-04-01

Galectin-3 (Gal3) is involved in many physiological processes related to tumor growth, such as promoting angiogenesis, cell migration/invasion, resistance to apoptosis and immune response modulation. Usually the overexpression of Gal3 is a poor prognostic marker for cancer patients. Recombinant Gal3 carbohydrate domain (Gal3C) has been proposed as a useful tool to inhibit angiogenesis. So far, all production protocols reported for Gal3C production have used proteolytic cleavage of full length Gal3 and/or affinity-based purification. This involves dialysis, a time consuming step used to eliminate the elution ligand, usually lactose. In this report, we describe an alternative method to produce human recombinant Gal3C in E. coli, purified with cationic exchange and size exclusion chromatography. The recombinant protein was characterized using circular dichroism and nuclear magnetic resonance, showing a beta sheet enriched well-folded globular structure. The average yield obtained was 26 mg/L of broth and the purity was above 99%. The anti-angiogenic activity was assessed in vitro and showed a reduction of 70% and 77% in endothelial cells tubule formation upon treatment with 10 and 20 μg/mL, respectively and also had no impact on cell viability. The method described here is more suitable for both laboratory and industrial production of the potential anti-tumor Gal3C. Copyright © 2017 Elsevier Inc. All rights reserved.
Exploring Biomolecular Recognition by Modeling and Simulation

NASA Astrophysics Data System (ADS)

Wade, Rebecca

2007-12-01

Biomolecular recognition is complex. The balance between the different molecular properties that contribute to molecular recognition, such as shape, electrostatics, dynamics and entropy, varies from case to case. This, along with the extent of experimental characterization, influences the choice of appropriate computational approaches to study biomolecular interactions. I will present computational studies in which we aim to make concerted use of bioinformatics, biochemical network modeling and molecular simulation techniques to study protein-protein and protein-small molecule interactions and to facilitate computer-aided drug design.
Syntactic/semantic techniques for feature description and character recognition

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

Gonzalez, R.C.

1983-01-01

The Pattern Analysis Branch, Mapping, Charting and Geodesy (MC/G) Division, of the Naval Ocean Research and Development Activity (NORDA) has been involved over the past several years in the development of algorithms and techniques for computer recognition of free-form handprinted symbols as they appear on the Defense Mapping Agency (DMA) maps and charts. NORDA has made significant contributions to the automation of MC/G through advancing the state of the art in such information extraction techniques. In particular, new concepts in character (symbol) skeletonization, rugged feature measurements, and expert system-oriented decision logic have allowed the development of a very high performancemore » Handprinted Symbol Recognition (HSR) system for identifying depth soundings from naval smooth sheets (accuracies greater than 99.5%). The study reported in this technical note is part of NORDA's continuing research and development in pattern and shape analysis as it applies to Navy and DMA ocean/environment problems. The issue addressed in this technical note deals with emerging areas of syntactic and semantic techniques in pattern recognition as they might apply to the free-form symbol problem.« less
The first armadillo repeat is involved in the recognition and regulation of beta-catenin phosphorylation by protein kinase CK1.

PubMed

Bustos, Victor H; Ferrarese, Anna; Venerando, Andrea; Marin, Oriano; Allende, Jorge E; Pinna, Lorenzo A

2006-12-26

Multiple phosphorylation of beta-catenin by glycogen synthase kinase 3 (GSK3) in the Wnt pathway is primed by CK1 through phosphorylation of Ser-45, which lacks a typical CK1 canonical sequence. Synthetic peptides encompassing amino acids 38-64 of beta-catenin are phosphorylated by CK1 on Ser-45 with low affinity (K(m) approximately 1 mM), whereas intact beta-catenin is phosphorylated at Ser-45 with very high affinity (K(m) approximately 200 nM). Peptides extended to include a putative CK1 docking motif (FXXXF) at 70-74 positions or a F74AA mutation in full-length beta-catenin had no significant effect on CK1 phosphorylation efficiency. beta-Catenin C-terminal deletion mutants up to residue 181 maintained their high affinity, whereas removal of the 131-181 fragment, corresponding to the first armadillo repeat, was deleterious, resulting in a 50-fold increase in K(m) value. Implication of the first armadillo repeat in beta-catenin targeting by CK1 is supported in that the Y142E mutation, which mimics phosphorylation of Tyr-142 by tyrosine kinases and promotes dissociation of beta-catenin from alpha-catenin, further improves CK1 phosphorylation efficiency, lowering the K(m) value to <50 nM, approximating the physiological concentration of beta-catenin. In contrast, alpha-catenin, which interacts with the N-terminal region of beta-catenin, prevents Ser-45 phosphorylation of CK1 in a dose-dependent manner. Our data show that the integrity of the N-terminal region and the first armadillo repeat are necessary and sufficient for high-affinity phosphorylation by CK1 of Ser-45. They also suggest that beta-catenin association with alpha-catenin and beta-catenin phosphorylation by CK1 at Ser-45 are mutually exclusive.
12 CFR 960.3 - Standby letters of credit on behalf of housing associates.

Code of Federal Regulations, 2010 CFR

2010-01-01

... AND OFF-BALANCE SHEET ITEMS STANDBY LETTERS OF CREDIT § 960.3 Standby letters of credit on behalf of... facilitating residential or commercial mortgage lending that benefits individuals or families meeting the...
12 CFR 960.2 - Standby letters of credit on behalf of members.

Code of Federal Regulations, 2010 CFR

2010-01-01

... OFF-BALANCE SHEET ITEMS STANDBY LETTERS OF CREDIT § 960.2 Standby letters of credit on behalf of... facilitating community lending; (3) To assist members with asset/liability management; or (4) To provide...
Beta-globin locus activation regions: conservation of organization, structure, and function.

PubMed Central

Li, Q L; Zhou, B; Powers, P; Enver, T; Stamatoyannopoulos, G

1990-01-01

The human beta-globin locus activation region (LAR) comprises four erythroid-specific DNase I hypersensitive sites (I-IV) thought to be largely responsible for activating the beta-globin domain and facilitating high-level erythroid-specific globin gene expression. We identified the goat beta-globin LAR, determined 10.2 kilobases of its sequence, and demonstrated its function in transgenic mice. The human and goat LARs share 6.5 kilobases of homologous sequences that are as highly conserved as the epsilon-globin gene promoters. Furthermore, the overall spatial organization of the two LARs has been conserved. These results suggest that the functionally relevant regions of the LAR are large and that in addition to their primary structure, the spatial relationship of the conserved elements is important for LAR function. Images PMID:2236034
ISEE observations of low frequency waves and ion distribution function evolution in the plasma sheet boundary layer

NASA Technical Reports Server (NTRS)

Elphic, R. C.; Gary, S. P.

1990-01-01

This paper describes ISEE plasma and magnetic fluctuation observations during two crossings of the plasma sheet boundary layer (PSBL) in the earth's magnetotail. Distribution function observations show that the counterstreaming ion components undergo pitch-angle scattering and evolve into a shell distribution in velocity space. This evolution is correlated with the development of low frequency, low amplitude magnetic fluctuations. However, the measured wave amplitudes are insufficient to accomplish the observed degree of ion pitch-angle scatttering locally; the near-earth distributions may be the result of processes occurring much farther down the magnetotail. Results show a clear correlation between the ion component beta and the relative streaming speed of the two components, suggesting that electromagnetic ion/ion instabilities do play an important role in the scattering of PSBL ions.
Nucleation Process of a Fibril Precursor in the C-Terminal Segment of Amyloid-β

NASA Astrophysics Data System (ADS)

Baftizadeh, Fahimeh; Pietrucci, Fabio; Biarnés, Xevi; Laio, Alessandro

2013-04-01

By extended atomistic simulations in explicit solvent and bias-exchange metadynamics, we study the aggregation process of 18 chains of the C-terminal segment of amyloid-β, an intrinsically disordered protein involved in Alzheimer’s disease and prone to form fibrils. Starting from a disordered aggregate, we are able to observe the formation of an ordered nucleus rich in beta sheets. The rate limiting step in the nucleation pathway involves crossing a barrier of approximately 40kcal/mol and is associated with the formation of a very specific interdigitation of the side chains belonging to different sheets. This structural pattern is different from the one observed experimentally in a microcrystal of the same system, indicating that the structure of a “nascent” fibril may differ from the one of an “extended” fibril.
Analysis of the specificity of sialyltransferases toward mucin core 2, globo, and related structures. identification of the sialylation sequence and the effects of sulfate, fucose, methyl, and fluoro substituents of the carbohydrate chain in the biosynthesis of selectin and siglec ligands, and novel sialylation by cloned alpha2,3(O)sialyltransferase.

PubMed

Chandrasekaran, E V; Xue, Jun; Xia, Jie; Chawda, Ram; Piskorz, Conrad; Locke, Robert D; Neelamegham, Sriram; Matta, Khushi L

2005-11-29

Sialic acids are key determinants in many carbohydrates involved in biological recognition. We studied the acceptor specificities of three cloned sialyltransferases (STs) [alpha2,3(N)ST, alpha2,3(O)ST, and alpha2,6(N)ST] and another alpha2,3(O)ST present in prostate cancer cell LNCaP toward mucin core 2 tetrasaccharide [Galbeta1,4GlcNAcbeta1,6(Galbeta1,3)GalNAcalpha-O-Bn] and Globo [Galbeta1,3GalNAcbeta1,3Galalpha-O-Me] structures containing sialyl, fucosyl, sulfo, methyl, or fluoro substituents by identifying the products by electrospray ionization tandem mass spectral analysis and other biochemical methods. The Globo precursor was an efficient acceptor for both alpha2,3(N)ST and alpha2,3(O)ST, whereas only alpha2,3(O)ST used its deoxy analogue (d-Fucbeta1,3GalNAcbeta1,3-Gal-alpha-O-Me); 2-O-MeGalbeta1,3GlcNAc and 4-OMeGalbeta1,4GlcNAc were specific acceptors for alpha2,3(N)ST. Other major findings of this study include: (i) alpha2,3 sialylation of beta1,3Gal in mucin core 2 can proceed even after alpha1,3 fucosylation of beta1,6-linked LacNAc. (ii) Sialylation of beta1,3Gal must precede the sialylation of beta1,4Gal for favorable biosynthesis of mucin core 2 compounds. (iii) alpha2,3 sialylation of the 6-O-sulfoLacNAc moiety in mucin core 2 (e.g., GlyCAM-1) is facilitated when beta1,3Gal has already been alpha2,3 sialylated. (iv) alpha2,6(N)ST was absolutely specific for the beta1,4Gal in mucin core 2. Either alpha1,3 fucosylation or 6-O-sulfation of the GlcNAc moiety reduced the activity. Sialylation of beta1,3Gal in addition to 6-O-sulfation of GlcNAc moiety abolished the activity. (v) Prior alpha2,3 sialylation or 3-O-sulfation of beta1,3Gal would not affect alpha2,6 sialylation of Galbeta1,4GlcNAc of mucin core 2. (vi) A 3- or 4-fluoro substituent in beta1,4Gal resulted in poor acceptors for the cloned alpha2,6(N)ST and alpha2,3(N)ST, whereas 4-fluoro- or 4-OMe-Galbeta1,3GalNAcalpha was a good acceptor for cloned alpha2,3(O)ST. (vii) 4-O-Methylation of beta1,4Gal abolished the acceptor ability toward alpha2,6(N)ST but increased the acceptor efficiency considerably toward alpha2,3(N)ST. (viii) Just like LNCaPalpha1,2-FT and Gal-3-O-sulfotransferase T2, the cloned alpha2,3(N)ST which modifies terminal Gal in Galbeta1,4GlcNAc also efficiently utilizes the terminal beta1,3Gal in the Globo backbone. Utilization of C-3 blocked compounds such as 3-O-sulfo-Galbeta1,3GalNAcbeta1,3Galalpha-OMe as acceptors by cloned alpha2,3(O)ST and analyses of the resulting products by lectin chromatography and mass spectrometry indicate that alpha2,3(O)ST is capable of attaching NeuAc to another position in C-3-substituted beta1,3Gal.
Object Recognition in Mental Representations: Directions for Exploring Diagnostic Features through Visual Mental Imagery.

PubMed

Roldan, Stephanie M

2017-01-01

One of the fundamental goals of object recognition research is to understand how a cognitive representation produced from the output of filtered and transformed sensory information facilitates efficient viewer behavior. Given that mental imagery strongly resembles perceptual processes in both cortical regions and subjective visual qualities, it is reasonable to question whether mental imagery facilitates cognition in a manner similar to that of perceptual viewing: via the detection and recognition of distinguishing features. Categorizing the feature content of mental imagery holds potential as a reverse pathway by which to identify the components of a visual stimulus which are most critical for the creation and retrieval of a visual representation. This review will examine the likelihood that the information represented in visual mental imagery reflects distinctive object features thought to facilitate efficient object categorization and recognition during perceptual viewing. If it is the case that these representational features resemble their sensory counterparts in both spatial and semantic qualities, they may well be accessible through mental imagery as evaluated through current investigative techniques. In this review, methods applied to mental imagery research and their findings are reviewed and evaluated for their efficiency in accessing internal representations, and implications for identifying diagnostic features are discussed. An argument is made for the benefits of combining mental imagery assessment methods with diagnostic feature research to advance the understanding of visual perceptive processes, with suggestions for avenues of future investigation.

Object Recognition in Mental Representations: Directions for Exploring Diagnostic Features through Visual Mental Imagery

PubMed Central

Roldan, Stephanie M.

2017-01-01

One of the fundamental goals of object recognition research is to understand how a cognitive representation produced from the output of filtered and transformed sensory information facilitates efficient viewer behavior. Given that mental imagery strongly resembles perceptual processes in both cortical regions and subjective visual qualities, it is reasonable to question whether mental imagery facilitates cognition in a manner similar to that of perceptual viewing: via the detection and recognition of distinguishing features. Categorizing the feature content of mental imagery holds potential as a reverse pathway by which to identify the components of a visual stimulus which are most critical for the creation and retrieval of a visual representation. This review will examine the likelihood that the information represented in visual mental imagery reflects distinctive object features thought to facilitate efficient object categorization and recognition during perceptual viewing. If it is the case that these representational features resemble their sensory counterparts in both spatial and semantic qualities, they may well be accessible through mental imagery as evaluated through current investigative techniques. In this review, methods applied to mental imagery research and their findings are reviewed and evaluated for their efficiency in accessing internal representations, and implications for identifying diagnostic features are discussed. An argument is made for the benefits of combining mental imagery assessment methods with diagnostic feature research to advance the understanding of visual perceptive processes, with suggestions for avenues of future investigation. PMID:28588538
A multistream model of visual word recognition.

PubMed

Allen, Philip A; Smith, Albert F; Lien, Mei-Ching; Kaut, Kevin P; Canfield, Angie

2009-02-01

Four experiments are reported that test a multistream model of visual word recognition, which associates letter-level and word-level processing channels with three known visual processing streams isolated in macaque monkeys: the magno-dominated (MD) stream, the interblob-dominated (ID) stream, and the blob-dominated (BD) stream (Van Essen & Anderson, 1995). We show that mixing the color of adjacent letters of words does not result in facilitation of response times or error rates when the spatial-frequency pattern of a whole word is familiar. However, facilitation does occur when the spatial-frequency pattern of a whole word is not familiar. This pattern of results is not due to different luminance levels across the different-colored stimuli and the background because isoluminant displays were used. Also, the mixed-case, mixed-hue facilitation occurred when different display distances were used (Experiments 2 and 3), so this suggests that image normalization can adjust independently of object size differences. Finally, we show that this effect persists in both spaced and unspaced conditions (Experiment 4)--suggesting that inappropriate letter grouping by hue cannot account for these results. These data support a model of visual word recognition in which lower spatial frequencies are processed first in the more rapid MD stream. The slower ID and BD streams may process some lower spatial frequency information in addition to processing higher spatial frequency information, but these channels tend to lose the processing race to recognition unless the letter string is unfamiliar to the MD stream--as with mixed-case presentation.
Curcumin-functionalized silk materials for enhancing adipogenic differentiation of bone marrow-derived human mesenchymal stem cells

PubMed Central

Li, Chunmei; Luo, Tingting; Zheng, Zhaozhu; Murphy, Amanda R.; Wang, Xiaoqin; Kaplan, David L.

2014-01-01

Curcumin, a natural phenolic compound derived from the plant Curcuma longa, was physically entrapped and stabilized in silk hydrogel films and its influence on human bone marrow-derived mesenchymal stem cells (hBMSCs) was assessed related to adipogenic differentiation. The presence of curcumin significantly reduced silk gelation time and changed the porous morphology of gel matrix, but did not change the formation of silk beta-sheet structure. Based on spectrofluorimetric analysis, curcumin likely interacted with hydrophobic residues in silk, interacting with the beta-sheet domains formed in the hydrogels. The antioxidant activity of silk film-associated curcumin remained functional over at least one month in both the dry and hydrated state. Negligible curcumin was released from silk hydrogel films over 48 hours incubation in aqueous solution. For hBMSCs cultured on silk films containing more than 0.25 mg/mL curcumin, cell proliferation was inhibited while adipogenesis was significantly promoted based on transcripts as well as oil red O staining. When hBMSCs were cultured in media containing free curcumin, both proliferation and adipogenesis of hBMSCs were inhibited when curcumin concentrations exceeded 5 μM, which is more than 1,000-times higher than the level of curcumin released from the films in aqueous solution. Thus, silk film-associated curcumin exhibited different effects on hBMSC proliferation and differentiation when compared to curcumin in solution. PMID:25132274
Mechanical response of silk crystalline units from force-distribution analysis.

PubMed

Xiao, Senbo; Stacklies, Wolfram; Cetinkaya, Murat; Markert, Bernd; Gräter, Frauke

2009-05-20

The outstanding mechanical toughness of silk fibers is thought to be caused by embedded crystalline units acting as cross links of silk proteins in the fiber. Here, we examine the robustness of these highly ordered beta-sheet structures by molecular dynamics simulations and finite element analysis. Structural parameters and stress-strain relationships of four different models, from spider and Bombyx mori silk peptides, in antiparallel and parallel arrangement, were determined and found to be in good agreement with x-ray diffraction data. Rupture forces exceed those of any previously examined globular protein many times over, with spider silk (poly-alanine) slightly outperforming Bombyx mori silk ((Gly-Ala)(n)). All-atom force distribution analysis reveals both intrasheet hydrogen-bonding and intersheet side-chain interactions to contribute to stability to similar extent. In combination with finite element analysis of simplified beta-sheet skeletons, we could ascribe the distinct force distribution pattern of the antiparallel and parallel silk crystalline units to the difference in hydrogen-bond geometry, featuring an in-line or zigzag arrangement, respectively. Hydrogen-bond strength was higher in antiparallel models, and ultimately resulted in higher stiffness of the crystal, compensating the effect of the mechanically disadvantageous in-line hydrogen-bond geometry. Atomistic and coarse-grained force distribution patterns can thus explain differences in mechanical response of silk crystals, opening up the road to predict full fiber mechanics.
Laccase of Cyathus bulleri: structural, catalytic characterization and expression in Escherichia coli.

PubMed

Salony; Garg, N; Baranwal, R; Chhabra, M; Mishra, S; Chaudhuri, T K; Bisaria, V S

2008-02-01

Cyathus bulleri, a ligninolytic fungus, produces a single laccase the internal peptides (3) of which bear similarity to laccases of several white rot fungi. Comparison of the total amino acid composition of this laccase with several fungal laccases indicated dissimilarity in the proportion of some basic and hydrophobic amino acids. Analysis of the circular dichroism spectrum of the protein indicated 37% alpha-helical, 26% beta-sheet and 38% random coil content which differed significantly from that in the solved structures of other laccases, which contain higher beta-sheet structures. The critical role of the carboxylic group containing amino acids was demonstrated by determining the kinetic parameters at different pH and this was confirmed by the observation that a critical Asp is strongly conserved in both Ascomycete and Basidiomycete laccases. The enzyme was denatured in the presence of a number of denaturing agents and refolded back to functional state with copper. In the folding experiments under alkaline conditions, zinc could replace copper in restoring 100% of laccase activity indicating the non-essential role of copper in this laccase. The laccase was expressed in Escherichia coli by a modification of the ligation-anchored PCR approach making it the first fungal laccase to be expressed in a bacterial host. The laccase sequence was confirmed by way of analysis of a 435 bp sequence of the insert.
A Library of the Nanoscale Self-Assembly of Amino Acids on Metal Surfaces

NASA Astrophysics Data System (ADS)

Iski, Erin; Yitamben, Esmeralda; Guisinger, Nathan

2012-02-01

The investigation of the hierarchical self-assembly of amino acids on surfaces represents a unique test-bed for the origin of enantio-favoritism in biology and the transmission of chirality from single molecules to complete surface layers. These chiral systems, in particular the assembly of isoleucine and alanine on Cu(111), represent a direct link to the understanding of certain biological processes, specifically the preference for some amino acids to form alpha helices vs. beta-pleated sheets in the secondary structure of proteins. Low temperature, ultra-high vacuum, scanning tunneling microscopy (LT UHV-STM) is used to study the hierarchical self-assembly of different amino acids on a Cu(111) single crystal in an effort to build a library of their two-dimensional structure with molecular-scale resolution for enhanced protein and peptide studies. Both enantiopure and racemic structures are studied in order to elucidate how chirality can affect the self-assembly of the amino acids. In some cases, density functional theory (DFT) models can be used to confirm the experimental structure. The advent of such a library with fully resolved, two-dimensional structures at different molecular coverages would address some of the complex questions surrounding the preferential formation of alpha helices vs. beta-pleated sheets in proteins and lead to a better understanding of the key role played by these amino acids in protein sequencing.
X-ray crystal structure of the passenger domain of plasmid encoded toxin(Pet), an autotransporter enterotoxin from enteroaggregative Escherichia coli (EAEC)

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

Domingo Meza-Aguilar, J.; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato Oncología e Investigación, Hospital Infantil de México Federico Gómez 06720, D.F.; Fromme, Petra

Highlights: • X-ray crystal structure of the passenger domain of Plasmid encoded toxin at 2.3 Å. • Structural differences between Pet passenger domain and EspP protein are described. • High flexibility of the C-terminal beta helix is structurally assigned. - Abstract: Autotransporters (ATs) represent a superfamily of proteins produced by a variety of pathogenic bacteria, which include the pathogenic groups of Escherichia coli (E. coli) associated with gastrointestinal and urinary tract infections. We present the first X-ray structure of the passenger domain from the Plasmid-encoded toxin (Pet) a 100 kDa protein at 2.3 Å resolution which is a cause ofmore » acute diarrhea in both developing and industrialized countries. Pet is a cytoskeleton-altering toxin that induces loss of actin stress fibers. While Pet (pdb code: 4OM9) shows only a sequence identity of 50% compared to the closest related protein sequence, extracellular serine protease plasmid (EspP) the structural features of both proteins are conserved. A closer structural look reveals that Pet contains a β-pleaded sheet at the sequence region of residues 181–190, the corresponding structural domain in EspP consists of a coiled loop. Secondary, the Pet passenger domain features a more pronounced beta sheet between residues 135 and 143 compared to the structure of EspP.« less
Amyloidosis

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

Glenner, G.G.; Osserman, E.F.

1986-01-01

The subjects covered in this Symposium range through almost every clinical medical specialty. From an average of one paper in each of the past three Symposiums, the explosive interest in cerebral amyloidosis has led to the presentation of 12 papers on this subject in the present volume. The genetically predisposed familial amyloidotic processes, such as the polyneuropathies and familial Mediterranean fever have also stimulated extensive and intriguing investigations which have revealed the striking effect of a single amino acid substitution in transforming a normal protein into a lethal ''amyloidogenic'' one. This Symposium clearly depicts the advances since the first amyloidmore » fibril protein was definitively identified and defined 14 years ago. Since all amyloid fibril proteins so far described are variants of normal proteins, attention to gene abnormalities now becomes a significant focus as well as the pathogenic sequences which lead in these cases to twisted BETA-pleated sheet (amyloid) fibril formation. Tentative concepts such as the ''amyloidogenic protein precursor of the fibril,'' ''proteolysis as one mechanism of fibril formation,'' ''Congo red birefringence as a marker for the twisted BETA-pleated sheet protein'' are now substantiated by recurring confirmation. Even a prophylactic treatment for one of the amyloidotic conditions, familial Mediterranean fever, is now available. Predictably, as the pathogeneses of the amyloid diseases are individually deciphered, highly specific and directed therapies will evolve to treat their devastated victims.« less
The Properties of Reconnection Current Sheets in GRMHD Simulations of Radiatively Inefficient Accretion Flows

NASA Astrophysics Data System (ADS)

Ball, David; Özel, Feryal; Psaltis, Dimitrios; Chan, Chi-Kwan; Sironi, Lorenzo

2018-02-01

Non-ideal magnetohydrodynamic (MHD) effects may play a significant role in determining the dynamics, thermal properties, and observational signatures of radiatively inefficient accretion flows onto black holes. In particular, particle acceleration during magnetic reconnection events may influence black hole spectra and flaring properties. We use representative general relativistic magnetohydrodynamic (GRMHD) simulations of black hole accretion flows to identify and explore the structures and properties of current sheets as potential sites of magnetic reconnection. In the case of standard and normal evolution (SANE) disks, we find that in the reconnection sites, the plasma beta ranges from 0.1 to 1000, the magnetization ranges from 10‑4 to 1, and the guide fields are weak compared with the reconnecting fields. In magnetically arrested (MAD) disks, we find typical values for plasma beta from 10‑2 to 103, magnetizations from 10‑3 to 10, and typically stronger guide fields, with strengths comparable to or greater than the reconnecting fields. These are critical parameters that govern the electron energy distribution resulting from magnetic reconnection and can be used in the context of plasma simulations to provide microphysics inputs to global simulations. We also find that ample magnetic energy is available in the reconnection regions to power the fluence of bright X-ray flares observed from the black hole in the center of the Milky Way.
Elastic deformation and failure in protein filament bundles: Atomistic simulations and coarse-grained modeling.

PubMed

Hammond, Nathan A; Kamm, Roger D

2008-07-01

The synthetic peptide RAD16-II has shown promise in tissue engineering and drug delivery. It has been studied as a vehicle for cell delivery and controlled release of IGF-1 to repair infarcted cardiac tissue, and as a scaffold to promote capillary formation for an in vitro model of angiogenesis. The structure of RAD16-II is hierarchical, with monomers forming long beta-sheets that pair together to form filaments; filaments form bundles approximately 30-60 nm in diameter; branching networks of filament bundles form macroscopic gels. We investigate the mechanics of shearing between the two beta-sheets constituting one filament, and between cohered filaments of RAD16-II. This shear loading is found in filament bundle bending or in tensile loading of fibers composed of partial-length filaments. Molecular dynamics simulations show that time to failure is a stochastic function of applied shear stress, and that for a given loading time behavior is elastic for sufficiently small shear loads. We propose a coarse-grained model based on Langevin dynamics that matches molecular dynamics results and facilities extending simulations in space and time. The model treats a filament as an elastic string of particles, each having potential energy that is a periodic function of its position relative to the neighboring filament. With insight from these simulations, we discuss strategies for strengthening RAD16-II and similar materials.
Local sequence information in cellular retinoic acid-binding protein I: specific residue roles in beta-turns.

PubMed

Rotondi, Kenneth S; Gierasch, Lila M

2003-01-01

We have recently shown that two of the beta-turns (III and IV) in the ten-stranded, beta-clam protein, cellular retinoic acid-binding protein I (CRABP I), are favored in short peptide fragments, arguing that they are encoded by local interactions (K. S. Rotondi and L. M. Gierasch, Biochemistry, 2003, Vol. 42, pp. 7976-7985). In this paper we examine these turns in greater detail to dissect the specific local interactions responsible for their observed native conformational biases. Conformations of peptides corresponding to the turn III and IV fragments were examined under conditions designed to selectively disrupt stabilizing interactions, using pH variation, chaotrope addition, or mutagenesis to probe specific side-chain influences. We find that steric constraints imposed by excluded volume effects between near neighbor residues (i,i+2), favorable polar (i,i+2) interactions, and steric permissiveness of glycines are the principal factors accounting for the observed native bias in these turns. Longer-range stabilizing interactions across the beta-turns do not appear to play a significant role in turn stability in these short peptides, in contrast to their importance in hairpins. Additionally, our data add to a growing number of examples of the 3:5 type I turn with a beta-bulge as a class of turns with high propensity to form locally defined structure. Current work is directed at the interplay between the local sequence information in the turns and more long-range influences in the mechanism of folding of this predominantly beta-sheet protein. Copyright 2004 Wiley Periodicals, Inc.
Galectin-1 suppresses alpha2(I) collagen through Smad3 in renal epithelial cells.

PubMed

Okano, K; Uchida, K; Nitta, K; Hayashida, T

2008-10-01

Transforming growth factor (TGF-beta1) promotes renal fibrogenesis through activation of Smads. Galectin-1 is reported to prevent experimental glomerulonephritis. Here we investigated the fact that transfected galectin-1 significantly suppressed the transcription of alpha2(I) collagen (COL1A2) in TGF-beta1- activated human renal epithelial cells. Conversely, galectin-1 silencing RNA reduced secretion of type I collagen by HKC cells. Galectin-1 significantly decreased activation of a TGF-beta1-responsive reporter construct and of a minimal reporter construct that contains four repeats of the Smad binding element (SBE). Galectin-1 had no effect on phosphorylation of Smad3 at the linker region and C-terminus, whereas it decreased affinity of Smad3 to the SBE. Additionally, the inhibitory effect of galectin-1 disappeared using a mutated reporter construct, 376 m-LUC, in which a potential Smad recognition site within the promoter is mutated. Taken together, the results suggest that galectin-1 decreases Smad3-complex from binding to the SBE, down-regulating transcription of COL1A2 in TGF-beta1-stimulated renal epithelial cells.
Purification, crystallization and preliminary X-ray diffraction analysis of the human mismatch repair protein MutS[beta

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

Tseng, Quincy; Orans, Jillian; Hast, Michael A.

2012-03-16

MutS{beta} is a eukaryotic mismatch repair protein that preferentially targets extrahelical unpaired nucleotides and shares partial functional redundancy with MutS{alpha} (MSH2-MSH6). Although mismatch recognition by MutS{alpha} has been shown to involve a conserved Phe-X-Glu motif, little is known about the lesion-binding mechanism of MutS{beta}. Combined MSH3/MSH6 deficiency triggers a strong predisposition to cancer in mice and defects in msh2 and msh6 account for roughly half of hereditary nonpolyposis colorectal cancer mutations. These three MutS homologs are also believed to play a role in trinucleotide repeat instability, which is a hallmark of many neurodegenerative disorders. The baculovirus overexpression and purification ofmore » recombinant human MutS{beta} and three truncation mutants are presented here. Binding assays with heteroduplex DNA were carried out for biochemical characterization. Crystallization and preliminary X-ray diffraction analysis of the protein bound to a heteroduplex DNA substrate are also reported.« less
Energetic, Structural, and Antimicrobial Analyses of [beta]-Lactam Side Chain Recognition by [beta]-Lactamases

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

Caselli, E.; Powers, R.A.; Blaszczak, L.C.

2010-03-05

Penicillins and cephalosporins are among the most widely used and successful antibiotics. The emergence of resistance to these {beta}-lactams, most often through bacterial expression of {beta}-lactamases, threatens public health. To understand how {beta}-lactamases recognize their substrates, it would be helpful to know their binding energies. Unfortunately, these have been difficult to measure because {beta}-lactams form covalent adducts with {beta}-lactamases. This has complicated functional analyses and inhibitor design. To investigate the contribution to interaction energy of the key amide (R1) side chain of {beta}-lactam antibiotics, eight acylglycineboronic acids that bear the side chains of characteristic penicillins and cephalosporins, as well asmore » four other analogs, were synthesized. These transition-state analogs form reversible adducts with serine {beta}-lactamases. Therefore, binding energies can be calculated directly from K{sub i} values. The K{sub i} values measured span four orders of magnitude against the Group I {beta}-lactamase AmpC and three orders of magnitude against the Group II {beta}-lactamase TEM-1. The acylglycineboronic acids have K{sub i} values as low as 20 nM against AmpC and as low as 390 nM against TEM-1. The inhibitors showed little activity against serine proteases, such as chymotrypsin. R1 side chains characteristic of {beta}-lactam inhibitors did not have better affinity for AmpC than did side chains characteristic of {beta}-lactam substrates. Two of the inhibitors reversed the resistance of pathogenic bacteria to {beta}-lactams in cell culture. Structures of two inhibitors in their complexes with AmpC were determined by X-ray crystallography to 1.90 {angstrom} and 1.75 {angstrom} resolution; these structures suggest interactions that are important to the affinity of the inhibitors. Acylglycineboronic acids allow us to begin to dissect interaction energies between {beta}-lactam side chains and {beta}-lactamases. Surprisingly, there is little correlation between the affinity contributed by R1 side chains and their occurrence in {beta}-lactam inhibitors or {beta}-lactam substrates of serine {beta}-lactamases. Nevertheless, presented in acylglycineboronic acids, these side chains can lead to inhibitors with high affinities and specificities. The structures of their complexes with AmpC give a molecular context to their affinities and may guide the design of anti-resistance compounds in this series.« less
Regulation of GM-CSF-induced dendritic cell development by TGF-beta1 and co-developing macrophages.

PubMed

Yamaguchi, Y

1998-01-01

Using a culture system of bone marrow progenitor cells with GM-CSF and TGF-beta1, a study was performed to analyze the effect of TGF-beta1 on the development of dendritic cells (DC) and to elucidate the regulatory role of macrophages co-developing with dendritic cells. The results demonstrate that DC generated in the presence of TGF-beta1 were immature with respect to the expression of CD86, nonspecific esterase activity and cell shape. Such inhibitory effects of TGF-beta1 were dependent on FcR+ macrophages, which were depleted by panning. TGF-beta1 did not appear to inhibit the commitment of progenitor cells to the DC lineage. In addition, TGF-beta1 also acted directly on the intermediate stage of DC to prevent their over-maturation, which results in a preferential decrease in MHC class II, but not in CD86, in the presence of TNF-alpha. FcR+ suppressive macrophages were also shown to facilitate DC maturation when stimulated via FcR-mediated signals even in the presence of TGF-beta1. These results indicate that TGF-beta1 indirectly and directly regulate the development of DC and that co-developing macrophages have a regulatory role in DC maturation.
Lactose carrier mutants of Escherichia coli with changes in sugar recognition (lactose versus melibiose).

PubMed

Varela, M F; Brooker, R J; Wilson, T H

1997-09-01

The purpose of this research was to identify amino acid residues that mediate substrate recognition in the lactose carrier of Escherichia coli. The lactose carrier transports the alpha-galactoside sugar melibiose as well as the beta-galactoside sugar lactose. Mutants from cells containing the lac genes on an F factor were selected by the ability to grow on succinate in the presence of the toxic galactoside beta-thio-o-nitrophenylgalactoside. Mutants that grew on melibiose minimal plates but failed to grow on lactose minimal plates were picked. In sugar transport assays, mutant cells showed the striking result of having low levels of lactose downhill transport but high levels of melibiose downhill transport. Accumulation (uphill) of melibiose was completely defective in all of the mutants. Kinetic analysis of melibiose transport in the mutants showed either no change or a greater than normal apparent affinity for melibiose. PCR was used to amplify the lacY DNA of each mutant, which was then sequenced by the Sanger method. The following six mutations were found in the lacY structural genes of individual mutants: Tyr-26-->Asp, Phe-27-->Tyr, Phe-29-->Leu, Asp-240-->Val, Leu-321-->Gln, and His-322-->Tyr. We conclude from these experiments that Tyr-26, Phe-27, Phe-29 (helix 1), Asp-240 (helix 7), Leu-321, and His-322 (helix 10) either directly or indirectly mediate sugar recognition in the lactose carrier of E. coli.
Effect of self-consistent magnetic field on plasma sheet penetration to the inner magnetosphere under enhanced convection: RCM simulations combined with force-balance magnetic field solver

NASA Astrophysics Data System (ADS)

Gkioulidou, M.; Wang, C.; Lyons, L. R.; Wolf, R. A.

2010-12-01

Transport of plasma sheet particles into the inner magnetosphere is strongly affected by the penetration of the convection electric field, which is the result of the large-scale magnetosphere-ionosphere electromagnetic coupling. This transport, on the other hand, results in plasma heating and magnetic field stretching, which become very significant in the inner plasma sheet (inside 20 RE). We have previously run simulations with the Rice Convection Model (RCM) to investigate how the earthward penetration of convection electric field, and therefore plasma sheet population, depends on plasma sheet boundary conditions. Outer boundary conditions at r ~20 RE are a function of MLT and interplanetary conditions based on 11 years of Geotail data. In the previous simulations, Tsyganenko 96 magnetic field model (T96) was used so force balance between plasma pressure and magnetic fields was not maintained. We have now integrated the RCM with a magnetic field solver (Liu et al., 2006) to obtain the required force balance in the equatorial plane. We have run the self-consistent simulations under enhanced convection with different boundary conditions in which we kept different parameters (flux tube particle content, plasma pressure, plasma beta, or magnetic fields) at the outer boundary to be MLT-dependent but time independent. Different boundary conditions result in qualitatively similar plasma sheet profiles. The results show that magnetic field has a dawn dusk asymmetry with field lines being more stretched in the pre-midnight sector, due to relatively higher plasma pressure there. The asymmetry in the magnetic fields in turn affects the radial distance and MLT of plasma sheet penetration into the inner magnetosphere. In comparison with results using the T96, plasma transport under self-consistent magnetic field results in proton and electron plasma sheet inner edges that are located in higher latitudes, weaker pressure gradients, and more efficient shielding of the near-Earth convection electric field (since auroral conductance is also confined to higher latitudes). We are currently evaluating the simulated plasma sheet properties by comparing them with statistical results obtained from Geotail and THEMIS observations.
How Do Professional Mutual Recognition Agreements Affect Higher Education? Examining Regional Policy in North America

ERIC Educational Resources Information Center

Sa, Creso; Gaviria, Patricia

2011-01-01

Professional mutual recognition agreements (MRAs) are one of the policy instruments employed in global and regional trade agreements to facilitate the mobility of skilled labour. While such agreements have been noted in the literature examining cross-border academic mobility, little is known about how they impact higher education. This paper…
Movement Contributes to Infants' Recognition of the Human Form

ERIC Educational Resources Information Center

Christie, Tamara; Slaughter, Virginia

2010-01-01

Three experiments demonstrate that biological movement facilitates young infants' recognition of the whole human form. A body discrimination task was used in which 6-, 9-, and 12-month-old infants were habituated to typical human bodies and then shown scrambled human bodies at the test. Recovery of interest to the scrambled bodies was observed in…
Emotion Recognition in Children with Down Syndrome: Influence of Emotion Label and Expression Intensity

ERIC Educational Resources Information Center

Cebula, Katie R.; Wishart, Jennifer G.; Willis, Diane S.; Pitcairn, Tom K.

2017-01-01

Some children with Down syndrome may experience difficulties in recognizing facial emotions, particularly fear, but it is not clear why, nor how such skills can best be facilitated. Using a photo-matching task, emotion recognition was tested in children with Down syndrome, children with nonspecific intellectual disability and cognitively matched,…

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