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

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

Lu, Q.; Hu, X; Wang, X

Water-insoluble regenerated silk materials are normally produced by increasing the {beta}-sheet content (silk II). In the present study water-insoluble silk films were prepared by controlling the very slow drying of Bombyx mori silk solutions, resulting in the formation of stable films with a predominant silk I instead of silk II structure. Wide angle X-ray scattering indicated that the silk films stabilized by slow drying were mainly composed of silk I rather than silk II, while water- and methanol-annealed silk films had a higher silk II content. The silk films prepared by slow drying had a globule-like structure at the coremore » surrounded by nano-filaments. The core region was composed of silk I and silk II, surrounded by hydrophilic nano-filaments containing random turns and {alpha}-helix secondary structures. The insoluble silk films prepared by slow drying had unique thermal, mechanical and degradative properties. Differential scanning calorimetry results revealed that silk I crystals had stable thermal properties up to 250 C, without crystallization above the T{sub g}, but degraded at lower temperatures than silk II structure. Compared with water- and methanol-annealed films the films prepared by slow drying had better mechanical ductility and were more rapidly enzymatically degraded, reflecting the differences in secondary structure achieved via differences in post processing of the cast silk films. Importantly, the silk I structure, a key intermediate secondary structure for the formation of mechanically robust natural silk fibers, was successfully generated by the present approach of very slow drying, mimicking the natural process. The results also point to a new mode of generating new types of silk biomaterials with enhanced mechanical properties and increased degradation rates, while maintaining water insolubility, along with a low {beta}-sheet content.« less

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.

The human fatty acid-binding protein family: Evolutionary divergences and functions

PubMed Central

2011-01-01

Fatty acid-binding proteins (FABPs) are members of the intracellular lipid-binding protein (iLBP) family and are involved in reversibly binding intracellular hydrophobic ligands and trafficking them throughout cellular compartments, including the peroxisomes, mitochondria, endoplasmic reticulum and nucleus. FABPs are small, structurally conserved cytosolic proteins consisting of a water-filled, interior-binding pocket surrounded by ten anti-parallel beta sheets, forming a beta barrel. At the superior surface, two alpha-helices cap the pocket and are thought to regulate binding. FABPs have broad specificity, including the ability to bind long-chain (C16-C20) fatty acids, eicosanoids, bile salts and peroxisome proliferators. FABPs demonstrate strong evolutionary conservation and are present in a spectrum of species including Drosophila melanogaster, Caenorhabditis elegans, mouse and human. The human genome consists of nine putatively functional protein-coding FABP genes. The most recently identified family member, FABP12, has been less studied. PMID:21504868

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.

Geometry of thin liquid sheet flows

NASA Technical Reports Server (NTRS)

Chubb, Donald L.; Calfo, Frederick D.; Mcconley, Marc W.; Mcmaster, Matthew S.; Afjeh, Abdollah A.

1994-01-01

Incompresible, thin sheet flows have been of research interest for many years. Those studies were mainly concerned with the stability of the flow in a surrounding gas. Squire was the first to carry out a linear, invicid stability analysis of sheet flow in air and compare the results with experiment. Dombrowski and Fraser did an experimental study of the disintegration of sheet flows using several viscous liquids. They also detected the formulation of holes in their sheet flows. Hagerty and Shea carried out an inviscid stability analysis and calculated growth rates with experimental values. They compared their calculated growth rates with experimental values. Taylor studied extensively the stability of thin liquid sheets both theoretically and experimentally. He showed that thin sheets in a vacuum are stable. Brown experimentally investigated thin liquid sheet flows as a method of application of thin films. Clark and Dumbrowski carried out second-order stability analysis for invicid sheet flows. Lin introduced viscosity into the linear stability analysis of thin sheet flows in a vacuum. Mansour and Chigier conducted an experimental study of the breakup of a sheet flow surrounded by high-speed air. Lin et al. did a linear stability analysis that included viscosity and a surrounding gas. Rangel and Sirignano carried out both a linear and nonlinear invisid stability analysis that applies for any density ratio between the sheet liquid and the surrounding gas. Now there is renewed interest in sheet flows because of their possible application as low mass radiating surfaces. The objective of this study is to investigate the fluid dynamics of sheet flows that are of interest for a space radiator system. Analytical expressions that govern the sheet geometry are compared with experimental results. Since a space radiator will operate in a vacuum, the analysis does not include any drag force on the sheet flow.

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.

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.

Electrochemical cell

DOEpatents

Redey, Laszlo I.; Myles, Kevin M.; Vissers, Donald R.; Prakash, Jai

1996-01-01

An electrochemical cell with a positive electrode having an electrochemically active layer of at least one transition metal chloride. A negative electrode of an alkali metal and a compatible electrolyte including an alkali metal salt molten at cell operating temperature is included in the cell. The electrolyte is present at least partially as a corrugated .beta." alumina tube surrounding the negative electrode interior to the positive electrode. The ratio of the volume of liquid electrolyte to the volume of the positive electrode is in the range of from about 0.1 to about 3. A plurality of stacked electrochemical cells is disclosed each having a positive electrode, a negative electrode of an alkali metal molten at cell operating temperature, and a compatible electrolyte. The electrolyte is at least partially present as a corrugated .beta." alumina sheet separating the negative electrode and interior to the positive electrodes. The alkali metal is retained in a porous electrically conductive ceramic, and seals for sealing the junctures of the electrolyte and the adjacent electrodes at the peripheries thereof.

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.

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.

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.

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

Electrochemical cell

DOEpatents

Redey, L.I.; Myles, K.M.; Vissers, D.R.; Prakash, J.

1996-07-02

An electrochemical cell is described with a positive electrode having an electrochemically active layer of at least one transition metal chloride. A negative electrode of an alkali metal and a compatible electrolyte including an alkali metal salt molten at cell operating temperature is included in the cell. The electrolyte is present at least partially as a corrugated {beta}{double_prime} alumina tube surrounding the negative electrode interior to the positive electrode. The ratio of the volume of liquid electrolyte to the volume of the positive electrode is in the range of from about 0.1 to about 3. A plurality of stacked electrochemical cells is disclosed each having a positive electrode, a negative electrode of an alkali metal molten at cell operating temperature, and a compatible electrolyte. The electrolyte is at least partially present as a corrugated {beta}{double_prime} alumina sheet separating the negative electrode and interior to the positive electrodes. The alkali metal is retained in a porous electrically conductive ceramic, and seals for sealing the junctures of the electrolyte and the adjacent electrodes at the peripheries thereof. 8 figs.

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.

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.

Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level.

PubMed

Brunak, S; Engelbrecht, J

1996-06-01

A direct comparison of experimentally determined protein structures and their corresponding protein coding mRNA sequences has been performed. We examine whether real world data support the hypothesis that clusters of rare codons correlate with the location of structural units in the resulting protein. The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate of the ribosome, and may thus in vivo have a catalyzing effect on the folding of the polypeptide chain. A complete search for GenBank nucleotide sequences coding for structural entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, amino acid sequence, and secondary structure assignment. By neural network analysis, we found strong signals in mRNA sequence regions surrounding helices and sheets. These signals do not originate from the clustering of rare codons, but from the similarity of codons coding for very abundant amino acid residues at the N- and C-termini of helices and sheets. No correlation between the positioning of rare codons and the location of structural units was found. The mRNA signals were also compared with conserved nucleotide features of 16S-like ribosomal RNA sequences and related to mechanisms for maintaining the correct reading frame by the ribosome.

Cooling arrangement for a superconducting coil

DOEpatents

Herd, K.G.; Laskaris, E.T.

1998-06-30

A superconducting device is disclosed, such as a superconducting rotor for a generator or motor. A vacuum enclosure has an interior wall surrounding a cavity containing a vacuum. A superconductive coil is placed in the cavity. A generally-annularly-arranged, thermally-conductive sheet has an inward-facing surface contacting generally the entire outward-facing surface of the superconductive coil. A generally-annularly-arranged coolant tube contains a cryogenic fluid and contacts a generally-circumferential portion of the outward-facing surface of the sheet. A generally-annularly-arranged, thermally-insulative coil overwrap generally circumferentially surrounds the sheet. The coolant tube and the inward-facing surface of the coil overwrap together contact generally the entire outward-facing surface of the sheet. 3 figs.

Cartilage repair using mesenchymal stem cell (MSC) sheet and MSCs-loaded bilayer PLGA scaffold in a rabbit model.

PubMed

Qi, Yiying; Du, Yi; Li, Weixu; Dai, Xuesong; Zhao, Tengfei; Yan, Weiqi

2014-06-01

The integration of regenerated cartilage with surrounding native cartilage is a major challenge for the success of cartilage tissue-engineering strategies. The purpose of this study is to investigate whether incorporation of the power of mesenchymal stem cell (MSC) sheet to MSCs-loaded bilayer poly-(lactic-co-glycolic acid) (PLGA) scaffolds can improve the integration and repair of cartilage defects in a rabbit model. Rabbit bone marrow-derived MSCs were cultured and formed cell sheet. Full-thickness cylindrical osteochondral defects (4 mm in diameter, 3 mm in depth) were created in the patellar groove of 18 New Zealand white rabbits and the osteochondral defects were treated with PLGA scaffold (n = 6), PLGA/MSCs (n = 6) or MSC sheet-encapsulated PLGA/MSCs (n = 6). After 6 and 12 weeks, the integration and tissue response were evaluated histologically. The MSC sheet-encapsulated PLGA/MCSs group showed significantly more amounts of hyaline cartilage and higher histological scores than PLGA/MSCs group and PLGA group (P < 0.05). In addition, the MSC sheet-encapsulated PLGA/MCSs group showed the best integration between the repaired cartilage and surrounding normal cartilage and subchondral bone compared to other two groups. The novel method of incorporation of MSC sheet to PLGA/MCSs could enhance the ability of cartilage regeneration and integration between repair cartilage and the surrounding cartilage. Transplantation of autologous MSC sheet combined with traditional strategies or cartilage debris might provide therapeutic opportunities for improving cartilage regeneration and integration in humans.

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…

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

Effect of double-tailed surfactant architecture on the conformation, self-assembly, and processing in polypeptide-surfactant complexes.

PubMed

Junnila, Susanna; Hanski, Sirkku; Oakley, Richard J; Nummelin, Sami; Ruokolainen, Janne; Faul, Charl F J; Ikkala, Olli

2009-10-12

This work describes the solid-state conformational and structural properties of self-assembled polypeptide-surfactant complexes with double-tailed surfactants. Poly(L-lysine) was complexed with three dialkyl esters of phosphoric acid (i.e., phosphodiester surfactants), where the surfactant tail branching and length was varied to tune the supramolecular architecture in a facile way. After complexation with the branched surfactant bis(2-ethylhexyl) phosphate in an aqueous solution, the polypeptide chains adopted an alpha-helical conformation. These rod-like helices self-assembled into cylindrical phases with the amorphous alkyl tails pointing outward. In complexes with dioctyl phosphate and didodecyl phosphate, which have two linear n-octyl or n-dodecyl tails, respectively, the polypeptide formed antiparallel beta-sheets separated by alkyl layers, resulting in well-ordered lamellar self-assemblies. By heating, it was possible to trigger a partial opening of the beta-sheets and disruption of the lamellar phase. After repeated heating/cooling, all of these complexes also showed a glass transition between 37 and 50 degrees C. Organic solvent treatment and plasticization by overstoichiometric amount of surfactant led to structure modification in poly(L-lysine)-dioctyl phosphate complexes, PLL(diC8)(x) (x = 1.0-3.0). Here, the alpha-helical PLL is surrounded by the surfactants and these bottle-brush-like chains self-assemble in a hexagonal cylindrical morphology. As x is increased, the materials are clearly plasticized and the degree of ordering is improved: The stiff alpha-helical backbones in a softened surfactant matrix give rise to thermotropic liquid-crystalline phases. The complexes were examined by Fourier transform infrared spectroscopy, small- and wide-angle X-ray scattering, transmission electron microscopy, differential scanning calorimetry, polarized optical microscopy, and circular dichroism.

Dynamics of a radially expanding liquid sheet: Experiments

NASA Astrophysics Data System (ADS)

Majumdar, Nayanika; Tirumkudulu, Mahesh

2017-11-01

A recent theory predicts that sinuous waves generated at the center of a radially expanding liquid sheet grow spatially even in absence of a surrounding gas phase. Unlike flat liquid sheets, the thickness of a radially expanding liquid sheet varies inversely with distance from the center of the sheet. To test the predictions of the theory, experiments were carried out on a horizontal, radially expanding liquid sheet formed by collision of a single jet on a solid impactor. The latter was placed on a speaker-vibrator with controlled amplitude and frequency. The growth of sinuous waves was determined by measuring the wave surface inclination angle using reflected laser light under both atmospheric and sub-atmospheric pressure conditions. It is shown that the measured growth rate matches with the predictions of the theory over a large range of Weber numbers for both pressure conditions suggesting that the thinning of the liquid sheet plays a dominant role in setting the growth rate of sinuous waves with minimal influence of the surrounding gas phase on its dynamics. IIT Bombay.

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.

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.

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.

Conformational change of cytochrome P450 1A2 induced by phospholipids and detergents.

PubMed

Yun, C H; Song, M; Kim, H

1997-08-08

Recently, it was reported that the activity of rabbit P450 1A2 is markedly increased at elevated salt concentration (Yun, C-H., Song, M., Ahn, T., and Kim, H. (1996) J. Biol. Chem. 271, 31312-31316). The activity increase of P450 1A2 coincides with the raised alpha-helix content and decreased beta-sheet content. The presence of phospholipid magnified this effect. Here, possible structural change of rabbit P450 1A2 accompanying the phospholipid-induced increase in its enzyme activity was investigated by circular dichroism, fluorescence spectroscopy, and absorption spectroscopy. Studies with the reconstituted system supported by cumene hydroperoxide or NADPH showed that the P450 1A2 activities were found to be dependent on the head group and hydrocarbon chain length of phospholipid. Phosphatidylcholines having short hydrocarbon chains with a carbon number of 8-12 were very efficient for reconstitution of the P450-catalyzed reactions supported by both cumene hydroperoxide and NADPH. It was found that the phospholipid increased the alpha-helix content and lowered the beta-sheet content of P450. Intrinsic fluorescence intensity is also increased in the presence of phospholipid. The low spin iron configuration of P450 1A2 shifted toward the high spin configuration by most of the phospholipids in the endoplasmic reticulum. Some synthetic phospholipids having short hydrocarbon chains with a carbon number of 10-12 caused a shift in the spin equilibrium of P450 1A2 toward low spin. The effect of detergents on the activity and conformation of P450 1A2 was also studied. It was found that the addition of detergents to P450 1A2 solution increased the enzyme activity of P450 1A2. Detergents also increased the alpha-helix content and lowered the beta-sheet content of P450 1A2. Intrinsic fluorescence emissions also increased with the presence of detergents. Octyl glucoside and deoxycholate caused a shift toward high spin. On the other hand, cholate caused a shift toward low spin. It was found that the activity increase of rabbit P450 1A2 coincides with the conformational change including raised alpha-helix content. It is proposed that the interaction with the phospholipid molecules surrounding P450 1A2 in the endoplasmic reticulum is important for a functional conformation of P450 1A2 in a monooxygenase system including NADPH-P450 reductase.

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

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.

Tie-fibre structure and organization in the knee menisci

PubMed Central

Andrews, Stephen H J; Rattner, Jerome B; Abusara, Ziad; Adesida, Adetola; Shrive, Nigel G; Ronsky, Janet L

2014-01-01

The collagenous structure of the knee menisci is integral to the mechanical integrity of the tissue and the knee joint. The tie-fibre structure of the tissue has largely been neglected, despite previous studies demonstrating its correlation with radial stiffness. This study has evaluated the structure of the tie-fibres of bovine menisci using 2D and 3D microscopy techniques. Standard collagen and proteoglycan (PG) staining and 2D light microscopy techniques were conducted. For the first time, the collagenous structure of the menisci was evaluated using 3D, second harmonic generation (SHG) microscopy. This technique facilitated the imaging of collagen structure in thick sections (50–100 μm). Imaging identified that tie-fibres of the menisci arborize from the outer margin of the meniscus toward the inner tip. This arborization is associated with the structural arrangement of the circumferential fibres. SHG microscopy has definitively demonstrated the 3D organization of tie-fibres in both sheets and bundles. The hierarchy of the structure is related to the organization of circumferential fascicles. Large tie-fibre sheets bifurcate into smaller sheets to surround circumferential fascicles of decreasing size. The tie-fibres emanate from the lamellar layer that appears to surround the entire meniscus. At the tibial and femoral surfaces these tie-fibre sheets branch perpendicularly into the meniscal body. The relationship between tie-fibres and blood vessels in the menisci was also observed in this study. Tie-fibre sheets surround the blood vessels and an associated PG-rich region. This subunit of the menisci has not previously been described. The size of tie-fibre sheets surrounding the vessels appeared to be associated with the size of blood vessel. These structural findings have implications in understanding the mechanics of the menisci. Further, refinement of the complex structure of the tie-fibres is important in understanding the consequences of injury and disease in the menisci. The framework of meniscus architecture also defines benchmarks for the development of tissue-engineered replacements in the future. PMID:24617800

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

Linear instabilities of a planar liquid sheet in a static electric field for intermediate relaxation and convection of surface charges

NASA Astrophysics Data System (ADS)

Yoshinaga, Takao

2018-04-01

Linear temporal instabilities of a two-dimensional planar liquid sheet in a static electric field are investigated when the relaxation and convection of surface electric charges are considered. Both viscous sheet liquid and inviscid surrounding liquid are placed between two parallel sheath walls, on which an external electric field is imposed. In particular, effects of the electric Peclet number {Pe} (charge relaxation time/convection time) and the electric Euler number Λ (electric pressure/liquid inertial) on the instabilities are emphasized for the symmetric and antisymmetric deformations of the sheet. It is found that the unstable mode is composed of the aerodynamic and electric modes, which are merged with each other for the symmetric deformation and separated for the antisymmetric deformation. For the symmetric deformation, the combined mode is more destabilized with the decrease of {Pe} and the increase of Λ. On the other hand, for the antisymmetric deformation, the electric mode is more destabilized and the aerodynamic mode is left unchanged with the decrease of {Pe}, while the electric mode is more destabilized but the aerodynamic mode is more stabilized with the increase of Λ. It is also found for both symmetric and antisymmetric deformations that the instabilities are most suppressed when {σ }R≃ 1/{ε }P ({σ }R: conductivity ratio of the surrounding to the sheet liquid, {ε }P: permittivity ratio of the sheet to the surrounding liquid), whose trend of the instabilities is more enhanced with the decrease of {Pe} except for vanishingly small {Pe}.

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.

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.

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.

Facts for Families from the American Academy of Child and Adolescent Psychiatry [1989].

ERIC Educational Resources Information Center

American Academy of Child and Adolescent Psychiatry, Washington, DC.

Six fact sheets on issues relevant to children's emotional well being are presented in this document. The first fact sheet, "Children and Divorce" provides information for parents to consider when getting a divorce. Parents are encouraged to be aware of the stress that the events surrounding a divorce cause for the child. The second fact sheet,…

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.

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.

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.

Linear Tidal Vestige Found in the WM Sheet

NASA Astrophysics Data System (ADS)

Lee, Jounghun; Kim, Suk; Rey, Soo-Chang

2018-06-01

We present a vestige of the linear tidal influence on the spin orientations of the constituent galaxies of the WM sheet discovered in the vicinity of the Virgo Cluster and the Local Void. The WM sheet is chosen as an optimal target since it has a rectangular parallelepiped-like shape whose three sides are in parallel with the supergalactic Cartesian axes. Determining three probability density functions of the absolute values of the supergalactic Cartesian components of the spin vectors of the WM sheet galaxies, we investigate their alignments with the principal directions of the surrounding large-scale tidal field. When the WM sheet galaxies located in the central region within the distance of 2 h ‑1 Mpc are excluded, the spin vectors of the remaining WM sheet galaxies are found to be weakly aligned, strongly aligned, and strongly anti-aligned with the minor, intermediate, and major principal directions of the surrounding large-scale tidal field, respectively. To examine whether or not the origin of the observed alignment tendency from the WM sheet is the linear tidal effect, we infer the eigenvalues of the linear tidal tensor from the axial ratios of the WM sheet with the help of the Zeldovich approximation and conduct a full analytic evaluation of the prediction of the linear tidal torque model for the three probability density functions. A detailed comparison between the analytical and the observational results reveals a good quantitative agreement not only in the behaviors but also in the amplitudes of the three probability density functions.

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

Microfabricated Multianalyte Sensor Arrays for Metabolic Monitoring

DTIC Science & Technology

2006-09-01

aqueous in vivo-like surrounding15-18 to entrap both the redox polymer and glucose oxidase on polyimide sheets. We have used biocompatible PEG-DA hydrogel...arrays were fabricated on gold electrodes on flexible polyimide sheets by cross-linking glucose oxidase and redox polymer using UV-initiated free...cyclic voltammetry. We have fabricated an array of glucose sensors on flexible polyimide sheets that exhibit the desired linear response in the

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.

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

FUEL-BREEDER FUEL ELEMENT FOR NUCLEAR REACTOR

DOEpatents

Abbott, W.E.; Balent, R.

1958-09-16

A fuel element design to facilitate breeding reactor fuel is described. The fuel element is comprised of a coatainer, a central core of fertile material in the container, a first bonding material surrounding the core, a sheet of fissionable material immediately surrounding the first bonding material, and a second bonding material surrounding the fissionable material and being in coniact with said container.

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

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

Zhang, Yanfeng; Zheng, Yi; Qin, Ling

Beta-hydroxyacid dehydrogenase (β-HAD) genes have been identified in all sequenced genomes of eukaryotes and prokaryotes. Their gene products catalyze the NAD+- or NADP+-dependent oxidation of various β-hydroxy acid substrates into their corresponding semialdehyde. In many fungal and bacterial genomes, multiple β-HAD genes are observed leading to the hypothesis that these gene products may have unique, uncharacterized metabolic roles specific to their species. The genomes of Geobacter sulfurreducens and Geobacter metallireducens each contain two potential β-HAD genes. The protein sequences of one pair of these genes, Gs-βHAD (Q74DE4) and Gm-βHAD (Q39R98), have 65% sequence identity and 77% sequence similarity with eachmore » other. Both proteins reduce succinic semialdehyde, a metabolite of the GABA shunt. To further explore the structural and functional characteristics of these two β-HADs with a potentially unique substrate specificity, crystal structures for Gs-βHAD and Gm-βHAD in complex with NADP+ were determined to a resolution of 1.89 Å and 2.07 Å, respectively. The structure of both proteins are similar, composed of 14 α-helices and nine β-strands organized into two domains. Domain One (1-165) adopts a typical Rossmann fold composed of two α/β units: a six-strand parallel β-sheet surrounded by six α-helices (α1 – α6) followed by a mixed three-strand β-sheet surrounded by two α-helices (α7 and α8). Domain Two (166-287) is composed of a bundle of seven α-helices (α9 – α14). Four functional regions conserved in all β-HADs are spatially located near each other at the interdomain cleft in both Gs-βHAD and Gm-βHAD with a buried molecule of NADP+. The structural features of Gs-βHAD and Gm-βHAD are described in relation to the four conserved consensus sequences characteristic of β-HADs and the potential biochemical importance of these enzymes as an alternative pathway for the degradation of succinic semialdehyde.« less

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.

Weld Repair of Thin Aluminum Sheet

NASA Technical Reports Server (NTRS)

Beuyukian, C. S.; Mitchell, M. J.

1986-01-01

Weld repairing of thin aluminum sheets now possible, using niobium shield and copper heat sinks. Refractory niobium shield protects aluminum adjacent to hole, while copper heat sinks help conduct heat away from repair site. Technique limits tungsten/inert-gas (TIG) welding bombardment zone to melt area, leaving surrounding areas around weld unaffected. Used successfully to repair aluminum cold plates on Space Shuttle, Commercial applications, especially in sealing fractures, dents, and holes in thin aluminum face sheets or clad brazing sheet in cold plates, heat exchangers, coolers, and Solar panels. While particularly suited to thin aluminum sheet, this process also used in thicker aluminum material to prevent surface damage near weld area.

Dynamics of Radially Expanding Liquid Sheets

NASA Astrophysics Data System (ADS)

Majumdar, Nayanika; Tirumkudulu, Mahesh S.

2018-04-01

The process of atomization often involves ejecting thin liquid sheets at high speeds from a nozzle that causes the sheet to flap violently and break up into fine droplets. The flapping of the liquid sheet has long been attributed to the sheet's interaction with the surrounding gas phase. Here, we present experimental evidence to the contrary and show that the flapping is caused by the thinning of the liquid sheet as it spreads out from the nozzle exit. The measured growth rates of the waves agree remarkably well with the predictions of a recent theory that accounts for the sheet's thinning but ignores aerodynamic interactions. We anticipate these results to not only lead to more accurate predictions of the final drop-size distribution but also enable more efficient designs of atomizers.

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

Bipolar battery plate

NASA Technical Reports Server (NTRS)

Rowlette, John J. (Inventor)

1987-01-01

A liquid-impermeable plate (10) having through-plate conductivity with essentially zero resistance comprises an insulator sheet (12) having a series of spaced perforations (14) each of which contains a metal element (16) sealingly received into the perforation (14). A low-cost plate can readily be manufactured by punching a thermoplastic sheet (40) such as polypropylene with a punching tool (52), filling the apertures with led spheres (63) having a diameter smaller than the holes (50) but larger than the thickness of the sheet, sweeping excess spheres (62) off the sheet with a doctor blade (60) and then pressing a heated platen (74) onto the sheet to swage the spheres into a cylindrical shape and melt the surrounding resin to form a liquid-impermeable collar (4) sealing the metal into the sheet.

Bipolar battery plate

NASA Technical Reports Server (NTRS)

Rowlette, John J. (Inventor)

1985-01-01

A liquid-impermeable plate (10) having throughplate conductivity with essentially zero resistance comprises an insulator sheet (12) having a series of spaced perforations (14) each of which contains a metal element (16) sealingly received into the perforation (14). A low-cost plate can readily be manufactured by punching a thermoplastic sheet (40) such as polypropylene with a punching tool (52), filling the apertures with lead spheres (63) having a diameter smaller than the holes (50) but larger than the thickness of the sheet, sweeping excess spheres (62) off the sheet with a doctor blade (60) and then pressing a heated platen (74) onto the sheet to swage the spheres into a cylindrical shape and melt the surrounding resin to form a liquid-impermeable collar (4) sealing the metal into the sheet.

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

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

Multilayer radiation shield

DOEpatents

Urbahn, John Arthur; Laskaris, Evangelos Trifon

2009-06-16

A power generation system including: a generator including a rotor including a superconductive rotor coil coupled to a rotatable shaft; a first prime mover drivingly coupled to the rotatable shaft; and a thermal radiation shield, partially surrounding the rotor coil, including at least a first sheet and a second sheet spaced apart from the first sheet by centripetal force produced by the rotatable shaft. A thermal radiation shield for a generator including a rotor including a super-conductive rotor coil including: a first sheet having at least one surface formed from a low emissivity material; and at least one additional sheet having at least one surface formed from a low emissivity material spaced apart from the first sheet by centripetal force produced by the rotatable shaft, wherein each successive sheet is an incrementally greater circumferential arc length and wherein the centripetal force shapes the sheets into a substantially catenary shape.

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

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

Mental Health, Substance Abuse, and Dropping Out: A Quick Stats Fact Sheet

ERIC Educational Resources Information Center

Gourley, Becca

2009-01-01

This fact sheet is intended to provide a snapshot of the current issues surrounding dropout factors among students who are identified with emotional disturbance, as well as to provide mental health resources that may assist this population to remain in high school. The statistics presented in this document highlight both the importance of…

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.

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

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

Rolled-up transmission line structure for a radiofrequency integrated circuit (RFIC)

DOEpatents

Li, Xiuling; Huang, Wen

2015-04-28

A rolled-up transmission line structure for a radiofrequency integrated circuit (RFIC) comprises a multilayer sheet in a rolled configuration comprising multiple turns about a longitudinal axis, where the multilayer sheet comprises a conductive pattern layer on a strain-relieved layer. The conductive pattern layer comprises a first conductive film and a second conductive film separated from the first conductive film in a rolling direction. In the rolled configuration, the first conductive film surrounds the longitudinal axis, and the second conductive film surrounds the first conductive film. The first conductive film serves as a signal line and the second conductive film serves as a conductive shield for the rolled-up transmission line structure.

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.

Three-dimensional solution structure of lactoferricin B, an antimicrobial peptide derived from bovine lactoferrin.

PubMed

Hwang, P M; Zhou, N; Shan, X; Arrowsmith, C H; Vogel, H J

1998-03-24

The solution structure of bovine lactoferricin (LfcinB) has been determined using 2D 1H NMR spectroscopy. LfcinB is a 25-residue antimicrobial peptide released by pepsin cleavage of lactoferrin, an 80 kDa iron-binding glycoprotein with many immunologically important functions. The NMR structure of LfcinB reveals a somewhat distorted antiparallel beta-sheet. This contrasts with the X-ray structure of bovine lactoferrin, in which residues 1-13 (of LfcinB) form an alpha-helix. Hence, this region of lactoferricin B appears able to adopt a helical or sheetlike conformation, similar to what has been proposed for the amyloidogenic prion proteins and Alzheimer's beta-peptides. LfcinB has an extended hydrophobic surface comprised of residues Phe1, Cys3, Trp6, Trp8, Pro16, Ile18, and Cys20. The side chains of these residues are well-defined in the NMR structure. Many hydrophilic and positively charged residues surround the hydrophobic surface, giving LfcinB an amphipathic character. LfcinB bears numerous similarities to a vast number of cationic peptides which exert their antimicrobial activities through membrane disruption. The structures of many of these peptides have been well characterized, and models of their membrane-permeabilizing mechanisms have been proposed. The NMR solution structure of LfcinB may be more relevant to membrane interaction than that suggested by the X-ray structure of intact lactoferrin. Based on the solution structure, it is now possible to propose potential mechanisms for the antimicrobial action of LfcinB.

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.

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.

Pink marine sediments reveal rapid ice melt and Arctic meltwater discharge during Dansgaard-Oeschger warmings.

PubMed

Rasmussen, Tine L; Thomsen, Erik

2013-01-01

The climate of the last glaciation was interrupted by numerous abrupt temperature fluctuations, referred to as Greenland interstadials and stadials. During warm interstadials the meridional overturning circulation was active transferring heat to the north, whereas during cold stadials the Nordic Seas were ice-covered and the overturning circulation was disrupted. Meltwater discharge, from ice sheets surrounding the Nordic Seas, is implicated as a cause of this ocean instability, yet very little is known regarding this proposed discharge during warmings. Here we show that, during warmings, pink clay from Devonian Red Beds is transported in suspension by meltwater from the surrounding ice sheet and replaces the greenish silt that is normally deposited on the north-western slope of Svalbard during interstadials. The magnitude of the outpourings is comparable to the size of the outbursts during the deglaciation. Decreasing concentrations of ice-rafted debris during the interstadials signify that the ice sheet retreats as the meltwater production increases.

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

Deformation, warming and softening of Greenland’s ice by refreezing meltwater

NASA Astrophysics Data System (ADS)

Bell, Robin E.; Tinto, Kirsteen; Das, Indrani; Wolovick, Michael; Chu, Winnie; Creyts, Timothy T.; Frearson, Nicholas; Abdi, Abdulhakim; Paden, John D.

2014-07-01

Meltwater beneath the large ice sheets can influence ice flow by lubrication at the base or by softening when meltwater refreezes to form relatively warm ice. Refreezing has produced large basal ice units in East Antarctica. Bubble-free basal ice units also outcrop at the edge of the Greenland ice sheet, but the extent of refreezing and its influence on Greenland’s ice flow dynamics are unknown. Here we demonstrate that refreezing of meltwater produces distinct basal ice units throughout northern Greenland with thicknesses of up to 1,100 m. We compare airborne gravity data with modelled gravity anomalies to show that these basal units are ice. Using radar data we determine the extent of the units, which significantly disrupt the overlying ice sheet stratigraphy. The units consist of refrozen basal water commonly surrounded by heavily deformed meteoric ice derived from snowfall. We map these units along the ice sheet margins where surface melt is the largest source of water, as well as in the interior where basal melting is the only source of water. Beneath Petermann Glacier, basal units coincide with the onset of fast flow and channels in the floating ice tongue. We suggest that refreezing of meltwater and the resulting deformation of the surrounding basal ice warms the Greenland ice sheet, modifying the temperature structure of the ice column and influencing ice flow and grounding line melting.

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.

The aCORN backscatter-suppressed beta spectrometer

DOE PAGES

Hassan, M. T.; Bateman, F.; Collett, B.; ...

2017-06-16

Backscatter of electrons from a beta detector, with incomplete energy deposition, can lead to undesirable effects in many types of experiments. We present and discuss the design and operation of a backscatter-suppressed beta spectrometer that was developed as part of a program to measure the electron–antineutrino correlation coefficient in neutron beta decay (aCORN). An array of backscatter veto detectors surrounds a plastic scintillator beta energy detector. The spectrometer contains an axial magnetic field gradient, so electrons are efficiently admitted but have a low probability for escaping back through the entrance after backscattering. Lastly, the design, construction, calibration, and performance ofmore » the spectrometer are discussed.« less

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.

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.

Study of the plastic zone around the ligament of thin sheet D.E.N.T specimen subjected to tensile

NASA Astrophysics Data System (ADS)

Djebali, S.; Larbi, S.; Bilek, A.

2015-03-01

One of the assumptions of Cotterell and Reddel's method of the essential work of fracture determination is the existence of a fracture process zone surrounded by an outer plastic zone extending to the whole ligament before crack initiation. To verify this hypothesis we developed a method based on micro hardness. The hardness values measured in the domain surrounding the tensile fracture area of ST-37-2 steel sheet D.E.N.T specimens confirm the existence of the two plastic zones. The extension of the plastic deformations to the whole ligament before the crack initiation and the circular shape of the outer plastic zone are revealed by the brittle coating method.

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.

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.

Bending elasticity of lipid membranes in presence of beta 2 glycoprotein I in the surrounding solution

NASA Astrophysics Data System (ADS)

Pavlič, J. I.; Genova, J.; Zheliaskova, A.; Iglič, A.; Mitov, M. D.

2010-11-01

Thermally induced shape fluctuations of giant quasi-spherical lipid vesicles are used to study the bending elasticity modulus kc of a phospholipid (PHLP) membranes in presence of beta 2 glycoprotein I (β2-GPI) in the aqueous solution which surrounds the vesicle's membrane. The bending elastic modulus kc of PHLP - protein membrane was obtained for different mass concentrations of β2-GPI for pure neutral SOPC membranes and for mixed SOPC: Cardiolipin negatively charged membranes. The experimental results for the bending elastic modulus kc of the PHLP membranes does not show dependence on the concentration of β2-GPI in the range from 5.5 to 55 μg/ml, when β2-GPI is present in the aqueous solution surrounding the vesicle's membrane. Obtained results are in good agreement with predictions, based on different experiments, explaining the mechanism of binding of β2-GPI to neutral membranes.

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.

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

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

High-latitude Conic Current Sheets in the Solar Wind

NASA Astrophysics Data System (ADS)

Khabarova, Olga V.; Malova, Helmi V.; Kislov, Roman A.; Zelenyi, Lev M.; Obridko, Vladimir N.; Kharshiladze, Alexander F.; Tokumaru, Munetoshi; Sokół, Justyna M.; Grzedzielski, Stan; Fujiki, Ken'ichi

2017-02-01

We provide observational evidence for the existence of large-scale cylindrical (or conic-like) current sheets (CCSs) at high heliolatitudes. Long-lived CCSs were detected by Ulysses during its passages over the South Solar Pole in 1994 and 2007. The characteristic scale of these tornado-like structures is several times less than a typical width of coronal holes within which the CCSs are observed. CCS crossings are characterized by a dramatic decrease in the solar wind speed and plasma beta typical for predicted profiles of CCSs. Ulysses crossed the same CCS at different heliolatitudes at 2-3 au several times in 1994, as the CCS was declined from the rotation axis and corotated with the Sun. In 2007, a CCS was detected directly over the South Pole, and its structure was strongly highlighted by the interaction with comet McNaught. Restorations of solar coronal magnetic field lines reveal the occurrence of conic-like magnetic separators over the solar poles in both 1994 and 2007. Such separators exist only during solar minima. Interplanetary scintillation data analysis confirms the presence of long-lived low-speed regions surrounded by the typical polar high-speed solar wind in solar minima. Energetic particle flux enhancements up to several MeV/nuc are observed at edges of the CCSs. We built simple MHD models of a CCS to illustrate its key features. The CCSs may be formed as a result of nonaxiality of the solar rotation axis and magnetic axis, as predicted by the Fisk-Parker hybrid heliospheric magnetic field model in the modification of Burger and coworkers.

High-latitude Conic Current Sheets in the Solar Wind

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

Khabarova, Olga V.; Obridko, Vladimir N.; Kharshiladze, Alexander F.

We provide observational evidence for the existence of large-scale cylindrical (or conic-like) current sheets (CCSs) at high heliolatitudes. Long-lived CCSs were detected by Ulysses during its passages over the South Solar Pole in 1994 and 2007. The characteristic scale of these tornado-like structures is several times less than a typical width of coronal holes within which the CCSs are observed. CCS crossings are characterized by a dramatic decrease in the solar wind speed and plasma beta typical for predicted profiles of CCSs. Ulysses crossed the same CCS at different heliolatitudes at 2–3 au several times in 1994, as the CCSmore » was declined from the rotation axis and corotated with the Sun. In 2007, a CCS was detected directly over the South Pole, and its structure was strongly highlighted by the interaction with comet McNaught. Restorations of solar coronal magnetic field lines reveal the occurrence of conic-like magnetic separators over the solar poles in both 1994 and 2007. Such separators exist only during solar minima. Interplanetary scintillation data analysis confirms the presence of long-lived low-speed regions surrounded by the typical polar high-speed solar wind in solar minima. Energetic particle flux enhancements up to several MeV/ nuc are observed at edges of the CCSs. We built simple MHD models of a CCS to illustrate its key features. The CCSs may be formed as a result of nonaxiality of the solar rotation axis and magnetic axis, as predicted by the Fisk–Parker hybrid heliospheric magnetic field model in the modification of Burger and coworkers.« less

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.

Enhanced osseointegration of titanium implants in a rat model of osteoporosis using multilayer bone mesenchymal stem cell sheets

PubMed Central

Duan, Yan; Ma, Wei; Li, Dehua; Wang, Tongfei; Liu, Baolin

2017-01-01

The present study aimed to investigate whether bone marrow-derived mesenchymal stem cell (BMSC) sheets combined with titanium implants enhanced implant osseointegration in an ovariectomized (OVX) rat model of osteoporosis. Sprague-Dawley rats were randomly assigned into a test group and control group. Allogenic BMSCs were collected from the rats, cultured and stored via cryopreservation. At 6 months post-ovariectomy, establishment of the OVX model was confirmed by micro-computed tomography (CT) measurements. BMSC sheets were subsequently layered and wrapped over titanium implants for implantation. Unmodified implants served as the control. At 8 weeks post-implantation, samples were observed by micro-CT reconstruction and histomorphometric evaluation. Micro-CT reconstruction identified a marked improvement in the surrounding bone volume following treatment, with data analyses indicating a significant increase in bone volume in the BMSC-implant group compared with the control implant group (P<0.05). In addition, histological staining identified new bone formation and an increased rate of bone-implant contact surrounding the BMSC-implant constructs. These results indicate that the use of BMSC sheets as a novel tissue engineering approach improves the osseointegration of titanium implants in an osteoporosis model. This method may expand the operative indications in patients with osteoporosis and improve the success rate of clinical dental implant treatments. PMID:29250137

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.

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

Predicting pulsar scintillation from refractive plasma sheets

NASA Astrophysics Data System (ADS)

Simard, Dana; Pen, Ue-Li

2018-07-01

The dynamic and secondary spectra of many pulsars show evidence for long-lived, aligned images of the pulsar that are stationary on a thin scattering sheet. One explanation for this phenomenon considers the effects of wave crests along sheets in the ionized interstellar medium, such as those due to Alfvén waves propagating along current sheets. If these sheets are closely aligned to our line of sight to the pulsar, high bending angles arise at the wave crests and a selection effect causes alignment of images produced at different crests, similar to grazing reflection off of a lake. Using geometric optics, we develop a simple parametrized model of these corrugated sheets that can be constrained with a single observation and that makes observable predictions for variations in the scintillation of the pulsar over time and frequency. This model reveals qualitative differences between lensing from overdense and underdense corrugated sheets: only if the sheet is overdense compared to the surrounding interstellar medium can the lensed images be brighter than the line-of-sight image to the pulsar, and the faint lensed images are closer to the pulsar at higher frequencies if the sheet is underdense, but at lower frequencies if the sheet is overdense.

Predicting Pulsar Scintillation from Refractive Plasma Sheets

NASA Astrophysics Data System (ADS)

Simard, Dana; Pen, Ue-Li

2018-05-01

The dynamic and secondary spectra of many pulsars show evidence for long-lived, aligned images of the pulsar that are stationary on a thin scattering sheet. One explanation for this phenomenon considers the effects of wave crests along sheets in the ionized interstellar medium, such as those due to Alfvén waves propagating along current sheets. If these sheets are closely aligned to our line-of-sight to the pulsar, high bending angles arise at the wave crests and a selection effect causes alignment of images produced at different crests, similar to grazing reflection off of a lake. Using geometric optics, we develop a simple parameterized model of these corrugated sheets that can be constrained with a single observation and that makes observable predictions for variations in the scintillation of the pulsar over time and frequency. This model reveals qualitative differences between lensing from overdense and underdense corrugated sheets: Only if the sheet is overdense compared to the surrounding interstellar medium can the lensed images be brighter than the line-of-sight image to the pulsar, and the faint lensed images are closer to the pulsar at higher frequencies if the sheet is underdense, but at lower frequencies if the sheet is overdense.

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

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.

Betavoltaics Of Increased Power

NASA Technical Reports Server (NTRS)

Pool, Frederick S.; Stella, Paul

1991-01-01

Batteries of newly developed betavoltaic cells proposed as long-lived sources of power of order of watts. High-power betavoltaic cell resembles solar photo voltaic cell, except it includes layer of beta-emitting material. Betavoltaic battery cells are stacked as in chemical battery, and surrounded by material containing beta rays. Intended for use aboard spacecraft, batteries also used in surgically implanted devices requiring high power.

High power beta electron device - Beyond betavoltaics

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

Ayers, William M.; Gentile, Charles A.

Developing watt level power sources with beta emitting radioisotopes has been limited by the inability to utilize high energy (> 100 KeV) beta emitters at high radioisotope loadings without damaging the energy conversion materials. A new type of beta electron power source is described that removes those restrictions. This approach contains the radioisotope in a beta transparent titanium tube and confines beta electrons emitted through the tube wall to spiral trajectories around the tube with an axial magnetic field. The confined beta electrons dissipate energy though multiple interactions with surrounding excimer precursor gas atoms to efficiently generate photons. Photovoltaic cellsmore » convert the photons to electrical power. Since the beta electrons dissipate energy in the excimer precursor gas, the device can be loaded with more than 10 13 Bq of radioisotope to generate 100 milliwatt to watt levels of electrical power without damaging the device materials or degrading its performance. Furthermore, the power source can use a variety of beta radioisotopes and scales by stacking the devices.« less

High power beta electron device - Beyond betavoltaics

DOE PAGES

Ayers, William M.; Gentile, Charles A.

2017-11-10

Developing watt level power sources with beta emitting radioisotopes has been limited by the inability to utilize high energy (> 100 KeV) beta emitters at high radioisotope loadings without damaging the energy conversion materials. A new type of beta electron power source is described that removes those restrictions. This approach contains the radioisotope in a beta transparent titanium tube and confines beta electrons emitted through the tube wall to spiral trajectories around the tube with an axial magnetic field. The confined beta electrons dissipate energy though multiple interactions with surrounding excimer precursor gas atoms to efficiently generate photons. Photovoltaic cellsmore » convert the photons to electrical power. Since the beta electrons dissipate energy in the excimer precursor gas, the device can be loaded with more than 10 13 Bq of radioisotope to generate 100 milliwatt to watt levels of electrical power without damaging the device materials or degrading its performance. Furthermore, the power source can use a variety of beta radioisotopes and scales by stacking the devices.« less

High power beta electron device - Beyond betavoltaics.

PubMed

Ayers, William M; Gentile, Charles A

2018-01-01

Developing watt level power sources with beta emitting radioisotopes has been limited by the inability to utilize high energy (> 100KeV) beta emitters at high radioisotope loadings without damaging the energy conversion materials. A new type of beta electron power source is described that removes those restrictions. The approach contains the radioisotope in a beta transparent titanium tube and confines beta electrons emitted through the tube wall to spiral trajectories around the tube with an axial magnetic field. The confined beta electrons dissipate energy though multiple interactions with surrounding excimer precursor gas atoms to efficiently generate photons. Photovoltaic cells convert the photons to electrical power. Since the beta electrons dissipate energy in the excimer precursor gas, the device can be loaded with more than 10 13 Bq of radioisotope to generate 100 milliwatt to watt levels of electrical power without damaging the device materials or degrading its performance. The power source can use a variety of beta radioisotopes and scales by stacking the devices. Copyright © 2017. Published by Elsevier Ltd.

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

Thermal properties of highly structured composite and aluminium sheets in an aerodynamic tunnel

NASA Astrophysics Data System (ADS)

Kulhavy, Petr; Egert, Josef

This article deals with the thermodynamic behaviour of heat shields - structured metal and composite plates. Experiments have been carried out in a wind tunnel with an additional heating, which simulates the heat source from engine or exhaust pipe and simultaneously the airflow generated during a car movement. The tested sheets with hexagonal structure were a standard commercial made of aluminium and a second manufactured by replication (lamination, diffusion) from glass fabric. The airflow in a parallel way along the sheets was analysed experimentally in order to determine the heat transfer efficiency between surfaces of sheets and surrounding airflow. The temperature on the sheets was chosen to observe the effects of different sheets material, various heat power and airflow velocity. During the experiment a thermal input below the sheets and airflow velocity through the tunnel have been changed. The thermal field distribution on the metal sheet is different than in case of composite sheet. For the composite material the thermal field distribution was more homogeneous. This article describe briefly also methods of obtaining real composite geometry based on scanned data and their reconstruction for using in some future numerical models.

Fluid Mechanics of the Vascular Basement Membrane in the Brain

NASA Astrophysics Data System (ADS)

Coloma, Mikhail; Hui, Jonathan; Chiarot, Paul; Huang, Peter; Carare, Roxana; McLeod, Kenneth; Schaffer, David

2013-11-01

Beta-amyloid is a normal product of brain metabolic function and is found within the interstitial fluid of the brain. Failure of the clearance of beta-amyloid from the aging brain leads to its accumulation within the walls of arteries and to Alzheimer's disease. The vascular basement membrane (VBM) within the walls of cerebral arteries surrounds the spirally arranged smooth muscle cells and represents an essential pathway for removal of beta-amyloid from the brain. This process fails with the stiffening of arterial walls associated with aging. In this study we hypothesize that the deformation of the VBM associated with arterial pulsations drives the interstitial fluid to drain in the direction opposite of the arterial blood flow. This hypothesis is theoretically investigated by modeling the VBM as a thin, coaxial, fluid-filled porous medium surrounding a periodically deforming cylindrical tube. Flow and boundary conditions required to achieve such a backward clearance are derived through a control volume analysis of mass, momentum, and energy.

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...

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

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.

Extracellular matrix directions estimation of the heart on micro-focus x-ray CT volumes

NASA Astrophysics Data System (ADS)

Oda, Hirohisa; Oda, Masahiro; Kitasaka, Takayuki; Akita, Toshiaki; Mori, Kensaku

2017-03-01

In this paper we propose an estimation method of extracellular matrix directions of the heart. Myofiber are surrounded by the myocardial cell sheets whose directions have strong correspondence between heart failure. Estimation of the myocardial cell sheet directions is difficult since they are very thin. Therefore, we estimate the extracellular matrices which are touching to the sheets as if piled up. First, we perform a segmentation of the extracellular matrices by using the Hessian analysis. Each extracellular matrix region has sheet-like shape. We estimate the direction of each extracellular matrix region by the principal component analysis (PCA). In our experiments, mean inclination angles of two normal canine hearts were 50.6 and 46.2 degrees, while the angle of a failing canine heart was 57.4 degrees. This results well fit the anatomical knowledge that failing hearts tend to have vertical myocardical cell sheets.

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.

Plasma pressure distribution in the surrounding the Earth plasma ring and its role in the magnetospheric dynamics

NASA Astrophysics Data System (ADS)

Antonova, E. E.; Kirpichev, I. P.; Stepanova, M. V.

2014-08-01

We analyzed the characteristics of the plasma region surrounding the Earth at the geocentric distances between 6 and 15RE using the data of THEMIS mission from April 2007 to September 2012. The obtained averaged distributions of plasma pressure, of pressure anisotropy, and of magnetic field near the equatorial plane showed the presence of a ring-shaped structure surrounding the Earth. It was found that for quiet geomagnetic conditions the plasma pressure is nearly isotropic for all magnetic local times at geocentric distances >6RE. Taking into consideration that the minimal values of the magnetic field at the field lines near noon are shifted from the equatorial plane, we estimate the value of plasma beta parameter in the region of minimal values of the magnetic field using the Tsyganenko-2001 magnetic field model. It was found that the values of plasma beta parameter are of the order of unity for the nightside part of the ring-shaped structure in the equatorial plane and for the region of minimal values of the magnetic field in the dayside, indicating that the ring-shaped structure should play an active role in the magnetic field distortion. Comparison of obtained distribution of plasma pressure at the equatorial plane with the values of plasma pressure at low altitudes, showed that the considerable part of the auroral oval can be mapped into the analyzed plasma ring. The role of the high-beta plasma ring surrounding the Earth for Earth-Sun System disturbances is discussed.

The region of formation of the ultraviolet high temperature resonance lines in the eclipsing binary Beta Persei (Algol)

NASA Technical Reports Server (NTRS)

Brandi, E.; Garcia, L. G.; Kondo, Y.; Sahade, J.

1989-01-01

A new series of IUE observations of Beta Persei has shown that the high temperature resonance lines of Si IV and C IV arise in a region that surrounds the brighter, early-type component of the system. The continuum spectrum corresponds to that of a B8V object, and the value of E(B-V) that yielded the best match between the two IUE regions was 0.06, the value quoted for Beta Per in Jamar et al.'s (1976) Catalog.

Solution structure of the catalytic domain of RICH protein from goldfish.

PubMed

Kozlov, Guennadi; Denisov, Alexey Y; Pomerantseva, Ekaterina; Gravel, Michel; Braun, Peter E; Gehring, Kalle

2007-03-01

Regeneration-induced CNPase homolog (RICH) is an axonal growth-associated protein, which is induced in teleost fish upon optical nerve injury. RICH consists of a highly acidic N-terminal domain, a catalytic domain with 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) activity and a C-terminal isoprenylation site. In vitro RICH and mammalian brain CNPase specifically catalyze the hydrolysis of 2',3'-cyclic nucleotides to produce 2'-nucleotides, but the physiologically relevant in vivo substrate remains unknown. Here, we report the NMR structure of the catalytic domain of goldfish RICH and describe its binding to CNPase inhibitors. The structure consists of a twisted nine-stranded antiparallel beta-sheet surrounded by alpha-helices on both sides. Despite significant local differences mostly arising from a seven-residue insert in the RICH sequence, the active site region is highly similar to that of human CNPase. Likewise, refinement of the catalytic domain of rat CNPase using residual dipolar couplings gave improved agreement with the published crystal structure. NMR titrations of RICH with inhibitors point to a similar catalytic mechanism for RICH and CNPase. The results suggest a functional importance for the evolutionarily conserved phosphodiesterase activity and hint of a link with pre-tRNA splicing.

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.

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.

The Jovian magnetotail and its current sheet

NASA Technical Reports Server (NTRS)

Behannon, K. W.; Burlaga, L. F.; Ness, N. F.

1980-01-01

Analyses of Voyager magnetic field measurements have extended the understanding of the structural and temporal characteristics of Jupiter's magnetic tail. The magnitude of the magnetic field in the lobes of the tail is found to decrease with Jovicentric distance approximately as r to he-1.4, compared with the power law exponent of -1.7 found for the rate of decrease along the Pioneer 10 outbound trajectory. Voyager observations of magnetic field component variations with Jovicentric distance in the tail do not support the uniform radial plasma outflow model derived from Pioneer data. Voyager 2 has shown that the azimuthal current sheet which surrounds Jupiter in the inner and middle magnetosphere extends tailward (in the anti-Sun direction) to a distance of at least 100 R sub J. In the tail this current sheet consists of a plasma sheet and embedded neutral sheet. In the region of the tail where the sheet is observed, the variation of the magnetic field as a result of the sheet structure and its 10 hr periodic motion is the dominant variation seen.

Tensile property improvement of TWIP-cored three-layer steel sheets fabricated by hot-roll-bonding with low-carbon steel or interstitial-free steel

PubMed Central

Park, Jaeyeong; Kim, Jung-Su; Kang, Minju; Sohn, Seok Su; Cho, Won Tae; Kim, Hyoung Seop; Lee, Sunghak

2017-01-01

TWIP-cored three-layer steel sheets were newly fabricated by hot rolling of TWIP steel sheet surrounded by low-carbon (LC) or interstitial-free (IF) steel sheets. TWIP/LC or TWIP/IF interfaces were well bonded without pores or voids, while a few pearlites were thinly formed along the interfaces. The strengths and elongation of the TWIP-cored sheets increased as the volume fraction of TWIP-cored region increased, and were also well matched with the ones calculated by a rule of mixtures based on volume fraction or force fraction. According to digital image correlation and electron back-scatter diffraction analyses, very high strain hardening effect in the initial deformation stage and active twin formation in the interfacial region beneficially affected the overall homogeneous deformation in the TWIP-cored sheets without any yield point phenomenon occurring in the LC sheet and serrations occurring in the TWIP sheet, respectively. These TWIP-cored sheets can cover a wide range of yield strength, tensile strength, and ductility levels, e.g., 320~498 MPa, 545~878 MPa, and 48~54%, respectively, by controlling the volume fraction of TWIP-cored region, and thus present new applications to multi-functional automotive steel sheets requiring excellent properties. PMID:28067318

Tensile property improvement of TWIP-cored three-layer steel sheets fabricated by hot-roll-bonding with low-carbon steel or interstitial-free steel

NASA Astrophysics Data System (ADS)

Park, Jaeyeong; Kim, Jung-Su; Kang, Minju; Sohn, Seok Su; Cho, Won Tae; Kim, Hyoung Seop; Lee, Sunghak

2017-01-01

TWIP-cored three-layer steel sheets were newly fabricated by hot rolling of TWIP steel sheet surrounded by low-carbon (LC) or interstitial-free (IF) steel sheets. TWIP/LC or TWIP/IF interfaces were well bonded without pores or voids, while a few pearlites were thinly formed along the interfaces. The strengths and elongation of the TWIP-cored sheets increased as the volume fraction of TWIP-cored region increased, and were also well matched with the ones calculated by a rule of mixtures based on volume fraction or force fraction. According to digital image correlation and electron back-scatter diffraction analyses, very high strain hardening effect in the initial deformation stage and active twin formation in the interfacial region beneficially affected the overall homogeneous deformation in the TWIP-cored sheets without any yield point phenomenon occurring in the LC sheet and serrations occurring in the TWIP sheet, respectively. These TWIP-cored sheets can cover a wide range of yield strength, tensile strength, and ductility levels, e.g., 320~498 MPa, 545~878 MPa, and 48~54%, respectively, by controlling the volume fraction of TWIP-cored region, and thus present new applications to multi-functional automotive steel sheets requiring excellent properties.

Magneto-hydrodynamics of coupled fluid-sheet interface with mass suction and blowing

NASA Astrophysics Data System (ADS)

Ahmad, R.

2016-01-01

There are large number of studies which prescribe the kinematics of the sheet and ignore the sheet's mechanics. However, the current boundary layer analysis investigates the mechanics of both the electrically conducting fluid and a permeable sheet, which makes it distinct from the other studies in the literature. One of the objectives of the current study is to (i) examine the behaviour of magnetic field effect for both the surface and the electrically conducting fluid (ii) investigate the heat and mass transfer between a permeable sheet and the surrounding electrically conducting fluid across the hydro, thermal and mass boundary layers. Self-similar solutions are obtained by considering the RK45 technique. Analytical solution is also found for the stretching sheet case. The skin friction dual solutions are presented for various types of sheet. The influence of pertinent parameters on the dimensionless velocity, shear stress, temperature, mass concentration, heat and mass transfer rates on the fluid-sheet interface is presented graphically as well as numerically. The obtained results are of potential benefit for studying the electrically conducting flow over various soft surfaces such as synthetic plastics, soft silicone sheet and soft synthetic rubber sheet. These surfaces are easily deformed by thermal fluctuations or thermal stresses.

Tensile property improvement of TWIP-cored three-layer steel sheets fabricated by hot-roll-bonding with low-carbon steel or interstitial-free steel.

PubMed

Park, Jaeyeong; Kim, Jung-Su; Kang, Minju; Sohn, Seok Su; Cho, Won Tae; Kim, Hyoung Seop; Lee, Sunghak

2017-01-09

TWIP-cored three-layer steel sheets were newly fabricated by hot rolling of TWIP steel sheet surrounded by low-carbon (LC) or interstitial-free (IF) steel sheets. TWIP/LC or TWIP/IF interfaces were well bonded without pores or voids, while a few pearlites were thinly formed along the interfaces. The strengths and elongation of the TWIP-cored sheets increased as the volume fraction of TWIP-cored region increased, and were also well matched with the ones calculated by a rule of mixtures based on volume fraction or force fraction. According to digital image correlation and electron back-scatter diffraction analyses, very high strain hardening effect in the initial deformation stage and active twin formation in the interfacial region beneficially affected the overall homogeneous deformation in the TWIP-cored sheets without any yield point phenomenon occurring in the LC sheet and serrations occurring in the TWIP sheet, respectively. These TWIP-cored sheets can cover a wide range of yield strength, tensile strength, and ductility levels, e.g., 320~498 MPa, 545~878 MPa, and 48~54%, respectively, by controlling the volume fraction of TWIP-cored region, and thus present new applications to multi-functional automotive steel sheets requiring excellent properties.

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.

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.

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.

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

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.

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.

The influence of the surrounding gas on drop impact onto a wet substrate

NASA Astrophysics Data System (ADS)

Deegan, Robert; Zhang, Li; Toole, Jameson

2011-11-01

The impact of a droplet with a wet or solid substrate creates a spray of secondary droplets. The effect of the surrounding gas on this process was widely neglected prior to the work of Xu, Zhang, & Nagel which showed that lowering the gas pressure suppresses splashing for impact with a dry solid substrate. Here we present the results of our experimental investigation of the effect of the surrounding gas on the evolution of splashes from a wet substrate. We varied the density and pressure of the surrounding gas. We find quantitative changes to the onset thresholds of splashing and on the size distribution of, but no qualitative changes. The effects are most pronounced on the evolution of the ejecta sheet.

The Majorana Demonstrator: Progress towards showing the feasibility of a tonne-scale 76Ge neutrinoless double-beta decay experiment

NASA Astrophysics Data System (ADS)

Finnerty, P.; Aguayo, E.; Amman, M.; Avignone, F. T., Iii; Barabash, A. S.; Barton, P. J.; Beene, J. R.; Bertrand, F. E.; Boswell, M.; Brudanin, V.; Busch, M.; Chan, Y.-D.; Christofferson, C. D.; Collar, J. I.; Combs, D. C.; Cooper, R. J.; Detwiler, J. A.; Doe, P. J.; Efremenko, Yu; Egorov, V.; Ejiri, H.; Elliott, S. R.; Esterline, J.; Fast, J. E.; Fields, N.; Fraenkle, F. M.; Galindo-Uribarri, A.; Gehman, V. M.; Giovanetti, G. K.; Green, M. P.; Guiseppe, V. E.; Gusey, K.; Hallin, A. L.; Hazama, R.; Henning, R.; Hoppe, E. W.; Horton, M.; Howard, S.; Howe, M. A.; Johnson, R. A.; Keeter, K. J.; Kidd, M. F.; Knecht, A.; Kochetov, O.; Konovalov, S. I.; Kouzes, R. T.; LaFerriere, B. D.; Leon, J.; Leviner, L. E.; Loach, J. C.; Luke, P. N.; MacMullin, S.; Marino, M. G.; Martin, R. D.; Merriman, J. H.; Miller, M. L.; Mizouni, L.; Nomachi, M.; Orrell, J. L.; Overman, N. R.; Perumpilly, G.; Phillips, D. G., Ii; Poon, A. W. P.; Radford, D. C.; Rielage, K.; Robertson, R. G. H.; Ronquest, M. C.; Schubert, A. G.; Shima, T.; Shirchenko, M.; Snavely, K. J.; Steele, D.; Strain, J.; Timkin, V.; Tornow, W.; Varner, R. L.; Vetter, K.; Vorren, K.; Wilkerson, J. F.; Yakushev, E.; Yaver, H.; Young, A. R.; Yu, C.-H.; Yumatov, V.; Majorana Collaboration

2014-03-01

The Majorana Demonstrator will search for the neutrinoless double-beta decay (0vββ) of the 76Ge isotope with a mixed array of enriched and natural germanium detectors. The observation of this rare decay would indicate the neutrino is its own anti-particle, demonstrate that lepton number is not conserved, and provide information on the absolute mass-scale of the neutrino. The Demonstrator is being assembled at the 4850 foot level of the Sanford Underground Research Facility in Lead, South Dakota. The array will be contained in a low-background environment and surrounded by passive and active shielding. The goals for the Demonstrator are: demonstrating a background rate less than 3 t-1 y-1 in the 4 keV region of interest (ROI) surrounding the 2039 keV 76Ge endpoint energy; establishing the technology required to build a tonne-scale germanium based double-beta decay experiment; testing the recent claim of observation of 0vββ [1]; and performing a direct search for light WIMPs (3-10 GeV/c2).

The Majorana Demonstrator: Progress towards showing the feasibility of a 76Ge neutrinoless double-beta decay experiment

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

Finnerty, P.; Aguayo, Estanislao; Amman, M.

2014-03-24

The Majorana Demonstrator will search for the neutrinoless double-beta decay (0*) of the 76Ge isotope with a mixed array of enriched and natural germanium detectors. The observation of this rare decay would indicate the neutrino is its own anti-particle, demonstrate that lepton number is not conserved, and provide information on the absolute mass-scale of the neutrino. The Demonstrator is being assembled at the 4850 foot level of the Sanford Underground Research Facility in Lead, South Dakota. The array will be contained in a lowbackground environment and surrounded by passive and active shielding. The goals for the Demonstrator are: demonstrating amore » background rate less than 3 counts tonne -1 year-1 in the 4 keV region of interest (ROI) surrounding the 2039 keV 76Ge endpoint energy; establishing the technology required to build a tonne-scale germanium based double-beta decay experiment; testing the recent claim of observation of 0; and performing a direct search for lightWIMPs (3-10 GeV/c2).« less

Spray From a Rolling Tire: Mechanics of Droplet Formation

NASA Astrophysics Data System (ADS)

Plocher, Dennis; Browand, Fred

2010-11-01

The spray pattern immediately behind a single-groove tire rolling on a wet surface is produced in the laboratory using a specially designed tire spray simulator. The spray development is examined using high speed video. Water from the groove forms a liquid sheet as the tire-tread lifts away from the surface. The sheet is not of uniform thickness, but it remains attached to the tread. The thinner portions of the sheet become even thinner as the tire rotates, and eventually break to produce holes near the tire surface. The holes grow as the sheet margins surrounding the holes retract into the thicker portions of the sheet which become roughly cylindrical "ligaments" aligned at right angles to the direction of spray motion. The ligaments break into large droplets via a Rayleigh instability. The smallest droplets form when the margins of two holes collide. As Weber number, We = ρU^2w/2σ , based on tire groove half width, w/2, varies by a factor of 25, the sheet-ligament structure persists, but ligaments become less organized, and more small droplets appear in the pattern.

Histologic effect of pure-phase beta-tricalcium phosphate on bone regeneration in human artificial jawbone defects.

PubMed

Trisi, Paolo; Rao, Walter; Rebaudi, Alberto; Fiore, Peter

2003-02-01

The effect of the pure-phase beta-tricalcium phosphate (beta-TCP) Cerasorb on bone regeneration was evaluated in hollow titanium cylinders implanted in the posterior jaws of five volunteers. Beta-TCP particles were inserted inside the cylinders and harvested 6 months after placement. The density of the newly formed bone inside the bone-growing chambers measured 27.84% +/- 24.67% in test and 17.90% +/- 4.28% in control subjects, without a statistically significant difference. Analysis of the histologic specimens revealed that the density of the regenerated bone was related to the density of the surrounding bone. The present study demonstrates the spontaneous healing of infrabony artificial defects, 2.5 mm diameter, in the jaw. The pure beta-TCP was resorbed simultaneously with new bone formation, without interference with the bone matrix formation.

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.

Injection Characteristics of Non-Swirling and Swirling Annular Liquid Sheets

NASA Technical Reports Server (NTRS)

Harper, Brent (Technical Monitor); Ibrahim, E. A.; McKinney, T. R.

2004-01-01

A simplified mathematical model, based on body-fitted coordinates, is formulated to study the evolution of non-swirling and swirling liquid sheet emanated from an annular nozzle in a quiescent surrounding medium. The model provides predictions of sheet trajectory, thickness and velocity at various liquid mass flow rates and liquid-swirler angles. It is found that a non-swirling annular sheet converges toward its centerline and assumes a bell shape as it moves downstream from the nozzle. The bell radius, and length are more pronounced at higher liquid mass flow rates. The thickness of the non-swirling annular sheet increases while its stream-wise velocity decreases with an increase in mass flow rate. The introduction of swirl results in the formation of a diverging hollow-cone sheet. The hollow-cone divergence from its centerline is enhanced by an increase in liquid mass flow rate or liquid-swirler angle. The hollow- cone sheet its radius, curvature and stream-wise velocity increase while its thickness and tangential velocity decrease as a result of increasing the mass flow rate or liquid-swirler angle. The present results are compared with previous studies and conclusions are drawn.

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.

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.

Direct evidence that prostate tumors show high sensitivity to fractionation (low alpha/beta ratio), similar to late-responding normal tissue.

PubMed

Brenner, David J; Martinez, Alvaro A; Edmundson, Gregory K; Mitchell, Christina; Thames, Howard D; Armour, Elwood P

2002-01-01

A direct approach to the question of whether prostate tumors have an atypically high sensitivity to fractionation (low alpha/beta ratio), more typical of the surrounding late-responding normal tissue. Earlier estimates of alpha/beta for prostate cancer have relied on comparing results from external beam radiotherapy (EBRT) and brachytherapy, an approach with significant pitfalls due to the many differences between the treatments. To circumvent this, we analyze recent data from a single EBRT + high-dose-rate (HDR) brachytherapy protocol, in which the brachytherapy was given in either 2 or 3 implants, and at various doses. For the analysis, standard models of tumor cure based on Poisson statistics were used in conjunction with the linear-quadratic formalism. Biochemical control at 3 years was the clinical endpoint. Patients were matched between the 3 HDR vs. 2 HDR implants by clinical stage, pretreatment prostate-specific antigen (PSA), Gleason score, length of follow-up, and age. The estimated value of alpha/beta from the current analysis of 1.2 Gy (95% CI: 0.03, 4.1 Gy) is consistent with previous estimates for prostate tumor control. This alpha/beta value is considerably less than typical values for tumors (> or =8 Gy), and more comparable to values in surrounding late-responding normal tissues. This analysis provides strong supporting evidence that alpha/beta values for prostate tumor control are atypically low, as indicated by previous analyses and radiobiological considerations. If true, hypofractionation or HDR regimens for prostate radiotherapy (with appropriate doses) should produce tumor control and late sequelae that are at least as good or even better than currently achieved, with the added possibility that early sequelae may be reduced.

The Blue Needle: A Highly Asymmetric Debris Disk Surrounding HD 15115

NASA Astrophysics Data System (ADS)

Kalas, P.; Graham, J. R.; Fitzgerald, M.

2007-06-01

Using the ACS coronagraph aboard the Hubble Space Telescope in the optical, and Keck adaptive optics in the near- infrared, we discovered an edge-on dust disk surrounding the F2V star HD 15115. HD 15115 is the most asymmetric debris disk imaged to date, with an eastward pointing midplane detected to ~315 AU radius, and a westward pointing midplane detected to >550 AU radius. The blue optical to near-infrared scattered light color relative to the star may indicate dust scattering properties similar to the AU Mic debris disk. The existence of a large debris disk surrounding HD 15115 is consistent with its proposed membership in the Beta Pic moving group, and the extreme asymmetry presents significant theoretical challenges. We hypothesize that the extreme asymmetries may be caused by dynamical perturbations from HIP 12545, another Beta Pic Moving Group member east of HD 15115, that shares a common proper motion vector, heliocentric distance, Galactic space velocity, and age. HD 15115 is a prime candidate for exoplanet detection via radial velocity and transit techniques.

[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.

Role of ice-ocean interaction on glacier instability: Results from numerical modeling applied to Petermann Glacier (Invited)

NASA Astrophysics Data System (ADS)

Nick, F.; Hubbard, A.; Vieli, A.; van der Veen, C. J.; Box, J. E.; Bates, R.; Luckman, A. J.

2009-12-01

Calving of icebergs and bottom melting from ice shelves accounts for roughly half the ice transferred from the Greenland Ice Sheet into the surrounding ocean, and virtually all of the ice loss from the Antarctic Ice Sheet. Petermann Glacier (north Greenland) with its 16 km wide and 80 km long floating tongue, experiences massive bottom melting. We apply a numerical ice flow model using a physically-based calving criterion based on crevasse depth to investigate the contribution of processes such as bottom melting, sea ice or sikkusak disintegration, surface run off and iceberg calving to the mass balance and instability of Petermann Glacier and its ice shelf. Our modeling study provides insights into the role of ice-ocean interaction, and on how to incorporate calving in ice sheet models, improving our ability to predict future ice sheet change.

Role of ice-ocean interaction on glacier instability: Results from numerical modelling applied to Petermann Glacier

NASA Astrophysics Data System (ADS)

Nick, Faezeh M.; Hubbard, Alun; van der Veen, Kees; Vieli, Andreas

2010-05-01

Calving of icebergs and bottom melting from ice shelves accounts for roughly half the ice transferred from the Greenland Ice Sheet into the surrounding ocean, and virtually all of the ice loss from the Antarctic Ice Sheet. Petermann Glacier (north Greenland) with its 16 km wide and 80 km long floating tongue, experiences massive bottom melting. We apply a numerical ice flow model using a physically-based calving criterion based on crevasse depth to investigate the contribution of processes such as bottom melting, sea ice or sikkusak disintegration, surface run off and iceberg calving to the mass balance and instability of Petermann Glacier and its ice shelf. Our modelling study provides insights into the role of ice-ocean interaction, and on how to incorporate calving in ice sheet models, improving our ability to predict future ice sheet change.

Kelvin-Helmholtz instability of a thin liquid sheet: Effect of the gas-boundary layer

NASA Astrophysics Data System (ADS)

Tirumkudulu, Mahesh

2017-11-01

It is well known that when a thin liquid sheet moves with respect to a surrounding gas phase, the liquid sheet is susceptible to the Kelvin-Helmholtz instability. Here, flow in both the liquid and the gas phases are assumed to be inviscid. In this work, we include exactly via a perturbation analysis, the influence of the growing boundary layer in the gas phase in the base flow and show that both temporal and spatial growth rates obtained from the linear stability analysis are significantly reduced due to the presence of the boundary layer. These results are in line with the simulation results of Lozano et al. and Tammisola et al.. We conclude with the implication of these results on the break-up of radially expanding liquid sheets. Funding from IIT Bombay, CSIR India, and Trinity College, Cambridge University is acknowledged.

Gulf coast ports surrounding the Deepwater Horizon oil spill

DOT National Transportation Integrated Search

2010-06-01

This fact sheet provides a snapshot of two major seaports : (New Orleans, LA, and Mobile, AL) and summary tables of : other Gulf coast seaports close to the Deepwater Horizon mobile : offshore drilling unit (MODU) explosion and oil spill. New : Orlea...

21 CFR 882.5910 - Dura substitute.

Code of Federal Regulations, 2010 CFR

2010-04-01

...) Identification. A dura substitute is a sheet or material that is used to repair the dura mater (the membrane surrounding the brain). (b) Classification. Class II (performance standards). ... and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL...

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

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.

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)).

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.

Cartilage engineering using chondrocyte cell sheets and its application in reconstruction of microtia.

PubMed

Zhou, Libin; Ding, Ruiying; Li, Baowei; Han, Haolun; Wang, Hongnan; Wang, Gang; Xu, Bingxin; Zhai, Suoqiang; Wu, Wei

2015-01-01

The imperfections of scaffold materials have hindered the clinical application of cartilage tissue engineering. The recently developed cell-sheet technique is adopted to engineer tissues without scaffold materials, thus is considered being potentially able to overcome the problems concerning the scaffold imperfections. This study constructed monolayer and bilayer chondrocyte cell sheets and harvested the sheets with cell scraper instead of temperature-responsive culture dishes. The properties of the cultured chondrocyte cell sheets and the feasibility of cartilage engineering using the chondrocyte cell sheets was further investigated via in vitro and in vivo study. Primary extracellular matrix (ECM) formation and type II collagen expression was detected in the cell sheets during in vitro culture. After implanted into nude mice for 8 weeks, mature cartilage discs were harvested. The morphology of newly formed cartilage was similar in the constructs originated from monolayer and bilayer chondrocyte cell sheet. The chondrocytes were located within evenly distributed ovoid lacunae. Robust ECM formation and intense expression of type II collagen was observed surrounding the evenly distributed chondrocytes in the neocartilages. Biochemical analysis showed that the DNA contents of the neocartilages were higher than native human costal cartilage; while the contents of the main component of ECM, glycosaminoglycan and hydroxyproline, were similar to native human costal cartilage. In conclusion, the chondrocyte cell sheet constructed using the simple and low-cost technique is basically the same with the cell sheet cultured and harvested in temperature-responsive culture dishes, and can be used for cartilage tissue engineering.

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.

The crystal structure of NADPH:ferredoxin reductase from Azotobacter vinelandii.

PubMed Central

Sridhar Prasad, G.; Kresge, N.; Muhlberg, A. B.; Shaw, A.; Jung, Y. S.; Burgess, B. K.; Stout, C. D.

1998-01-01

NADPH:ferredoxin reductase (AvFPR) is involved in the response to oxidative stress in Azotobacter vinelandii. The crystal structure of AvFPR has been determined at 2.0 A resolution. The polypeptide fold is homologous with six other oxidoreductases whose structures have been solved including Escherichia coli flavodoxin reductase (EcFldR) and spinach, and Anabaena ferredoxin:NADP+ reductases (FNR). AvFPR is overall most homologous to EcFldR. The structure is comprised of a N-terminal six-stranded antiparallel beta-barrel domain, which binds FAD, and a C-terminal five-stranded parallel beta-sheet domain, which binds NADPH/NADP+ and has a classical nucleotide binding fold. The two domains associate to form a deep cleft where the NADPH and FAD binding sites are juxtaposed. The structure displays sequence conserved motifs in the region surrounding the two dinucleotide binding sites, which are characteristic of the homologous enzymes. The folded over conformation of FAD in AvFPR is similar to that in EcFldR due to stacking of Phe255 on the adenine ring of FAD, but it differs from that in the FNR enzymes, which lack a homologous aromatic residue. The structure of AvFPR displays three unique features in the environment of the bound FAD. Two features may affect the rate of reduction of FAD: the absence of an aromatic residue stacked on the isoalloxazine ring in the NADPH binding site; and the interaction of a carbonyl group with N10 of the flavin. Both of these features are due to the substitution of a conserved C-terminal tyrosine residue with alanine (Ala254) in AvFPR. An additional unique feature may affect the interaction of AvFPR with its redox partner ferredoxin I (FdI). This is the extension of the C-terminus by three residues relative to EcFldR and by four residues relative to FNR. The C-terminal residue, Lys258, interacts with the AMP phosphate of FAD. Consequently, both phosphate groups are paired with a basic group due to the simultaneous interaction of the FMN phosphate with Arg51 in a conserved FAD binding motif. The fourth feature, common to homologous oxidoreductases, is a concentration of 10 basic residues on the face of the protein surrounding the active site, in addition to Arg51 and Lys258. PMID:9865948

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.

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

Differential expression of extracellular matrix molecules and the alpha 6-integrins in the normal and neoplastic prostate.

PubMed Central

Knox, J. D.; Cress, A. E.; Clark, V.; Manriquez, L.; Affinito, K. S.; Dalkin, B. L.; Nagle, R. B.

1994-01-01

The epithelial basal lamina composition and integrin expression profile of normal and neoplastic human prostate was characterized using immunohistochemical analysis of frozen samples. The major components of the basal lamina surrounding normal acini were laminin, type IV collagen, entactin, and type VII collagen with variable amounts of tenascin. The basal lamina of neoplastic acini had a similar composition, except for the loss of type VII collagen, which was observed in all grades of carcinoma. The basal cells of the normal prostate express the alpha 6-, beta 1-, and beta 4-integrin subunits, suggesting that both the alpha 6 beta 1- and alpha 6 beta 4-integrin complexes are formed. In prostate carcinoma there is a complete loss of beta 4 expression and the alpha 6- and beta 1-integrin subunits, which are restricted to the basal and basal lateral surfaces of basal cells, are distributed diffusely throughout the cytoplasmic membrane. The differential expression of type VII collagen and beta 4 are discussed in relationship to their possible role in tumor progression. Images Figure 1 Figure 2 Figure 3 PMID:8030747

Mirage effect from thermally modulated transparent carbon nanotube sheets.

PubMed

Aliev, Ali E; Gartstein, Yuri N; Baughman, Ray H

2011-10-28

The single-beam mirage effect, also known as photothermal deflection, is studied using a free-standing, highly aligned carbon nanotube aerogel sheet as the heat source. The extremely low thermal capacitance and high heat transfer ability of these transparent forest-drawn carbon nanotube sheets enables high frequency modulation of sheet temperature over an enormous temperature range, thereby providing a sharp, rapidly changing gradient of refractive index in the surrounding liquid or gas. The advantages of temperature modulation using carbon nanotube sheets are multiple: in inert gases the temperature can reach > 2500 K; the obtained frequency range for photothermal modulation is ~100 kHz in gases and over 100 Hz in high refractive index liquids; and the heat source is transparent for optical and acoustical waves. Unlike for conventional heat sources for photothermal deflection, the intensity and phase of the thermally modulated beam component linearly depends upon the beam-to-sheet separation over a wide range of distances. This aspect enables convenient measurements of accurate values for thermal diffusivity and the temperature dependence of refractive index for both liquids and gases. The remarkable performance of nanotube sheets suggests possible applications as photo-deflectors and for switchable invisibility cloaks, and provides useful insights into their use as thermoacoustic projectors and sonar. Visibility cloaking is demonstrated in a liquid.

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

Blast-Absorbing Bag

NASA Technical Reports Server (NTRS)

Kahn, Jon B.

1992-01-01

Proposed expandable bag contains debris from explosion. Permanently surrounds vessel or devices prone to explosive disintegration or slipped around small bomb. Finned cells shaped like outward-opening cups. Cells built up from overlapped sheets of fabric and stitched together to form expandable polyhedral bag. Cells pentagonal, triangular or square.

Surface (sea floor) and near-surface (box cores) sediment mineralogy in Baffin Bay as a key to sediment provenance and ice sheet variations

USGS Publications Warehouse

Andrews, John T.; Eberl, D.D.

2011-01-01

To better understand the glacial history of the ice sheets surrounding Baffin Bay and to provide information on sediment pathways, samples from 82 seafloor grabs and core tops, and from seven box cores were subjected to quantitative X-ray diffraction weight percent (wt.%) analysis of the 2000 m) all show an abrupt drop in calcite wt.% (post-5 cal ka BP?) following a major peak in detrital carbonate (mainly dolomite). This dolomite-rich detrital carbonate (DC) event in JR175BC06 is possibly coeval with the Younger Dryas cold event. Four possible glacial-sourced end members were employed in a compositional unmixing algorithm to gain insight into down core changes in sediment provenance at the deep central basin. Estimates of the rates of sediment accumulation in the central basin are only in the range of 2 to 4 cm/cal ka, surprisingly low given the glaciated nature of the surrounding land.

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.

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.

A Novel Light Trapping Phenomenon in Fluid Media.

ERIC Educational Resources Information Center

Devlin, J. C.; Tolles, W. M.

1979-01-01

Describes an experiment on light trapping in thin liquid films. Injection of a thin layer of solution at the boundary of a moving solvent is utilized to create a thin fluid sheet having an index of refraction greater than that of the surrounding medium. (Author/SA)

Time dependence of volcano inflation: mass influx or viscoelastic relaxation? Insights from Grímsvötn volcano, Iceland

NASA Astrophysics Data System (ADS)

Segall, P.

2017-12-01

Distinguishing magma chamber pressurization from relaxation of a viscoelastic aureole surrounding the chamber based on geodetic measurements has remained challenging. Elastic models with mass inflow proportional to the pressure difference between the chamber and a deep reservoir predict exponentially decaying flux. For a spherical chamber surrounded by a Maxwell viscoelastic shell with pressure dependent recharge, the surface deformation is the sum of two exponentials (Segall, 2016). GPS displacements following eruptions of Grímsvötn, Iceland in 2004 and 2011 exhibit rapid post-eruptive inflation (time scale of 0.1 yr), followed by inflation with a much longer time constant. Markov Chain Monte Carlo inversion with the viscoelastic model shows the GPS time series can be fit with viscosity of 2e16 Pa-s, and a relatively incompressible magma, B = beta_c/ (beta_m + beta_c) > 0.6, where beta_m and beta_c are chamber and magma compressibility. The latter appears to conflict with the ratio of erupted volume to geodetically inferred source volume change, rv 10, obtained for the best fitting spherical (Mogi ) source (Hreinsdóttir, 2014). Since rv = 1/B, this implies a relatively compressible melt, B 0.1. Reexamination of the co-eruptive GPS and tilt data with the more general ellipsoidal model of Cervelli (2013), reveals that the best fitting sources are oblate (b/a 3), deeper, and with larger volume changes, rv 3, relative to spherical models. Oblate magma chambers are consistent with seismic tomography. FEM calculations including free surface effects lead to even larger co-eruptive volume changes, smaller rv and hence larger B. I conclude that the data are consistent with rapid post-eruptive inflation driven by viscoelastic relaxation with a relatively incompressible magma, although other interpretations will be discussed.

Bipolar battery with array of sealed cells

DOEpatents

Kaun, Thomas D.; Smaga, John A.

1987-01-01

A lithium alloy/metal sulfide battery as a dipolar battery is disclosed with an array of stacked cells with the anode and cathode electrode materials in each cell sealed in a confining structure and separated from one another except across separator material interposed therebetween. The separator material is contained in a module having separate perforated metallic sheets that sandwich opposite sides of the separator material for the cell and an annular insulating spacer that surrounds the separator material beyond the perforations and is also sandwiched between and sealed to the sheets. The peripheral edges of the sheets project outwardly beyond the spacer, traverse the side edges of the adjacent electrode material to form cup-like electrode holders, and are fused to the adjacent current collector or end face members of the array. Electrolyte is infused into the electrolyte cavity through the perforations of one of the metallic sheets with the perforations also functioning to allow ionic conductance across the separator material between the adjacent electrodes. A gas-tight housing provides an enclosure of the array.

Ice sheets as a significant source of highly reactive nanoparticulate iron to the oceans.

PubMed

Hawkings, Jon R; Wadham, Jemma L; Tranter, Martyn; Raiswell, Rob; Benning, Liane G; Statham, Peter J; Tedstone, Andrew; Nienow, Peter; Lee, Katherine; Telling, Jon

2014-05-21

The Greenland and Antarctic Ice Sheets cover ~ 10% of global land surface, but are rarely considered as active components of the global iron cycle. The ocean waters around both ice sheets harbour highly productive coastal ecosystems, many of which are iron limited. Measurements of iron concentrations in subglacial runoff from a large Greenland Ice Sheet catchment reveal the potential for globally significant export of labile iron fractions to the near-coastal euphotic zone. We estimate that the flux of bioavailable iron associated with glacial runoff is 0.40-2.54 Tg per year in Greenland and 0.06-0.17 Tg per year in Antarctica. Iron fluxes are dominated by a highly reactive and potentially bioavailable nanoparticulate suspended sediment fraction, similar to that identified in Antarctic icebergs. Estimates of labile iron fluxes in meltwater are comparable with aeolian dust fluxes to the oceans surrounding Greenland and Antarctica, and are similarly expected to increase in a warming climate with enhanced melting.

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.

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)

Respiratory epithelial ingrowth and hemorrhage as late complications of orbital floor fracture repair with silicone sheet implant.

PubMed

Jones, David F; Wilson, Matthew W

2008-01-01

The authors present a unique case of rapidly progressive proptosis in a woman 23 years after repair of an orbital floor fracture. Clinical studies, surgical exploration, and pathology revealed a hemorrhagic cyst lined with respiratory epithelium surrounding her previously placed silicone implant.

A calving law for ice sheet models; Investigating the role of surface melt on dynamics of Greenland outlet glaciers

NASA Astrophysics Data System (ADS)

Nick, F. M.; van der Veen, C. J.; Vieli, A.

2008-12-01

alving of icebergs accounts for perhaps as much as half the ice transferred from the Greenland Ice Sheet into the surrounding ocean, and virtually all of the ice loss from the Antarctic Ice Sheet. We have formulated a calving model that can be readily incorporated into time-evolving numerical ice-flow models. Our model is based on downward penetration of water-filled surface crevasses and upward propagation of basal crevasses. A calving event occurs when the depth of the surface crevasse (which increases as melting progresses through the summer) reaches the height of the basal crevasse. Our numerical ice sheet model is able to reproduce observed seasonal changes of Greenland outlet glaciers, such as fluctuations in flow speed and terminus positions. We have applied the model to Helheim Glacier on the east coast, and Petermann Glacier in the northwest. Our model suggests that rapid retreat of the claving front is highly affected by the amplified calving rate due to increasing water level in surface crevasses during warmer summers. Our results show little response to seasonally enhanced basal lubrication from surface melt. This modeling study provides insights into the role of surface and basal hydrology to ice sheet dynamics and on how to incorporate calving in ice sheet models and therefore advances our ability to predict future ice sheet change.

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.

Tubular hydrogen permeable metal foil membrane and method of fabrication

DOEpatents

Paglieri, Stephen N.; Birdsell, Stephen A.; Barbero, Robert S.; Snow, Ronny C.; Smith, Frank M.

2006-04-04

A tubular hydrogen permeable metal membrane and fabrication process comprises obtaining a metal alloy foil having two surfaces, coating the surfaces with a metal or metal alloy catalytic layer to produce a hydrogen permeable metal membrane, sizing the membrane into a sheet with two long edges, wrapping the membrane around an elongated expandable rod with the two long edges aligned and overlapping to facilitate welding of the two together, placing the foil wrapped rod into a surrounding fixture housing with the two aligned and overlapping foil edges accessible through an elongated aperture in the surrounding fixture housing, expanding the elongated expandable rod within the surrounding fixture housing to tighten the foil about the expanded rod, welding the two long overlapping foil edges to one another generating a tubular membrane, and removing the tubular membrane from within the surrounding fixture housing and the expandable rod from with the tubular membrane.

The Growth of Instabilities in Annular Liquid Sheets

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

Duke, Daniel J.; Honnery, Damon R; Soria, Julio

An annular liquid sheet surrounded by parallel co-flowing gas is an effective atomiser. However, the initial instabilities which determine the primary break-up of the liquid sheet are not well understood. Lack of agreement on the influence of the boundary conditions and the non-dimension scaling of the initial instability persists between theoretical stability analyses and experiments. To address this matter, we have undertaken an experimental parametric study of an aerodynamically-driven, non-swirling annular water sheet. The effects of sheet thickness, inner and outer gas-liquid momentum ratio were investigated over an order of magnitude variation in Reynolds and Weber number. From high-speed imagemore » correlation measurements in the near-nozzle region, we propose new empirical correlations for the frequency of the instability as a function of the total gas-liquid momentum ratio, with good non-dimensional collapse. From analysis of the instability velocity probability densities, we find two persistent and distinct superimposed instabilities with different growth rates. The first is a short-lived, rapidly saturating sawtooth-like instability. The second is a slower-growing stochastic instability which persists through the break-up of the sheet. The presence of multiple instabilities whose growth rates do not strongly correlate with the shear velocities may explain some of the discrepancies between experiments and stability analyses.« less

Shatter Complex Formation in the Twin Craters Lava Flow, Zuni-Bandera Field, New Mexico

NASA Astrophysics Data System (ADS)

von Meerscheidt, H. C.; Bleacher, J. E.; Brand, B. D.; deWet, A.; Samuels, R.; Hamilton, C.; Garry, W. B.; Bandfield, J. L.

2013-12-01

Lava channels, tubes and sheets are transport structures that deliver flowing lava to a flow front. The type of structure can vary within a flow field and evolve throughout an eruption. The 18.0 × 1.0 ka Twin Craters lava flow in the Zuni-Bandera lava field provides a unique opportunity to study morphological changes of a lava flow partly attributable to interaction with a topographic obstacle. Facies mapping and airborne image analysis were performed on an area of the Twin Craters flow that includes a network of channels, lava tubes, shatter features, and disrupted pahoehoe flows surrounding a 45 m tall limestone bluff. The bluff is 1000 m long (oriented perpendicular to flow.) The general flow characteristics upstream from the bluff include smooth, lobate pahoehoe flows and a >2.5 km long lava tube (see Samuels et al., this meeting.) Emplacement characteristics change abruptly where the flow encountered the bluff, to include many localized areas of disrupted pahoehoe and several pahoehoe-floored depressions. Each depression is fully or partly surrounded by a raised rim of blocky material up to 4 m higher than the surrounding terrain. The rim is composed of 0.05 - 4 m diameter blocks, some of which form a breccia that is welded by lava, and some of which exhibit original flow textures. The rim-depression features are interpreted as shatter rings based on morphological similarity to those described by Orr (2011.Bul Volcanol.73.335-346) in Hawai';i. Orr suggests that shatter rings develop when fluctuations in the lava supply rate over-pressurize the tube, causing the tube roof to repeatedly uplift and subside. A rim of shattered blocks and breccias remains surrounding the sunken tube roof after the final lava withdraws from the system. One of these depressions in the Twin Craters flow is 240 m wide and includes six mounds of shattered material equal in height to the surrounding undisturbed terrain. Several mounds have depressed centers floored with rubbly pahoehoe. Prominent ';a';a channels travel around the bluff, leaving a 'wake' of uncovered ground on the downstream side. We interpret this shatter area to have been a branching tube network within an active sheet. The limestone bluff acted as an obstacle that caused a backup of lava within the tubes, driving episodes of shattering. The mounds likely represent earlier solidified sections between active, possibly braided, tube branches, which remained as mounds within the shatter area after the adjacent crust subsided. When lava broke out from the pressurized sheet-like lobe, it formed the ';a';a channels. This section of the flow field is interpreted using inferences from shatter ring formation, but is perhaps better termed a shatter sheet or shatter complex. This study has implications for understanding lava flow dynamics at constriction points, as well as the evolution and morphology of shatter rings.

Magnetic-field sensing coil embedded in ceramic for measuring ambient magnetic field

DOEpatents

Takahashi, Hironori

2004-02-10

A magnetic pick-up coil for measuring magnetic field with high specific sensitivity, optionally with an electrostatic shield (24), having coupling elements (22) with high winding packing ratio, oriented in multiple directions, and embedded in ceramic material for structural support and electrical insulation. Elements of the coil are constructed from green ceramic sheets (200) and metallic ink deposited on surfaces and in via holes of the ceramic sheets. The ceramic sheets and the metallic ink are co-fired to create a monolithic hard ceramic body (20) with metallized traces embedded in, and placed on exterior surfaces of, the hard ceramic body. The compact and rugged coil can be used in a variety of environments, including hostile conditions involving ultra-high vacuum, high temperatures, nuclear and optical radiation, chemical reactions, and physically demanding surroundings, occurring either individually or in combinations.

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

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.

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

Viscous Impact

NASA Astrophysics Data System (ADS)

Driscoll, Michelle; Stevens, Cacey; Nagel, Sidney

2008-11-01

The splashing of both inviscid and viscous drops on smooth, dry surfaces can be completely suppressed by decreasing the pressure of the surrounding gas [1,2,3]. However, at sufficiently high pressure when splashing does occur, the shape and dynamics of the ejected liquid sheets depends strongly on the liquid viscosity. This, as well as the dependence of the threshold pressure on viscosity [2], suggests that the splashing of viscous and inviscid liquids is caused by different mechanisms. When a low-viscosity (˜1 cst) liquid splashes, a corona is ejected immediately upon impact. In more viscous fluids (10 cst silicone oil), our experiments show that a thin sheet, resembling a flattened version of the corona seen in the inviscid case, emerges out of a much thicker spreading film. However, for these viscous fluids, the ejection of the thin sheet does not occur immediately. As the ambient pressure is lowered, the sheet ejection time is delayed longer and longer after impact until no sheet is ejected at all. [1] L. Xu, W.W. Zhang, S.R. Nagel, Phys. Rev. Lett. 94, 184505 (2005). [2] L. Xu, Phys. Rev. E 75, 056316 (2007). [3] C. Stevens et al., FC.00003 DFD 2007

Use of a gentamicin-impregnated collagen sheet (Collatamp(®)) in the management of major soft tissue complications in pediatric cochlear implants.

PubMed

Benito-González, Fernando; Benito, Jose; Sánchez, Luis Alberto Guardado; Estevez Alonso, Santiago; Muñoz Herrera, Angel; Batuecas-Caletrio, Angel

2014-09-01

The objective was to report the effectiveness of salvage treatment in soft tissue infection around cochlear implants with an absorbable gentamicin collagen sheet and a periosteum and skin rotation flaps. Three patients with cochlear implant and persistent surrounding soft tissue infection are included. All of them underwent antibiotic treatment prior to surgery without any response. In this study preoperative and postoperative audiograms were practiced. Surgical excision of infectious skin and a periosteum and skin rotation flaps were performed. The cochlear implant was refixed in the temporal bone and a gentamicin-impregnated collagen sheet was located covering the cochlear implant. headings In all patients with soft tissue infection around the cochlear implant, infection was completely resolved. It was not necessary to remove the device in any case. The use of an absorbable gentamicin-impregnated collagen sheet is not described for the management of soft tissue complications in pediatric cochlear implant patients. The local application of high concentrations of antibiotic administered by this sheet may be effective against resistant bacteria and, in conjunction with surgery, may resolve this type of complications.

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

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.

Application of a Silicone Sheet in Negative-Pressure Wound Therapy to Treat an Abdominal Wall Defect after Necrotizing Fasciitis.

PubMed

Shin, Jin Su; Choi, Hwan Jun

2017-01-01

Necrotizing fasciitis (NF) is an aggressive soft-tissue infection involving the deep fascia and is characterized by extensive deterioration of the surrounding tissue. Immediate diagnosis and intensive treatment, including debridement and systemic antibiotics, represent the most important factors influencing the survival of NF patients. In this report, we present a case of NF in the abdomen due to an infection caused by a perforated small bowel after abdominal liposuction. It was successfully treated using negative-pressure wound therapy, in which a silicone sheet functioned as a barrier between the sponge and internal organs to protect the small bowel.

Making One World: An Education Pack on Development and Environment.

ERIC Educational Resources Information Center

1992

This pack contains activities aimed at 10-14 year-olds to help raise awareness of issues surrounding the environment and development and the concept of sustainable development. The Teachers' Notes outline the seven units of student activity sheets: (A) lifestyles (links between consumption, development, and the environment); (B) identifying the…

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.

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

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

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.

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.

Current collector for AMTEC

NASA Technical Reports Server (NTRS)

Williams, Roger M. (Inventor)

1989-01-01

An electrode having higher power output is formed of an open mesh current collector such as expanded nickel covering an electrode film applied to a tube of beta-alumina solid electrolyte (BASE). A plurality of cross-members such as spaced, parallel loops of molybdenum metal wire surround the BASE tube. The loops are electrically connected by a bus wire. As the AMTEC cell is heated, the grid of expanded nickel expands more than the BASE tube and the surrounding loop of wire and become diffusion welded to the electrode film and to the wire loops.

A coronal magnetic field model with horizontal volume and sheet currents

NASA Technical Reports Server (NTRS)

Zhao, Xuepu; Hoeksema, J. Todd

1994-01-01

When globally mapping the observed photospheric magnetic field into the corona, the interaction of the solar wind and magnetic field has been treated either by imposing source surface boundary conditions that tacitly require volume currents outside the source surface or by limiting the interaction to thin current sheets between oppositely directed field regions. Yet observations and numerical Magnetohydrodynamic (MHD) calculations suggest the presence of non-force-free volume currents throughout the corona as well as thin current sheets in the neighborhoods of the interfaces between closed and open field lines or between oppositely directed open field lines surrounding coronal helmet-streamer structures. This work presents a model including both horizontal volume currents and streamer sheet currents. The present model builds on the magnetostatic equilibria developed by Bogdan and Low and the current-sheet modeling technique developed by Schatten. The calculation uses synoptic charts of the line-of-sight component of the photospheric magnetic field measured at the Wilcox Solar Observatory. Comparison of an MHD model with the calculated model results for the case of a dipole field and comparison of eclipse observations with calculations for CR 1647 (near solar minimum) show that this horizontal current-current-sheet model reproduces polar plumes and axes of corona streamers better than the source-surface model and reproduces polar plumes and axes of corona streamers better than the source-surface model and reproduces coro nal helmet structures better than the current-sheet model.

Evidence of local and regional freshening of Northeast Greenland coastal waters.

PubMed

Sejr, Mikael K; Stedmon, Colin A; Bendtsen, Jørgen; Abermann, Jakob; Juul-Pedersen, Thomas; Mortensen, John; Rysgaard, Søren

2017-10-13

The supply of freshwater to fjord systems in Greenland is increasing as a result of climate change-induced acceleration in ice sheet melt. However, insight into the marine implications of the melt water is impaired by lack of observations demonstrating the fate of freshwater along the Greenland coast and providing evaluation basis for ocean models. Here we present 13 years of summer measurements along a 120 km transect in Young Sound, Northeast Greenland and show that sub-surface coastal waters are decreasing in salinity with an average rate of 0.12 ± 0.05 per year. This is the first observational evidence of a significant freshening on decadal scale of the waters surrounding the ice sheet and comes from a region where ice sheet melt has been less significant. It implies that ice sheet dynamics in Northeast Greenland could be of key importance as freshwater is retained in southward flowing coastal currents thus reducing density of water masses influencing major deep water formation areas in the Subarctic Atlantic Ocean. Ultimately, the observed freshening could have implications for the Atlantic meridional overturning circulation.

Glacial removal of late Cenozoic subglacially emplaced volcanic edifices by the West Antarctic ice sheet

USGS Publications Warehouse

Behrendt, John C.; Blankenship, D.D.; Damaske, D.; Cooper, A. K.

1995-01-01

Local maxima of the horizontal gradient of pseudogravity from closely spaced aeromagnetic surveys over the Ross Sea, northwestern Ross Ice Shelf, and the West Antarctic ice sheet, reveal a linear magnetic rift fabric and numerous subcircular, high-amplitude anomalies. Geophysical data indicate two or three youthful volcanic edifices at widely separated areas beneath the sea and ice cover in the West Antarctic rift system. In contrast, we suggest glacial removal of edifices of volcanic sources of many more anomalies. Magnetic models, controlled by marine seismic reflection and radar ice-sounding data, allow us to infer that glacial removal of the associated late Cenozoic volcanic edifices (probably debris, comprising pillow breccias, and hyaloclastites) has occurred essentially concomitantly with their subglacial eruption. "Removal' of unconsolidated volcanic debris erupted beneath the ice is probably a more appropriate term than "erosion', given its fragmented, ice-contact origin. The exposed volcanoes may have been protected from erosion by the surrounding ice sheet because of more competent rock or high elevation above the ice sheet. -from Authors

A radioimmunoassay for ependymins beta and gamma: two goldfish brain proteins involved in behavioral plasticity.

PubMed

Schmidt, R; Shashoua, V E

1981-04-01

A radioimmunoassay (RIA) using 125I-labeled antigen was developed for the quantitative determination of two goldfish brain proteins (ependymins beta and gamma). The proteins were isolated from the cerebrospinal fluid (CSF) and cells of the ependymal zone surrounding goldfish brain ventricles. The turnover rates of beta and gamma were previously shown to be specifically enhanced after the animals successfully acquired a new pattern of swimming behavior. Femtomole quantities of ependymin beta were measurable by the RIA. In applications of the assay, beta and gamma ependymins were found to have common immunological properties, since 125I-beta-antigen bound to antibody could be displaced by unlabeled ependymin gamma as well as ependymin beta but not by a variety of other proteins including several purified glycoproteins isolated from goldfish brain. The ependymins were shown to constitute 14% of the total protein content of the brain extracellular fluid and also to be present as a minor component of the serum proteins (0.3%). Ependymins beta and gamma have an immunological reactivity in these fractions that can be increased by a factor of 30 on heating. The data suggest that the antigenicity of the molecules is highly masked, and that it may require some unraveling of the quaternary structure of the proteins before maximal interaction with the antisera becomes possible.

The Beta Pictoris circumstellar disk. XV - Highly ionized species near Beta Pictoris

NASA Technical Reports Server (NTRS)

Deleuil, M.; Gry, C.; Lagrange-Henri, A.-M.; Vidal-Madjar, A.; Beust, H.; Ferlet, R.; Moos, H. W.; Livengood, T. A.; Ziskin, D.; Feldman, P. D.

1993-01-01

Temporal variations of the Fe II, Mg II, and Al III circumstellar lines towards Beta Pictoris have been detected and monitored since 1985. However, the unusual presence of Al III ions is still puzzling, since the UV stellar flux from an A5V star such as Beta Pic is insufficient to produce such an ion. In order to better define the origin of such a phenomenon, new observations have been carried out to detect faint signatures of other highly ionized species in the short UV wavelength range, where the stellar continuum flux is low. These observations reveal variations not only near the C IV doublet lines, but also in C I and Al II lines, two weakly ionized species, not clearly detectable until now. In the framework of an infalling body scenario, highly ionized species would be created in the tail, far from the comet head, by collisions with ambient gas surrounding the star, or a weak stellar wind. Spectral changes have also been detected near a CO molecular band location, which, if confirmed, would provide the first molecular signature around Beta Pictoris.

Bone tissue engineering with human mesenchymal stem cell sheets constructed using magnetite nanoparticles and magnetic force.

PubMed

Shimizu, Kazunori; Ito, Akira; Yoshida, Tatsuro; Yamada, Yoichi; Ueda, Minoru; Honda, Hiroyuki

2007-08-01

An in vitro reconstruction of three-dimensional (3D) tissues without the use of scaffolds may be an alternative strategy for tissue engineering. We have developed a novel tissue engineering strategy, termed magnetic force-based tissue engineering (Mag-TE), in which magnetite cationic liposomes (MCLs) with a positive charge at the liposomal surface, and magnetic force were used to construct 3D tissue without scaffolds. In this study, human mesenchymal stem cells (MSCs) magnetically labeled with MCLs were seeded onto an ultra-low attachment culture surface, and a magnet (4000 G) was placed on the reverse side. The MSCs formed multilayered sheet-like structures after a 24-h culture period. MSCs in the sheets constructed by Mag-TE maintained an in vitro ability to differentiate into osteoblasts, adipocytes, or chondrocytes after a 21-day culture period using each induction medium. Using an electromagnet, MSC sheets constructed by Mag-TE were harvested and transplanted into the bone defect in the crania of nude rats. Histological observation revealed that new bone surrounded by osteoblast-like cells was formed in the defect area 14 days after transplantation with MSC sheets, whereas no bone formation was observed in control rats without the transplant. These results indicated that Mag-TE could be used for the transplantation of MSC sheets using magnetite nanoparticles and magnetic force, providing novel methodology for bone tissue engineering.

Troughs on Martian Ice Sheets: Analysis of Their Closure and Mass Balance

NASA Technical Reports Server (NTRS)

Fountain, A.; Kargel, J.; Lewis, K.; MacAyeal, D.; Pfeffer, T.; Zwally, J.

2000-01-01

At the Copenhagen workshop on Martian polar processes, Ralf Greve commented that the flow regime surrounding scarps and troughs of the Martian polar ice sheets cannot be modeled using traditional "plan view" ice-sheet models. Such models are inadequate because they typically use reduced equations that embody certain simplifications applicable only to terrestrial ice sheets where the upper ice sheet surface is smooth. In response to this suggestion, we have constructed a 2-dimensional, time dependent "side view" (two spatial dimensions: one horizontal, one vertical) model of scarp closure that is designed to overcome the difficulties described by Greve. The purpose of the model is to evaluate the scales of stress variation and styles of flow closure so as to estimate errors that may be encountered by "plan view" models. We show that there may be avenues whereby the complications associated with scarp closure can be overcome in "plan view" models through appropriate parameterizations of 3-dimensional effects. Following this, we apply the flow model to simulate the evolution of a typical scarp on the North Polar Cap of Mars. Our simulations investigate: (a) the role of "radiation trapping" (see our companion abstract) in creating and maintaining "spiral-like" scarps on the ice sheet, (b) the consequences of different flowlaws and ice compositions on scarp evolution and, in particular, scarp age, and (c) the role of dust and debris in scarp evolution.

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.

Comparison of NOAA lidar data at 1.5 and 3 meter resolutions, for adequate watershed delineation in Tift County, Georgia, USA

USDA-ARS?s Scientific Manuscript database

The USDA Southeast Watershed Research Laboratory is located in Tifton, Ga, and performs ongoing watershed research for the Tift County area, as well as surrounding counties. Current watershed delineations are based on 1972-1977, 7.5-minute USGS Quadrangle sheets, and require updating. Light Detectio...

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.

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/

Pop-up assembly of 3D structures actuated by heat shrinkable polymers

NASA Astrophysics Data System (ADS)

Cui, Jianxun; Adams, J. G. M.; Zhu, Yong

2017-12-01

Folding 2D sheets into desired 3D structures is a promising fabrication technique that can find a wide range of applications. Compressive buckling provides an attractive strategy to actuate the folding and can be applied to a broad range of materials. Here a new and simple method is reported to achieve controlled compressive buckling, which is actuated by a heat shrinkable polymer sheet. The buckling deformation is localized at the pre-defined creases in the 2D sheet, resulting in sharp folding. Two approaches are developed to actuate the transformation, which follow similar geometric rules. In the first approach, the 2D precursor is pushed from outside, which leads to a 3D structure surrounded by the shrunk polymer sheet. Assembled 3D structures include prisms/pyramids with different base shapes, house roof, partial soccer ball, Miura-ori structure and insect wing. In the second approach, the 2D precursor is pulled from inside, which leads to a 3D structure enclosing the shrunk polymer sheet. Prisms/pyramids with different base shapes are assembled. The assembled structures are further tessellated to fabricate cellular structures that can be used as thermal insulator and crash energy absorber. They are also stacked vertically to fabricate complex multilayer structures.

Blood-brain barrier dysfunction and amyloid precursor protein accumulation in microvascular compartment following ischemia-reperfusion brain injury with 1-year survival.

PubMed

Pluta, R

2003-01-01

This study examined the late microvascular consequences of brain ischemia due to cardiac arrest in rats. In reacted vibratome sections scattered foci of extravasated horseradish peroxidase were noted throughout the brain and did not appear to be restricted to any specific area of brain. Ultrastructural investigation of leaky sites frequently presented platelets adhering to the endothelium of venules and capillaries. Endothelial cells demonstrated pathological changes with evidence of perivascular astrocytic swelling. At the same time, we noted C-terminal of amyloid precursor protein/beta-amyloid peptide (CAPP/betaA) deposits in cerebral blood vessels, with a halo of CAPP/betaA immunoreactivity in the surrounding parenchyma suggested diffusion of CAPP/betaA out of the vascular compartment. Changes predominated in the hippocampus, cerebral and entorhinal cortex, corpus callosum, thalamus, basal ganglia and around the lateral ventricles. These data implicate delayed abnormal endothelial function of vessels following ischemia-reperfusion brain injury as a primary event in the pathogenesis of the recurrent cerebral infarction.

The effect of microstructure on the deformation modes and mechanical properties of Ti-6Al-2Nb-1Ta-0.8Mo: Part II. Equiaxed structures

NASA Astrophysics Data System (ADS)

Lin, Fu-Shiong; Starke, E. A.; Gysler, A.

1984-10-01

The Ti-6Al-2Nb-lTa-0.8Mo alloy was processed to develop both near-basal and transverse textures. Samples were annealed at different temperatures to vary the equiaxed alpha grain size and the thick-ness of the grain boundary beta, and subsequently quenched in order to transform the beta phase to either martensite, tempered martensite, or Widmanstätten alpha + beta. The effect of microstructure and texture on tensile properties and on fracture toughness was investigated. In addition, yield locus diagrams were constructed in order to study the texture strengthening effect. The yield strength was found to be strongly dependent on the thickness and Burgers relationship of the transformed beta phase surrounding the alpha grains. A texture hardening effect as large as 60 pct was found for the basal-texture material but only 15 pct for the transverse texture material. These variations are asso-ciated with differences in deformation behavior.

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

Threshold self-powered gamma detector for use as a monitor of power in a nuclear reactor

DOEpatents

LeVert, Francis E.; Cox, Samson A.

1978-01-01

A self-powered gamma monitor for placement near the core of a nuclear reactor comprises a lead prism surrounded by a coaxial thin nickel sheet, the combination forming a collector. A coaxial polyethylene electron barrier encloses the collector and is separated from the nickel sheet by a vacuum region. The electron barrier is enclosed by a coaxial stainless steel emitter which, in turn, is enclosed within a lead casing. When the detector is placed in a flux of gamma rays, a measure of the current flow in an external circuit between emitter and collector provides a measure of the power level of the reactor.

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

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.

Dual-mode nonlinear instability analysis of a confined planar liquid sheet sandwiched between two gas streams of unequal velocities and prediction of droplet size and velocity distribution using maximum entropy formulation

NASA Astrophysics Data System (ADS)

Dasgupta, Debayan; Nath, Sujit; Bhanja, Dipankar

2018-04-01

Twin fluid atomizers utilize the kinetic energy of high speed gases to disintegrate a liquid sheet into fine uniform droplets. Quite often, the gas streams are injected at unequal velocities to enhance the aerodynamic interaction between the liquid sheet and surrounding atmosphere. In order to improve the mixing characteristics, practical atomizers confine the gas flows within ducts. Though the liquid sheet coming out of an injector is usually annular in shape, it can be considered to be planar as the mean radius of curvature is much larger than the sheet thickness. There are numerous studies on breakup of the planar liquid sheet, but none of them considered the simultaneous effects of confinement and unequal gas velocities on the spray characteristics. The present study performs a nonlinear temporal analysis of instabilities in the planar liquid sheet, produced by two co-flowing gas streams moving with unequal velocities within two solid walls. The results show that the para-sinuous mode dominates the breakup process at all flow conditions over the para-varicose mode of breakup. The sheet pattern is strongly influenced by gas velocities, particularly for the para-varicose mode. Spray characteristics are influenced by both gas velocity and proximity to the confining wall, but the former has a much more pronounced effect on droplet size. An increase in the difference between gas velocities at two interfaces drastically shifts the droplet size distribution toward finer droplets. Moreover, asymmetry in gas phase velocities affects the droplet velocity distribution more, only at low liquid Weber numbers for the input conditions chosen in the present study.

A novel immune-to-CNS communication pathway: cells of the meninges surrounding the spinal cord CSF space produce proinflammatory cytokines in response to an inflammatory stimulus.

PubMed

Wieseler-Frank, Julie; Jekich, Brian M; Mahoney, John H; Bland, Sondra T; Maier, Steven F; Watkins, Linda R

2007-07-01

Pain is enhanced in response to elevations of proinflammatory cytokines in spinal cerebrospinal fluid (CSF), following either intrathecal injection of these cytokines or intrathecal immune challenge with HIV-1 gp120 that induces cytokine release. Spinal cord glia have been assumed to be the source of endogenous proinflammatory cytokines that enhance pain. However, assuming that spinal cord glia are the sole source of CSF cytokines may be an underestimate, as the cellular composition of the meninges surrounding the spinal cord CSF space includes several cell types known to produce proinflammatory cytokines. The present experiments provide the first investigation of the immunocompetent nature of the spinal cord meninges. Here, we explore whether rat meninges are responsive to intrathecal gp120. These studies demonstrate that: (a) intrathecal gp120 upregulates meningeal gene expression of proinflammatory signals, including tumor necrosis factor-alpha (TNF-alpha), interleukin-1beta (IL-1beta), interleukin 6 (IL-6), and inducible nitric oxide synthase (iNOS), and (b) intrathecal gp120 induces meningeal release of TNF-alpha, IL-1beta, and IL-6. In addition, stimulation of isolated meninges in vitro with gp120 induced the release of TNF-alpha and IL-1beta, indicating that the resident cells of the meninges are able to respond without immune cell recruitment. Taken together, these data document that the meninges are responsive to immunogenic stimuli in the CSF and that the meninges may be a source of immune products detected in CSF. The ability of the meninges to release to proinflammatory signals suggests a potential role in the modulation of pain.

Effects of rolling conditions on recrystallization microstructure and texture in magnetostrictive Fe-Ga-Al rolled sheets

NASA Astrophysics Data System (ADS)

Li, Jiheng; Liu, Yangyang; Li, Xiaojuan; Mu, Xing; Bao, Xiaoqian; Gao, Xuexu

2018-07-01

The effects of different rolling conditions on the microstructure and texture of primary and secondary recrystallization in magnetostrictive Fe82Ga9Al9+0.1at%NbC alloy sheets were investigated. After the primary recrystallization annealing at 850 °C for 5 min, the as-rolled sheets prepared by warm-cold rolling with an intermediate annealing, can be fully recrystallized, and obtain the homogeneous matrix in which the fine dispersed NbC precipitate particles are distributed. The primary recrystallization textures of sheets with different rolling conditions consist mostly of strong {1 0 0} textures, γ-fiber textures, {4 1 1}〈1 4 8〉 texture and weak Goss texture. In the primary recrystallized sheets prepared by warm-cold rolling with an intermediate annealing, the high energy grain boundaries and ∑9 boundaries have the highest proportion. After high temperature annealing, the secondary recrystallizations of Goss grains in these sheets are more complete, and the size of abnormal grown Goss grain is up to several centimeters, which results in the strongest Goss texture. Correspondingly, the largest magnetostriction of 183 ppm is observed. The sample prepared by warm-cold rolling with an intermediate annealing, has homogeneous primary matrix, special texture components and grain boundary distribution, all of which provide a better surrounding for the abnormal growth of Goss grains. This work indicates that the control of rolling conditions of Fe-Ga-Al alloy sheets is necessary to achieve the strong Goss texture and obtain a possible high magnetostriction if other appropriate conditions (stress, domain structure) are achieved.

Widespread Refreezing of Both Surface and Basal Melt Water Beneath the Greenland Ice Sheet

NASA Astrophysics Data System (ADS)

Bell, R. E.; Tinto, K. J.; Das, I.; Wolovick, M.; Chu, W.; Creyts, T. T.; Frearson, N.

2013-12-01

The isotopically and chemically distinct, bubble-free ice observed along the Greenland Ice Sheet margin both in the Russell Glacier and north of Jacobshavn must have formed when water froze from subglacial networks. Where this refreezing occurs and what impact it has on ice sheet processes remain unclear. We use airborne radar data to demonstrate that freeze-on to the ice sheet base and associated deformation produce large ice units up to 700 m thick throughout northern Greenland. Along the ice sheet margin, in the ablation zone, surface meltwater, delivered via moulins, refreezes to the ice sheet base over rugged topography. In the interior, water melted from the ice sheet base is refrozen and surrounded by folded ice. A significant fraction of the ice sheet is modified by basal freeze-on and associated deformation. For the Eqip and Petermann catchments, representing the ice sheet margin and interior respectively, extensive airborne radar datasets show that 10%-13% of the base of the ice sheet and up to a third of the catchment width is modified by basal freeze-on. The interior units develop over relatively subdued topography with modest water flux from basal melt where conductive cooling likely dominates. Steps in the bed topography associated with subglacial valley networks may foster glaciohydraulic supercooling. The ablation zone units develop where both surface melt and crevassing are widespread and large volumes of surface meltwater will reach the base of the ice sheet. The relatively steep topography at the upslope edge of the ablation zone units combined with the larger water flux suggests that supercooling plays a greater role in their formation. The ice qualities of the ablation zone units should reflect the relatively fresh surface melt whereas the chemistry of the interior units should reflect solute-rich basal melt. Changes in basal conditions such as the presence of till patches may contribute to the formation of the large basal units near the Northeast Ice Stream. The contrasting rheology of glacial and interglacial ice may also enhance the deformation associated with freeze-on beneath large ice sheets. The occurrence of basal units both in the ice sheet interior and in the thermally very different ablation zone indicates refreezing is widespread and can occur in many environments beneath an ice sheet. This process appears to influence the morphology and behavior of the ice sheet from top to bottom.

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.

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

Alpha cells secrete acetylcholine as a non-neuronal paracrine signal priming human beta cell function

PubMed Central

Rodriguez-Diaz, Rayner; Dando, Robin; Jacques-Silva, M. Caroline; Fachado, Alberto; Molina, Judith; Abdulreda, Midhat; Ricordi, Camillo; Roper, Stephen D.; Berggren, Per-Olof; Caicedo, Alejandro

2011-01-01

Acetylcholine is a neurotransmitter that plays a major role in the function of the insulin secreting pancreatic beta cell1,2. Parasympathetic innervation of the endocrine pancreas, the islets of Langerhans, has been shown to provide cholinergic input to the beta cell in several species1,3,4, but the role of autonomic innervation in human beta cell function is at present unclear. Here we show that, in contrast to mouse islets, cholinergic innervation of human islets is sparse. Instead, we find that the alpha cells of the human islet provide paracrine cholinergic input to surrounding endocrine cells. Human alpha cells express the vesicular acetylcholine transporter and release acetylcholine when stimulated with kainate or a lowering in glucose concentration. Acetylcholine secretion by alpha cells in turn sensitizes the beta cell response to increases in glucose concentration. Our results demonstrate that in human islets acetylcholine is a paracrine signal that primes the beta cell to respond optimally to subsequent increases in glucose concentration. We anticipate these results to revise models about neural input and cholinergic signaling in the endocrine pancreas. Cholinergic signaling within the islet represents a potential therapeutic target in diabetes5, highlighting the relevance of this advance to future drug development. PMID:21685896

Tissue-specific and pathogen-induced regulation of a Nicotiana plumbaginifolia beta-1,3-glucanase gene.

PubMed Central

Castresana, C; de Carvalho, F; Gheysen, G; Habets, M; Inzé, D; Van Montagu, M

1990-01-01

The Nicotiana plumbaginifolia gn1 gene encoding a beta-1,3-glucanase isoform has been characterized. The gn1 product represents an isoform distinct from the previously identified tobacco beta-1,3-glucanases. By expressing gn1 in Escherichia coli, we have determined directly that the encoded protein does, indeed, correspond to a beta-1,3-glucanase. In N. plumbaginifolia, gn1 was found to be expressed in roots and older leaves. Transgenic tobacco plants containing the 5'-noncoding region of gn1 fused to the beta-glucuronidase (GUS) reporter gene also showed maximum levels of GUS activity in roots and older leaves. No detectable activity was present in the upper part of the transgenic plants with the exception of stem cells at the bases of emerging shoots. The expression conferred by the gn1 promoter was differentially induced in response to specific plant stress treatments. Studies of three plant-bacteria interactions showed high levels of GUS activity when infection resulted in a hypersensitive reaction. Increased gene expression was confined to cells surrounding the necrotic lesions. The observed expression pattern suggests that the characterized beta-1,3-glucanase plays a role both in plant development and in the defense response against pathogen infection. PMID:2152158

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.

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.

Functional morphology of femoral glands in the Tegu lizard, Tupinambis merianae.

PubMed

Chamut, Silvia; Valdez, Valeria García; Manes, Mario E

2009-04-01

Several lizards have femoral glands, which have an influence in various reproductive behaviors. In this paper we describe the morphological organization of the femoral glands in the Tegu, Tupinambis merianae, by means of light and electron microscopy. Even though these glands are present in both genders, secretions during the reproductive period can only be found in males. The glandular parenchyma, which is organized in numerous secretory units, consists of keratinocyte-like cells and granular cells. The holocrine secretion is constituted from both cells, which lose their integrity and become a semi-amorphous material, reinforced by keratin sheets. The discharges of each unit merge together into a solid cylinder of secretion, surrounded by epithelial cells, that is extruded to the exterior. The keratin sheets and epithelial layers that surround both the complete and partial secretions form a sort of structural support suitable for the type of territorial demarcation characteristic of the species. The granular cells, supposedly the producers of pheromones, are characterized by the presence of electron-dense granules and multilaminar membranous bodies that show ultrastructural changes of unknown function. The free granules in the secretion cylinder may act as pheromone deposits.

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

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

Selective intraarterial gene delivery into a canine meningioma.

PubMed

Chauvet, A E; Kesava, P P; Goh, C S; Badie, B

1998-05-01

The goal of this study was to evaluate gene delivery to a benign brain tumor. A recombinant adenovirus vector bearing the Escherichia coli beta-galactosidase reporter gene was selectively injected into the vascular supply of a spontaneously occurring canine olfactory groove meningioma. The tumor and a small amount of peritumoral brain tissue were removed 5 days after viral injection and stained with X-Gal to assess gene delivery. The authors noted significant beta-galactosidase gene expression by the tumor, but not by surrounding brain tissue. No obvious viral-related cytotoxicity was noted. The authors found that meningiomas can be successfully transduced by adenovirus vectors by using endovascular techniques.

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

Investigating role of ice-ocean interaction on glacier dynamic: Results from numerical modeling applied to Petermann Glacier

NASA Astrophysics Data System (ADS)

Nick, F. M.; van der Veen, C. J.; Vieli, A.; Pattyn, F.; Hubbard, A.; Box, J. E.

2010-12-01

Calving of icebergs and bottom melting from ice shelves accounts for roughly half the ice transferred from the Greenland Ice Sheet into the surrounding ocean, and virtually all of the ice loss from the Antarctic Ice Sheet. Petermann Glacier (north Greenland) with its ~17 km wide and ~ 60 km long floating ice-shelf is experiencing high rates of bottom melting. The recent partial disintegration of its shelf (in August 2010) presents a natural experiment to investigate the dynamic response of the ice sheet to its shelf retreat. We apply a numerical ice flow model using a physically-based calving criterion based on crevasse depth to investigate the contribution of processes such as shelf disintegration, bottom melting, sea ice or sikkusak disintegration and surface run off to the mass balance of Petermann Glacier and assess its stability. Our modeling study provides insights into the role of ice-ocean interaction, and on response of Petermann Glacier to its recent massive ice loss.

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.

Manicouagan impact melt, Quebec. I - Stratigraphy, petrology, and chemistry

NASA Technical Reports Server (NTRS)

Floran, R. J.; Grieve, R. A. F.; Dence, M. R.; Phinney, W. C.; Warner, J. L.; Blanchard, D. P.; Simonds, C. H.

1978-01-01

A sheet of clast-laden impact melt 230 m thick and 55 km in diameter forms an annular plateau surrounding an uplift of shocked anorthosite within the moderately eroded Manicouagan structure. Three gradational units of the melt sheet are characterized with respect to grain size, inclusions, texture, and mineralogy. The melt rocks as a group are chemically homogeneous with a bulk composition similar to that of latite and with no statistically significant regional chemical variations. The melt is not completely chemically homogeneous as a local mafic variant represented by two samples with poikilitic texture was found. These poikilitic rocks texturally resemble some Apollo 17 impact melt rocks and are inferred to have had a similar origin and thermal history.

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.

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.

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.

Ringin' the water bell: dynamic modes of curved fluid sheets

NASA Astrophysics Data System (ADS)

Kolinski, John; Aharoni, Hillel; Fineberg, Jay; Sharon, Eran

2015-11-01

A water bell is formed by fluid flowing in a thin, coherent sheet in the shape of a bell. Experimentally, a water bell is created via the impact of a cylindrical jet on a flat surface. Its shape is set by the splash angle (the separation angle) of the resulting cylindrically symmetric water sheet. The separation angle is altered by adjusting the height of a lip surrounding the impact point, as in a water sprinkler. We drive the lip's height sinusoidally, altering the separation angle, and ringin' the water bell. This forcing generates disturbances on the steady-state water bell that propagate forward and backward in the fluid's reference frame at well-defined velocities, and interact, resulting in the emergence of an interference pattern unique to each steady-state geometry. We analytically model these dynamics by linearizing the amplitude of the bell's response about the underlying curved geometry. This simple model predicts the nodal structure over a wide range of steady-state water bell configurations and driving frequencies. Due to the curved water bell geometry, the nodal structure is quite complex; nevertheless, the predicted nodal structure agrees extremely well with the experimental data. When we drive the bell beyond perturbative separation angles, the nodal locations surprisingly persist, despite the strikingly altered underlying water bell shape. At extreme driving amplitudes the water sheet assumes a rich variety of tortuous, non-convex shapes; nevertheless, the fluid sheet remains intact.

Experimental investigation of the stability of a moving radial liquid sheet

NASA Astrophysics Data System (ADS)

Paramati, Manjula; Tirumkudulu, Mahesh

2013-11-01

Experiments were conducted to understand the stability of moving radial liquid sheets formed by the head-on impingement of two co-linear water jets using laser induced fluorescence technique (LIF). Acoustic sinusoidal fluctuations were introduced at the jet impingement point and we measured the displacement of the center line of the liquid sheet (sinuous mode) and the thickness variation (varicose mode) of the disturbed liquid sheet. Our experiments show that the sinuous disturbances grow as they are convected outward in the radial direction even in the smooth regime (We < 800). In the absence of the acoustic forcing, the measured thickness has the expected 1/r dependence. Interestingly, we were unable to detect any thickness variation about the pre-stimulus values in the presence of acoustic forcing suggesting that the variation in the thickness is lower than the resolution of the technique (+/- 1 μm). The growth rates of the sinuous mode determined from the wave envelope matches with the prediction of a recent theory by Tirumkudulu and Paramati (Communicated to Phys. Of Fluids, 2013) which accounts for the inertia of the liquid phase and the surface tension force in a radial liquid sheet while neglecting the inertial effects due to the surrounding gas phase. The authors acknowledge the financial assistance from Indo-French Center for Pro- motion of Advanced Research and also Indian institute of technology Bombay.

Amyloid Plaques in PSAPP Mice Bind Less Metal than Plaques in Human Alzheimer's Disease

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

Leskovjan, A.; Lanzirotti, A; Miller, L

2009-01-01

Amyloid beta (A{Beta}) is the primary component of Alzheimer's disease (AD) plaques, a key pathological feature of the disease. Metal ions of zinc (Zn), copper (Cu), iron (Fe), and calcium (Ca) are elevated in human amyloid plaques and are thought to be involved in neurodegeneration. Transgenic mouse models of AD also exhibit amyloid plaques, but fail to exhibit the high degree of neurodegeneration observed in humans. In this study, we imaged the Zn, Cu, Fe, and Ca ion distribution in the PSAPP transgenic mouse model representing end-stage AD (N = 6) using synchrotron X-ray fluorescence (XRF) microprobe. In order tomore » account for differences in density in the plaques, the relative protein content was imaged with synchrotron Fourier transform infrared microspectroscopy (FTIRM) on the same samples. FTIRM results revealed a 61% increase in protein content in the plaques compared to the surrounding tissue. After normalizing to protein density, we found that the PSAPP plaques contained only a 29% increase in Zn and there was actually less Cu, Fe, and Ca in the plaque compared to the surrounding tissue. Since metal binding to A{beta} is thought to induce redox chemistry that is toxic to neurons, the reduced metal binding in PSAPP mice is consistent with the lack of neurodegeneration in these animals. These findings were in stark contrast to the high metal ion content observed in human AD plaques, further implicating the role of metal ions in human AD pathology.« less

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.

New method for obliterative treatment of an anterior wall aneurysm in the internal carotid artery: encircling silicone sheet clip procedure--technical case report.

PubMed

Kurokawa, Y; Wanibuchi, M; Ishiguro, M; Inaba, K

2001-08-01

Aneurysms on the anterior surface of the internal carotid artery (ICA) have been shown to be somewhat different from ordinary berry aneurysms because they are rather small, grow rapidly in a short time, and easily lead to rupture, especially during surgery. The most difficult problem is that this type of aneurysm cannot be eliminated easily by an ordinary clipping procedure without causing apparent arterial stenosis or occlusion. A 52-year-old man experienced a subarachnoid hemorrhage because of a ruptured aneurysm located on the anterior surface of the ICA. The tiny aneurysmal body, which was covered with a layer of brain tissue, was successfully exposed. The ICA seemed to be atherosclerotic, and the aneurysmal portion was solitary and had a reddish color. A large silicone sheet encircling clip (Vascwrap; Mizuho Ikakogyo Co., Ltd., Tokyo, Japan) was selected for this patient. The proximal margin of the silicone sheet was incised with a V-shaped cut, and the middle part of the sheet, which covered the diagonal part of the ICA, was trimmed to make it shorter. The blade of the fenestrated clip was applied to obliterate the aneurysm and was attached to the normal arterial wall together with this modified Vascwrap sheet to create a small space between the normal arterial wall and the surrounding Vascwrap sheet. Then tiny pieces of Teflon fiber (E.I. duPont de Nemours and Co., Wilmington, DE) was inserted from both margins, and the whole Vascwrap sheet was sealed with fibrin glue to ensure good adhesion. This method seemed adequate in treating this difficult aneurysm without causing postoperative regrowth or occlusion of the patient's ICA.

Relative impacts of insolation changes, meltwater fluxes and ice sheets on African and Asian monsoons during the Holocene

NASA Astrophysics Data System (ADS)

Marzin, Charline; Braconnot, Pascale; Kageyama, Masa

2013-11-01

In order to better understand the evolution of the Afro-Asian monsoon in the early Holocene, we investigate the impact on boreal summer monsoon characteristics of (1) a freshwater flux in the North Atlantic from the surrounding melting ice sheets and (2) a remnant ice sheet over North America and Europe. Sensitivity experiments run with the IPSL_CM4 model show that both the meltwater flux and the remnant ice sheets induce a cooling of similar amplitude of the North Atlantic leading to a southward shift of the Inter-Tropical Convergence Zone over the tropical Atlantic and to a reduction of the African monsoon. The two perturbations have different impacts in the Asian sector. The meltwater flux results in a weakening of the Indian monsoon and no change in the East Asian monsoon, whereas the remnant ice sheets induce a strengthening of the Indian monsoon and a strong weakening of the East Asian monsoon. Despite the similar coolings in the Atlantic Ocean, the ocean heat transport is reduced only in the meltwater flux experiment, which induces slight differences between the two experiments in the role of the surface latent heat flux in the tropical energetics. In the meltwater experiment, the southward shift of the subtropical jet acts to cool the upper atmosphere over the Tibetan Plateau and hence to weaken the Indian monsoon. In the ice sheet experiment this effect is overwhelmed by the changes in extratropical stationary waves induced by the ice sheets, which are associated with a larger cooling over the Eurasian continent than in the meltwater experiment. However these sensitivity experiments suggest that insolation is the dominant factor explaining the relative changes of the African, Indian and East Asian monsoons from the early to the mid-Holocene.

Study of the vortex conditions of wings with large sweepback by extrapolation of the Jones method

NASA Technical Reports Server (NTRS)

Hirsch, P.

1980-01-01

The pockets of separation originating on the leading edges are surrounded by vortex sheets. Their configuration and intensity were determined by four conditions with the JONES approximation, which is itself corrected by a simple logic. Field pressures and stresses were computed for different cases and are compared with test results (pure deltas, swallow tails, truncations, strakes, ducks, fuselage).

Microstructure evolution and tensile properties of Zr-2.5wt%Nb pressure tubes processed from billets with different microstructures

NASA Astrophysics Data System (ADS)

Kapoor, K.; Saratchandran, N.; Muralidharan, K.

1999-02-01

Starting with identical ingots, billets having different microstructures were obtained by three different processing methods for fabrication of Zr-2.5wt%Nb pressure tubes. The billets were further processed by hot extrusion and cold Pilger tube reducing to the finished product. Microstructural characterization was done at each stage of processing. The effects of the initial billet microstructure on the intermediate and final microstructure and mechanical property results were determined. It was found that the structure at each stage and the final mechanical properties depend strongly on the initial billet microstructure. The structure at the final stage consists of elongated alpha zirconium grains with a network of metastable beta zirconium phase. Some of this metastable phase transforms into stable beta niobium during thermomechanical processing. Billets with quenched structure resulted in less beta niobium at the final stage. The air cooled billets resulted in a large amount of beta niobium. The tensile properties, especially the percentage elongation, were found to vary for the different methods. Higher percentage elongation was observed for billets having quenched structure. Extrusion and forging did not produce any characteristic differences in the properties. The results were used to select a process flow sheet which yields the desired mechanical properties with suitable microstructure in the final product.

Comparison and Analysis of 3,4 dihydrocylmandelic acid (DHMA) and noremetanephrine (NMN) on Amyloid-Beta 40 Monomer for treatment of Alzheimer's Disease using Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Choi, Woosung; Jee, Sang Eun; Jang, Seung Soon

Alzheimer's disease (AD) is type of degenerative dementia caused memory loss and behavior problem. Main reason of AD is Amyloid-Beta 40(A β) mostly composed of α -helix form misfolds to insoluble fibrils and soluble oilgomer. This insoluble fibrils aggregate with beta sheet structure and form the plaque which is caused nurotoxicity in brain. Both 3,4 dihydrocylmandelic acid (DHMA) and noremetanephrine (NMN) are the metabolite of norepinephrine in brain . Also these are inhibit the changing formation of fibrils and maintain the α -helix structure. In this computational modeling study, both NMN and DHMA molecules were modified and analyzed for specific effect on the A β-monomer using molecular dynamics simulation. Using molecular dynamic simulation, NMN and DHMA act as modulator on three A β-monomer batches and could observe the conformational changing of these A β-monomer under the physiologocal condition. This computational experiment is designed to compare and analyze both of chemicals for determining which chamecal would be more effective on the conformation of A β 40 monomer.

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

Fogh, R.H.; Mabbutt, B.C.; Kem, W.R.

Sequence-specific assignments are reported for the 500-MHz H nuclear magnetic resonance (NMR) spectrum of the 48-residue polypeptide neurotoxin I from the sea anemone Stichodactyla helianthus (Sh I). Spin systems were first identified by using two-dimensional relayed or multiple quantum filtered correlation spectroscopy, double quantum spectroscopy, and spin lock experiments. Specific resonance assignments were then obtained from nuclear Overhauser enhancement (NOE) connectivities between protons from residues adjacent in the amino acid sequence. Of a total of 265 potentially observable resonances, 248 (i.e., 94%) were assigned, arising from 39 completely and 9 partially assigned amino acid spin systems. The secondary structure ofmore » Sh I was defined on the basis of the pattern of sequential NOE connectivities. NOEs between protons on separate strands of the polypeptide backbone, and backbone amide exchange rates. Sh I contains a four-stranded antiparallel {beta}-sheet encompassing residues 1-5, 16-24, 30-33, and 40-46, with a {beta}-bulge at residues 17 and 18 and a reverse turn, probably a type II {beta}-turn, involving residues 27-30. No evidence of {alpha}-helical structure was found.« less

The Skylab barium plasma injection experiments. I - Convection observations

NASA Technical Reports Server (NTRS)

Wescott, E. M.; Stenbaek-Nielsen, H. C.; Davis, T. N.; Peek, H. M.

1976-01-01

Two barium-plasma injection experiments were carried out during magnetically active periods in conjunction with the Skylab 3 mission. The high-explosive shaped charges were launched near dawn on November 27 and December 4, 1973, UT. In both cases, the AE index was near 400 gammas, and extensive pulsating auroras covered the sky. The first experiment, Skylab Alpha, occurred in the waning phase of a 1000-gamma substorm, and the second, Skylab Beta, occurred in the expansive phase of an 800-gamma substorm. In both, the convection was generally magnetically eastward, with 100-km-level electric fields near 40 mV/m. However, in the Alpha experiment the observed orientation of the barium flux tube fit theoretical field lines having no parallel current, but the Beta flux-tube orientation indicated a substantial upward parallel sheet current.

Molecular basis for insulin fibril assembly

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

Ivanova, Magdalena I.; Sievers, Stuart A.; Sawaya, Michael R.

2009-12-01

In the rare medical condition termed injection amyloidosis, extracellular fibrils of insulin are observed. We found that the segment of the insulin B-chain with sequence LVEALYL is the smallest segment that both nucleates and inhibits the fibrillation of full-length insulin in a molar ratio-dependent manner, suggesting that this segment is central to the cross-{beta} spine of the insulin fibril. In isolation from the rest of the protein, LVEALYL forms microcrystalline aggregates with fibrillar morphology, the structure of which we determined to 1 {angstrom} resolution. The LVEALYL segments are stacked into pairs of tightly interdigitated {beta}-sheets, each pair displaying the drymore » steric zipper interface typical of amyloid-like fibrils. This structure leads to a model for fibrils of human insulin consistent with electron microscopic, x-ray fiber diffraction, and biochemical studies.« less

Therapeutic index of gramicidin S is strongly modulated by D-phenylalanine analogues at the beta-turn.

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

2009-02-12

Analogues of the cationic antimicrobial peptide gramicidin S (GS), cyclo(Val-Orn-Leu-D-Phe-Pro)2, with d-Phe residues replaced by different (restricted mobility, mostly) surrogates have been synthesized and used in SAR studies against several pathogenic bacteria. While all D-Phe substitutions are shown by NMR to preserve the overall beta-sheet conformation, they entail subtle structural alterations that lead to significant modifications in biological activity. In particular, the analogue incorporating D-Tic (1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid) shows a modest but significant increase in therapeutic index, mostly due to a sharp decrease in hemolytic effect. The fact that NMR data show a shortened distance between the D-Tic aromatic ring and the Orn delta-amino group may help explain the improved antibiotic profile of this analogue.

Electromagnetic ion/ion cyclotron instability - Theory and simulations

NASA Technical Reports Server (NTRS)

Winske, D.; Omidi, N.

1992-01-01

Linear theory and 1D and 2D hybrid simulations are employed to study electromagnetic ion/ion cyclotron (EMIIC) instability driven by the relative streaming of two field-aligned ion beams. The characteristics of the instability are studied as a function of beam density, propagation angle, electron-ion temperature ratios, and ion beta. When the propagation angle is near 90 deg the EMIIC instability has the characteristics of an electrostatic instability, while at smaller angles electromagnetic effects play a significant role as does strong beam coupling. The 2D simulations point to a narrowing of the wave spectrum and accompanying coherent effects during the linear growth stage of development. The EMIIC instability is an important effect where ion beta is low such as in the plasma-sheet boundary layer and upstream of slow shocks in the magnetotail.

Recombinational hotspot specific to female meiosis in the mouse major histocompatibility complex.

PubMed

Shiroishi, T; Hanzawa, N; Sagai, T; Ishiura, M; Gojobori, T; Steinmetz, M; Moriwaki, K

1990-01-01

The wm7 haplotype of the major histocompatibility complex (MHC), derived from the Japanese wild mouse Mus musculus molossinus, enhances recombination specific to female meiosis in the K/A beta interval of the MHC. We have mapped crossover points of fifteen independent recombinants from genetic crosses of the wm7 and laboratory haplotypes. Most of them were confined to a short segment of approximately 1 kilobase (kb) of DNA between the A beta 3 and A beta 2 genes, indicating the presence of a female-specific recombinational hotspot. Its location overlaps with a sex-independent hotspot previously identified in the Mus musculus castaneus CAS3 haplotype. We have cloned and sequenced DNA fragments surrounding the hotspot from the wm7 haplotype and the corresponding regions from the hotspot-negative B10.A and C57BL/10 strains. There is no significant difference between the sequences of these three strains, or between these and the published sequences of the CAS3 and C57BL/6 strains. However, a comparison of this A beta 3/A beta 2 hotspot with a previously characterized hotspot in the E beta gene revealed that they have a very similar molecular organization. Each hotspot consists of two elements, the consensus sequence of the mouse middle repetitive MT family and the tetrameric repeated sequences, which are separated by 1 kb of DNA.

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

Zhao Jincun; Wang Wei; Yuan Zhihong

The spike (S) protein of SARS coronavirus (SARS-CoV) is responsible for viral binding with ACE2 molecules. Its receptor-binding motif (S-RBM) is located between residues 424 and 494, which folds into 2 anti-parallel {beta}-sheets, {beta}5 and {beta}6. We have previously demonstrated that fragment 450-650 of the S protein (S450-650) is predominantly recognized by convalescent sera of SARS patients. The N-terminal 60 residues (450-510) of the S450-650 fragment covers the entire {beta}6 strand of S-RBM. In the present study, we demonstrate that patient sera predominantly recognized 2 linear epitopes outside the {beta}6 fragment, while the mouse antisera, induced by immunization of BALB/cmore » mice with recombinant S450-650, mainly recognized the {beta}6 strand-containing region. Unlike patient sera, however, the mouse antisera were unable to inhibit the infectivity of S protein-expressing (SARS-CoV-S) pseudovirus. Fusion protein between green fluorescence protein (GFP) and S450-650 (S450-650-GFP) was able to stain Vero E6 cells and deletion of the {beta}6 fragment rendered the fusion product (S511-650-GFP) unable to do so. Similarly, recombinant S450-650, but not S511-650, was able to block the infection of Vero E6 cells by the SARS-CoV-S pseudovirus. Co-precipitation experiments confirmed that S450-650 was able to specifically bind with ACE2 molecules in lysate of Vero E6 cells. However, the ability of S450-510, either alone or in fusion with GFP, to bind with ACE2 was significantly poorer compared with S450-650. Our data suggest a possibility that, although the {beta}6 strand alone is able to bind with ACE2 with relatively high affinity, residues outside the S-RBM could also assist the receptor binding of SARS-CoV-S protein.« less

Landforms, sediments and dates to constrain rates and style of marine-influenced ice sheet decay; the BRITICE-CHRONO project.

NASA Astrophysics Data System (ADS)

Clark, Chris

2014-05-01

Uncertainty exists regarding the future mass of the Antarctic and Greenland ice sheets and how they will respond to forcings from sea level, and atmospheric and ocean temperatures. If we want to know more about the mechanisms and rate of change of shrinking ice sheets, then why not examine an ice sheet that has fully disappeared and track its retreat through time? If achieved in enough detail such information on ice retreat could be a data-rich playground for improving the next breed of numerical ice sheet models to be used in ice and sea level forecasting. We regard that the last British-Irish Ice Sheet is a good target for this work, on account of its small size, density of information and with its numerous researchers already investigating it. Geomorphological mapping across the British Isles and the surrounding continental shelf has revealed the nature and distribution of glacial landforms. Here we demonstrate how such data have been used to build a pattern of ice margin retreat. The BRITICE-CHRONO consortium of Quaternary scientists and glaciologists, are now working on a project running from 2012 - 2017 to produce an ice sheet wide database of geochronometric dates to constrain and then understand ice margin retreat. This is being achieved by focusing on 8 transects running from the continental shelf edge to a short distance (10s km) onshore and acquiring marine and terrestrial samples for geochronometric dating. The project includes funding for 587 radiocarbon, 140 OSL and 158 TCN samples for surface exposure dating; with sampling accomplished by two research cruises and 16 fieldwork campaigns. Results will reveal the timing and rate of change of ice margin recession for each transect, and combined with existing landform and dating databases, will be used to build an ice sheet-wide empirical reconstruction of retreat. Simulations using two numerical ice sheet models, fitted against the margin data, will help us understand the nature and significance of sea-level rise and ocean/atmosphere forcing on influencing the rate of retreat and ice sheet demise and the effect that bed topography has in controlling this.

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.

Cometary Dust in the Debris Disks of HD 31648 and HD 163296: Two "Baby" (BETA) Pictoris Stars

NASA Technical Reports Server (NTRS)

Sitko, Michael L.; Grady, Carol A.; Lynch, David K.; Russell, Ray W.; Hanner, Martha S.; Hanner, Martha S.

1999-01-01

The debris disks surrounding the pre-main-sequence stars HD 31648 and HD 163296 were observed spectroscopically between 3 and 14 microns. Both stars possess a silicate emission feature at 10 microns that resembles that of the star beta Pictoris and those observed in solar system comets. The structure of the band is consistent with a mixture of olivine and pyroxene material, plus an underlying continuum of unspecified origin. The similarity in both size and structure of the silicate band suggests that the material in these systems had a processing history similar to that in our own solar system prior to the time that the grains were incorporated into comets.

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.

Electron/ion whistler instabilities and magnetic noise bursts

NASA Technical Reports Server (NTRS)

Akimoto, K.; Gary, S. Peter; Omidi, N.

1987-01-01

Two whistler instabilities are investigated by means of the linear Vlasov dispersion equation. They are called the electron/ion parallel and oblique whistler instabilities, and are driven by electron/ion relative drifts along the magnetic field. It is demonstrated that the enhanced fluctuations from these instabilities can explain several properties of magnetic noise bursts in and near the plasma sheet in the presence of ion beams and/or field-aligned currents. At sufficiently high plasma beta, these instabilities may affect the current system in the magnetotail.

The surgical management of severe macroglossia in systemic AL amyloidosis.

PubMed

Cobb, Alistair R M; Boyapati, Raghu; Walker, Donald Murray; Dunaway, David J; Lloyd, Timothy W

2013-07-01

Amyloidosis is a disease characterised by the deposition in body tissues of amyloid: abnormal protein in a beta pleated sheet formation. It is a systemic disorder and macroglossia may be seen in all forms. Changes to the normal architecture of the tissues and systemic features of the disease and its underlying cause can complicate the surgical management of the enlarged tongue. Copyright © 2012 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Visualization of prostatic nerves by polarization-sensitive optical coherence tomography

PubMed Central

Yoon, Yeoreum; Jeon, Seung Hwan; Park, Yong Hyun; Jang, Won Hyuk; Lee, Ji Youl; Kim, Ki Hean

2016-01-01

Preservation of prostatic nerves is critical to recovery of a man’s sexual potency after radical prostatectomy. A real-time imaging method of prostatic nerves will be helpful for nerve-sparing radical prostatectomy (NSRP). Polarization-sensitive optical coherence tomography (PS-OCT), which provides both structural and birefringent information of tissue, was applied for detection of prostatic nerves in both rat and human prostate specimens, ex vivo. PS-OCT imaging of rat prostate specimens visualized highly scattering and birefringent fibrous structures superficially, and these birefringent structures were confirmed to be nerves by histology or multiphoton microscopy (MPM). PS-OCT could easily distinguish these birefringent structures from surrounding other tissue compartments such as prostatic glands and fats. PS-OCT imaging of human prostatectomy specimens visualized two different birefringent structures, appearing fibrous and sheet-like. The fibrous ones were confirmed to be nerves by histology, and the sheet-like ones were considered to be fascias surrounding the human prostate. PS-OCT imaging of human prostatectomy specimens along the perimeter showed spatial variation in the amount of birefringent fibrous structures which was consistent with anatomy. These results demonstrate the feasibility of PS-OCT for detection of prostatic nerves, and this study will provide a basis for intraoperative use of PS-OCT. PMID:27699090

On a nonlinear state of the electromagnetic ion/ion cyclotron instability

NASA Astrophysics Data System (ADS)

Cremer, M.; Scholer, M.

We have investigated the nonlinear properties of the electromagnetic ion/ion cyclotron instability (EMIIC) by means of hybrid simulations (macroparticle ions, massless electron fluid). The instability is driven by the relative (super-Alfvénic) streaming of two field-aligned ion beams in a low beta plasma (ion thermal pressure to magnetic field pressure) and may be of importance in the plasma sheet boundary layer. As shown in previously reported simulations the waves propagate obliquely to the magnetic field and heat the ions in the perpendicular direction as the relative beam velocity decreases. By running the simulation to large times it can be shown that the large temperature anisotropy leads to the ion cyclotron instability (IC) with parallel propagating Alfvén ion cyclotron waves. This is confirmed by numerically solving the electromagnetic dispersion relation. An application of this property to the plasma sheet boundary layer is discussed.

Sv-map between type I and heterotic sigma models

NASA Astrophysics Data System (ADS)

Fan, Wei; Fotopoulos, A.; Stieberger, S.; Taylor, T. R.

2018-05-01

The scattering amplitudes of gauge bosons in heterotic and open superstring theories are related by the single-valued projection which yields heterotic amplitudes by selecting a subset of multiple zeta value coefficients in the α‧ (string tension parameter) expansion of open string amplitudes. In the present work, we argue that this relation holds also at the level of low-energy expansions (or individual Feynman diagrams) of the respective effective actions, by investigating the beta functions of two-dimensional sigma models describing world-sheets of open and heterotic strings. We analyze the sigma model Feynman diagrams generating identical effective action terms in both theories and show that the heterotic coefficients are given by the single-valued projection of the open ones. The single-valued projection appears as a result of summing over all radial orderings of heterotic vertices on the complex plane representing string world-sheet.

A Structure-Toxicity Study of Aß42 Reveals a New Anti-Parallel Aggregation Pathway

PubMed Central

Vignaud, Hélène; Bobo, Claude; Lascu, Ioan; Sörgjerd, Karin Margareta; Zako, Tamotsu; Maeda, Mizuo; Salin, Benedicte; Lecomte, Sophie; Cullin, Christophe

2013-01-01

Amyloid beta (Aβ) peptides produced by APP cleavage are central to the pathology of Alzheimer’s disease. Despite widespread interest in this issue, the relationship between the auto-assembly and toxicity of these peptides remains controversial. One intriguing feature stems from their capacity to form anti-parallel ß-sheet oligomeric intermediates that can be converted into a parallel topology to allow the formation of protofibrillar and fibrillar Aβ. Here, we present a novel approach to determining the molecular aspects of Aß assembly that is responsible for its in vivo toxicity. We selected Aß mutants with varying intracellular toxicities. In vitro, only toxic Aß (including wild-type Aß42) formed urea-resistant oligomers. These oligomers were able to assemble into fibrils that are rich in anti-parallel ß-sheet structures. Our results support the existence of a new pathway that depends on the folding capacity of Aß . PMID:24244667

Repurposing doxycycline for synucleinopathies: remodelling of α-synuclein oligomers towards non-toxic parallel beta-sheet structured species

PubMed Central

González-Lizárraga, Florencia; Socías, Sergio B.; Ávila, César L.; Torres-Bugeau, Clarisa M.; Barbosa, Leandro R. S.; Binolfi, Andres; Sepúlveda-Díaz, Julia E.; Del-Bel, Elaine; Fernandez, Claudio O.; Papy-Garcia, Dulce; Itri, Rosangela; Raisman-Vozari, Rita; Chehín, Rosana N.

2017-01-01

Synucleinophaties are progressive neurodegenerative disorders with no cure to date. An attractive strategy to tackle this problem is repurposing already tested safe drugs against novel targets. In this way, doxycycline prevents neurodegeneration in Parkinson models by modulating neuroinflammation. However, anti-inflammatory therapy per se is insufficient to account for neuroprotection. Herein we characterise novel targets of doxycycline describing the structural background supporting its effectiveness as a neuroprotector at subantibiotic doses. Our results show that doxycycline reshapes α-synuclein oligomers into off-pathway, high-molecular-weight species that do not evolve into fibrils. Off-pathway species present less hydrophobic surface than on-pathway oligomers and display different β-sheet structural arrangement. These structural changes affect the α-synuclein ability to destabilize biological membranes, cell viability, and formation of additional toxic species. Altogether, these mechanisms could act synergically giving novel targets for repurposing this drug. PMID:28155912

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).

Glacial changes in warm pool climate dominated by shelf exposure and ice sheet albedo

NASA Astrophysics Data System (ADS)

Di Nezio, P. N.; Tierney, J. E.; Otto-Bliesner, B. L.; Timmermann, A.; Bhattacharya, T.; Brady, E. C.; Rosenbloom, N. A.

2017-12-01

The mechanisms driving glacial-interglacial changes in the climate of the Indo-Pacific warm pool (IPWP) are unclear. We addressed this issue combining model simulations and paleoclimate reconstructions of the Last Glacial Maximum (LGM). Two drivers - the exposure of tropical shelves due to lower sea level and a monsoonal response to ice sheet albedo - explain the proxy-inferred patterns of hydroclimate change. Shelf exposure influences IPWP climate by weakening the ascending branch of the Walker circulation. This response is amplified by coupled interactions akin to the Bjerknes feedback involving a stronger sea-surface temperature (SST) gradient along the equatorial Indian Ocean (IO). Ice sheet albedo enhances the import of cold, dry air into the tropics, weakening the Afro-Asian monsoon system. This "ventilation" mechanism alters temperature contrasts between the Arabian Sea and surrounding land leading to further monsoon weakening. Additional simulations show that the altered SST patterns associated with these responses are essential for explaining the proxy-inferred changes. Together our results show that ice sheets are a first order driver of tropical climate on glacial-interglacial timescales. While glacial climates are not a straightforward analogue for the future, our finding of an active Bjerknes feedback deserves further attention in the context of future climate projections.

How ice age climate got the shakes

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

Kerr, R.A.

1993-05-14

Records in Greenland ice, ocean mud, and ancient corals are revealing abrupt climate shifts during the last ice age. The climate at the end of the last ice age apparently jumped from cold to warmer conditions, jumped back to cold, and then jumped into the present warm weather conditions. The mechanism for this erratic behavior is unknown, but appears to be an interaction of North Atlantic ocean currents and the ice sheets themselves. Warm water from the tropics would evaporate and become more saline and dense as it moved north. The colder, denser water would then sink and flow backmore » to the tropics. The melting of ice caused by the warm water would decrease the salinity of the North Atlantic current, the water would not sink, the return current would be shut down, and the waters surrounding the ice sheets would become colder, slowing melting of the sheets. The cycle could be started again by collapse of the ice sheets from their internal heat. There may be other switches that could cause sudden climate change, as may be evidenced by links between changes in the Pacific and a decade of erratic weather in North America. Researcher would like to identify these switches to prevent them from being activated by human activity.« less

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

PubMed

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

1996-06-21

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

Coupling between Mercury and its nightside magnetosphere: Cross-tail current sheet asymmetry and substorm current wedge formation

NASA Astrophysics Data System (ADS)

Poh, Gangkai; Slavin, James A.; Jia, Xianzhe; Raines, Jim M.; Imber, Suzanne M.; Sun, Wei-Jie; Gershman, Daniel J.; DiBraccio, Gina A.; Genestreti, Kevin J.; Smith, Andy W.

2017-08-01

We analyzed MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) magnetic field and plasma measurements taken during 319 crossings of Mercury's cross-tail current sheet. We found that the measured BZ in the current sheet is higher on the dawnside than the duskside by a factor of ≈3 and the asymmetry decreases with downtail distance. This result is consistent with expectations based upon MHD stress balance. The magnetic fields threading the more stretched current sheet in the duskside have a higher plasma beta than those on the dawnside, where they are less stretched. This asymmetric behavior is confirmed by mean current sheet thickness being greatest on the dawnside. We propose that heavy planetary ion (e.g., Na+) enhancements in the duskside current sheet provides the most likely explanation for the dawn-dusk current sheet asymmetries. We also report the direct measurement of Mercury's substorm current wedge (SCW) formation and estimate the total current due to pileup of magnetic flux to be ≈11 kA. The conductance at the foot of the field lines required to close the SCW current is found to be ≈1.2 S, which is similar to earlier results derived from modeling of Mercury's Region 1 field-aligned currents. Hence, Mercury's regolith is sufficiently conductive for the current to flow radially then across the surface of Mercury's highly conductive iron core. Mercury appears to be closely coupled to its nightside magnetosphere by mass loading of upward flowing heavy planetary ions and electrodynamically by field-aligned currents that transfer momentum and energy to the nightside auroral oval crust and interior. Heavy planetary ion enhancements in Mercury's duskside current sheet provide explanation for cross-tail asymmetries found in this study. The total current due to the pileup of magnetic flux and conductance required to close the SCW current is found to be ≈11 kA and 1.2 S. Mercury is coupled to magnetotail by mass loading of heavy ions and field-aligned currents driven by reconnection-related fast plasma flow.

Biotin uptake by mouse and human pancreatic beta cells/islets: a regulated, lipopolysaccharide-sensitive carrier-mediated process

PubMed Central

Ghosal, Abhisek; Sekar, Thillai V.

2014-01-01

Biotin is essential for the normal function of pancreatic beta cells. These cells obtain biotin from their surroundings via transport across their cell membrane. Little is known about the uptake mechanism involved, how it is regulated, and how it is affected by internal and external factors. We addressed these issues using the mouse-derived pancreatic beta-TC-6 cells and freshly isolated mouse and human primary pancreatic beta cells as models. The results showed biotin uptake by pancreatic beta-TC-6 cells occurs via a Na+-dependent, carrier-mediated process, that is sensitive to desthiobiotin, as well as to pantothenic acid and lipoate; the process is also saturable as a function of concentration (apparent Km = 22.24 ± 5.5 μM). These cells express the sodium-dependent multivitamin transporter (SMVT), whose knockdown (with doxycycline-inducible shRNA) led to a sever inhibition in biotin uptake. Similarly, uptake of biotin by mouse and human primary pancreatic islets is Na+-dependent and carrier-mediated, and both cell types express SMVT. Biotin uptake by pancreatic beta-TC-6 cells is also adaptively regulated (via transcriptional mechanism) by extracellular substrate level. Chronic treatment of pancreatic beta-TC-6 cells with bacterial lipopolysaccharides (LPS) leads to inhibition in biotin uptake. This inhibition is mediated via a Toll-Like receptor 4-mediated process and involves a decrease in membrane expression of SMVT. These findings show, for the first time, that pancreatic beta cells/islets take up biotin via a specific and regulated carrier-mediated process, and that the process is sensitive to the effect of LPS. PMID:24904078

Mechanical design of the third FnIII domain of tenascin-C.

PubMed

Peng, Qing; Zhuang, Shulin; Wang, Meijia; Cao, Yi; Khor, Yuanai; Li, Hongbin

2009-03-13

By combining single-molecule atomic force microscopy (AFM), proline mutagenesis and steered molecular dynamics (SMD) simulations, we investigated the mechanical unfolding dynamics and mechanical design of the third fibronectin type III domain of tenascin-C (TNfn3) in detail. We found that the mechanical stability of TNfn3 is similar to that of other constituting FnIII domains of tenascin-C, and the unfolding process of TNfn3 is an apparent two-state process. By employing proline mutagenesis to block the formation of backbone hydrogen bonds and introduce structural disruption in beta sheet, we revealed that in addition to the important roles played by hydrophobic core packing, backbone hydrogen bonds in beta hairpins are also responsible for the overall mechanical stability of TNfn3. Furthermore, proline mutagenesis revealed that the mechanical design of TNfn3 is robust and the mechanical stability of TNfn3 is very resistant to structural disruptions caused by proline substitutions in beta sheets. Proline mutant F88P is one exception, as the proline mutation at position 88 reduced the mechanical stability of TNfn3 significantly and led to unfolding forces of < 20 pN. This result suggests that Phe88 is a weak point of the mechanical resistance for TNfn3. We used SMD simulations to understand the molecular details underlying the mechanical unfolding of TNfn3. The comparison between the AFM results and SMD simulations revealed similarities and discrepancies between the two. We compared the mechanical unfolding and design of TNfn3 and its structural homologue, the tenth FnIII domain from fibronectin. These results revealed the complexity underlying the mechanical design of FnIII domains and will serve as a starting point for systematically analyzing the mechanical architecture of other FnIII domains in tenascins-C, and will help to gain a better understanding of some of the complex features observed for the stretching of native tenascin-C.

The 2.2 A resolution structure of the O(H) blood-group-specific lectin I from Ulex europaeus.

PubMed

Audette, G F; Vandonselaar, M; Delbaere, L T

2000-12-01

The tertiary and quaternary structure of the lectin I from Ulex europaeus (UE-I) has been determined to 2.2 A resolution. UE-I is a dimeric metalloglycoprotein that binds the H-type 2 human blood group determinant [alpha-L-Fucalpha(1-->2)-beta-D-Galbeta(1-->4)-beta-D-Glc NAcalpha-]. Nine changes from the published amino acid sequence were necessary to account for the electron density. The quaternary structural organization of UE-I is that of the most commonly occurring legume lectin dimer. The tertiary structure of the monomeric subunits is similar to that in the conventional lectin subunit; however, some structural differences are noted. These differences include a four-stranded anti-parallel "S" sheet in UE-I versus the five-stranded S sheet in other lectin monomers. The Ala residue of the Ala-Asp cis-peptide bond present in the carbohydrate-binding site of the conventional lectin monomer is replaced with a Thr in the UE-I structure. Also, a novel disulfide bridge linking Cys115 and Cys150 is present. There are two metallic ions, one calcium and the other manganese, per subunit. N-linked oligosaccharides are at residues 23 and 111 of each subunit. One molecule of R-2-methyl-2, 4-pentanediol (R-MPD) is present in a shallow depression on the surface of each subunit. In order to examine the binding of the H-type 2 blood group determinant by UE-I, its beta-methyl glycoside (H-type 2-OMe) was docked into the binding site of R-MPD. The epitope previously identified for H-type 2-OMe by chemical mapping proved, with only minor adjustment of amino acid residues, to be complementary to the shallow cavity occupied by R-MPD in the structure. Several key interactions have been proposed between the H-type 2-OMe and UE-I. Copyright 2000 Academic Press.

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.

Effects of selenium on the structure and function of recombinant human S-adenosyl-L-methionine dependent arsenic (+3 oxidation state) methyltransferase in E. coli.

PubMed

Geng, Zhirong; Song, Xiaoli; Xing, Zhi; Geng, Jinlong; Zhang, Sichun; Zhang, Xinrong; Wang, Zhilin

2009-05-01

The effects of Se(IV) on the structure and function of recombinant human arsenic (+3 oxidation state) methyltransferase (AS3MT) purified from the cytoplasm of Escherichia coli were studied. The coding region of human AS3MT complementary DNA was amplified from total RNA extracted from HepG2 cell by reverse transcription PCR. Soluble and active human AS3MT was expressed in the E. coli with a Trx fusion tag under a lower induction temperature of 25 degrees C. Spectra (UV-vis, circular dichroism, and fluorescence) were first used to probe the interaction of Se(IV) and recombinant human AS3MT and the structure-function relationship of the enzyme. The recombinant human AS3MT had a secondary structure of 29.0% alpha-helix, 23.9% beta-pleated sheet, 17.9% beta-turn, and 29.2% random coil. When Se(IV) was added, the content of the alpha-helix did not change, but that of the beta-pleated sheet increased remarkably in the conformation of recombinant human AS3MT. Se(IV) inhibited the enzymatic methylation of inorganic As(III) in a concentration-dependent manner. The IC(50) value for Se(IV) was 2.38 muM. Double-reciprocal (1/V vs. 1/[inorganic As(III)]) plots showed Se(IV) to be a noncompetitive inhibitor of the methylation of inorganic As(III) by recombinant human AS3MT with a K (i) value of 2.61 muM. We hypothesized that Se(IV) interacts with the sulfhydryl group of cysteine(s) in the structural residues rather than the cysteines of the active site (Cys156 and Cys206). When Se(IV) was combined with cysteine(s) in the structural residues, the conformation of recombinant human AS3MT changed and the enzymatic activity decreased. Considering the quenching of tryptophan fluorescence, Cys72 and/or Cys226 are deduced to be primary targets for Se(IV).

How main-chains of proteins explore the free-energy landscape in native states.

PubMed

Senet, Patrick; Maisuradze, Gia G; Foulie, Colette; Delarue, Patrice; Scheraga, Harold A

2008-12-16

Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an alpha/beta protein (crambin) and a beta-sheet polypeptide (BS2) in their "native" states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive C(alpha) atoms, increases as a power law of time, t(alpha), with an exponent alpha between 0.08 and 0.39 (alpha = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles.

Sensitivity experiments with a one-dimensional coupled plume - iceflow model

NASA Astrophysics Data System (ADS)

Beckmann, Johanna; Perette, Mahé; Alexander, David; Calov, Reinhard; Ganopolski, Andrey

2016-04-01

Over the last few decades Greenland Ice sheet mass balance has become increasingly negative, caused by enhanced surface melting and speedup of the marine-terminating outlet glaciers at the ice sheet margins. Glaciers speedup has been related, among other factors, to enhanced submarine melting, which in turn is caused by warming of the surrounding ocean and less obviously, by increased subglacial discharge. While ice-ocean processes potentially play an important role in recent and future mass balance changes of the Greenland Ice Sheet, their physical understanding remains poorly understood. In this work we performed numerical experiments with a one-dimensional plume model coupled to a one-dimensional iceflow model. First we investigated the sensitivity of submarine melt rate to changes in ocean properties (ocean temperature and salinity), to the amount of subglacial discharge and to the glacier's tongue geometry itself. A second set of experiments investigates the response of the coupled model, i.e. the dynamical response of the outlet glacier to altered submarine melt, which results in new glacier geometry and updated melt rates.

Lightweight Radiator System for a Spacecraft

NASA Technical Reports Server (NTRS)

Copeland, Robert J.; Mason, Georgia; Weislogel, Mark M.

2005-01-01

Three documents describe various aspects of a proposed lightweight, deployable radiator system for dissipating excess heat from the life-support system of a habitable spacecraft. The first document focuses on a radiator tube that would include a thin metal liner surrounded and supported by a thicker carbon-fiber-reinforced composite tubular structure that, in turn, would be formed as part of a unitary composite radiator-fin structure consisting mostly of a sheet of reticulated vitreous carbon laminated between carbon-fiber-reinforced face sheets. The thermal and mechanical properties, including the anisotropies, of the component materials are taken into account in the design. The second document describes thermo-structural bumpers, in the form of exterior multiple-ply carbon-fiber sheets enclosing hollows on opposite sides of a radiator fin, which would protect the radiator tube against impinging micrometeors and orbital debris. The third document describes a radiator system that would include multiple panels containing the aforementioned components, among others. The system would also include mechanisms for deploying the panels from compact stowage. Deployment would not involve breaking and remaking of fluid connections to the radiator panels.

“In Silico” Characterization of 3-Phytase A and 3-Phytase B from Aspergillus niger

PubMed Central

Niño-Gómez, Doris C.; Rivera-Hoyos, Claudia M.; Morales-Álvarez, Edwin D.; Vargas-Alejo, Nury E.; Ramírez-Casallas, Ingrid N.; Erkan Türkmen, Kübra; Sáenz-Suárez, Homero; Sáenz-Moreno, José A.; González-Santos, Janneth; Arévalo-Galvis, Azucena

2017-01-01

Phytases are used for feeding monogastric animals, because they hydrolyze phytic acid generating inorganic phosphate. Aspergillus niger 3-phytase A (PDB: 3K4Q) and 3-phytase B (PDB: 1QFX) were characterized using bioinformatic tools. Results showed that both enzymes have highly conserved catalytic pockets, supporting their classification as histidine acid phosphatases. 2D structures consist of 43% alpha-helix, 12% beta-sheet, and 45% others and 38% alpha-helix, 12% beta-sheet, and 50% others, respectively, and pI 4.94 and 4.60, aliphatic index 72.25 and 70.26 and average hydrophobicity of −0,304 and −0.330, respectively, suggesting aqueous media interaction. Glycosylation and glycation sites allowed detecting zones that can affect folding and biological activity, suggesting fragmentation. Docking showed that H59 and H63 act as nucleophiles and that D339 and D319 are proton donor residues. MW of 3K4Q (48.84 kDa) and 1QFX (50.78 kDa) is similar; 1QFX forms homodimers which will originate homotetramers with several catalytic center accessible to the ligand. 3K4Q is less stable (instability index 45.41) than 1QFX (instability index 33.66), but the estimated lifespan for 3K4Q is superior. Van der Waals interactions generate hydrogen bonds between the active center and O2 or H of the phytic acid phosphate groups, providing greater stability to these temporal molecular interactions. PMID:29348934

"In Silico" Characterization of 3-Phytase A and 3-Phytase B from Aspergillus niger.

PubMed

Niño-Gómez, Doris C; Rivera-Hoyos, Claudia M; Morales-Álvarez, Edwin D; Reyes-Montaño, Edgar A; Vargas-Alejo, Nury E; Ramírez-Casallas, Ingrid N; Erkan Türkmen, Kübra; Sáenz-Suárez, Homero; Sáenz-Moreno, José A; Poutou-Piñales, Raúl A; González-Santos, Janneth; Arévalo-Galvis, Azucena

2017-01-01

Phytases are used for feeding monogastric animals, because they hydrolyze phytic acid generating inorganic phosphate. Aspergillus niger 3-phytase A (PDB: 3K4Q) and 3-phytase B (PDB: 1QFX) were characterized using bioinformatic tools. Results showed that both enzymes have highly conserved catalytic pockets, supporting their classification as histidine acid phosphatases. 2D structures consist of 43% alpha-helix, 12% beta-sheet, and 45% others and 38% alpha-helix, 12% beta-sheet, and 50% others, respectively, and pI 4.94 and 4.60, aliphatic index 72.25 and 70.26 and average hydrophobicity of -0,304 and -0.330, respectively, suggesting aqueous media interaction. Glycosylation and glycation sites allowed detecting zones that can affect folding and biological activity, suggesting fragmentation. Docking showed that H 59 and H 63 act as nucleophiles and that D 339 and D 319 are proton donor residues. MW of 3K4Q (48.84 kDa) and 1QFX (50.78 kDa) is similar; 1QFX forms homodimers which will originate homotetramers with several catalytic center accessible to the ligand. 3K4Q is less stable (instability index 45.41) than 1QFX (instability index 33.66), but the estimated lifespan for 3K4Q is superior. Van der Waals interactions generate hydrogen bonds between the active center and O 2 or H of the phytic acid phosphate groups, providing greater stability to these temporal molecular interactions.

Interaction of insulin with colloidal ZnS quantum dots functionalized by various surface capping agents.

PubMed

Hosseinzadeh, Ghader; Maghari, Ali; Farniya, Seyed Morteza Famil; Keihan, Amir Homayoun; Moosavi-Movahedi, Ali A

2017-08-01

Interaction of quantum dots (QDs) and proteins strongly influenced by the surface characteristics of the QDs at the protein-QD interface. For a precise control of these surface-related interactions, it is necessary to improve our understanding in this field. In this regard, in the present work, the interaction between the insulin and differently functionalized ZnS quantum dots (QDs) were studied. The ZnS QDs were functionalized with various functional groups of hydroxyl (OH), carboxyl (COOH), amine (NH 2 ), and amino acid (COOH and NH 2 ). The effect of surface hydrophobicity was also studied by changing the alkyl-chain lengths of mercaptocarboxylic acid capping agents. The interaction between insulin and the ZnS QDs were investigated by fluorescence quenching, synchronous fluorescence, circular dichroism (CD), and thermal aggregation techniques. The results reveal that among the studied QDs, mercaptosuccinic acid functionalized QDs has the strongest interaction (∆G ° =-51.50kJ/mol at 310K) with insulin, mercaptoethanol functionalized QDs destabilize insulin by increasing the beta-sheet contents, and only cysteine functionalized QDs improves the insulin stability by increasing the alpha-helix contents of the protein, and. Our results also indicate that by increasing the alkyl-chain length of capping agents, due to an increase in hydrophobicity of the QDs surface, the beta-sheet contents of insulin increase which results in the enhancement of insulin instability. Copyright © 2017 Elsevier B.V. All rights reserved.

Kinetic stabilization of Bacillus licheniformis alpha-amylase through introduction of hydrophobic residues at the surface.

PubMed

Machius, Mischa; Declerck, Nathalie; Huber, Robert; Wiegand, Georg

2003-03-28

It is generally assumed that in proteins hydrophobic residues are not favorable at solvent-exposed sites, and that amino acid substitutions on the surface have little effect on protein thermostability. Contrary to these assumptions, we have identified hyperthermostable variants of Bacillus licheniformis alpha-amylase (BLA) that result from the incorporation of hydrophobic residues at the surface. Under highly destabilizing conditions, a variant combining five stabilizing mutations unfolds 32 times more slowly and at a temperature 13 degrees C higher than the wild-type. Crystal structure analysis at 1.7 A resolution suggests that stabilization is achieved through (a) extension of the concept of increased hydrophobic packing, usually applied to cavities, to surface indentations, (b) introduction of favorable aromatic-aromatic interactions on the surface, (c) specific stabilization of intrinsic metal binding sites, and (d) stabilization of a beta-sheet by introducing a residue with high beta-sheet forming propensity. All mutated residues are involved in forming complex, cooperative interaction networks that extend from the interior of the protein to its surface and which may therefore constitute "weak points" where BLA unfolding is initiated. This might explain the unexpectedly large effect induced by some of the substitutions on the kinetic stability of BLA. Our study shows that substantial protein stabilization can be achieved by stabilizing surface positions that participate in underlying cooperatively formed substructures. At such positions, even the apparently thermodynamically unfavorable introduction of hydrophobic residues should be explored.

The effect of freeze-dried antibody concentrations on its stability in the presence of trehalose and hydroxypropyl-β-cyclodextrin: a Box-Behnken statistical design.

PubMed

Faghihi, Homa; Khalili, Fatemeh; Amini, Mohsen; Vatanara, Alireza

2017-09-01

The present study aimed at preparation and optimization of stable freeze-dried immunoglobulin G (IgG) applying proper amount of antibody with efficient combination of trehalose and hydroxypropyl-β-cyclodextrin (HPβCD). Response surface methodology was employed through a three-factor, three-level Box-Behnken design. Amounts of IgG (X 1 ), trehalose (X 2 ) and HPβCD (X 3 ) were independent variables. Aggregation following process (Y 1 ), after one month at 45 °C (Y 2 ), upon two month at 45 °C (Y 3 ) and beta-sheet content of IgG (Y 4 ) were determined as dependent variables. Results were fitted to quadratic models (except for beta-sheet content), describing the inherent relationship between main factors. Optimized formulation composed of 55.85 mg IgG, 52.51 mg trehalose and 16.01 mg HPβCD was prepared. The calculated responses of the optimized formulation were as follows: Y 1  = 0.19%, Y 2  = 0.78%, Y 3  = 1.88% and Y 4  = 68.60%, respectively. The thermal analysis confirmed the amorphous nature of optimum formulation and the integrity of IgG was shown to be favorably preserved. Validation of the optimization study demonstrated high degree of prognostic ability. The DOE study successfully predicted the optimum values of antibody as well as stabilizers for desirable process and storage stabilization of freeze-dried IgG.

Metal binding characterization and conformational studies using Raman microscopy of resin-bound poly(aspartic acid).

PubMed

Stair, Jacqueline L; Holcombe, James A

2007-03-01

The metal binding capacities, conditional stability constants, and secondary structure of immobilized polyaspartic acid (PLAsp) (n = 6, 20, and 30) on TentaGel resin were determined when binding Mg2+, Co2+, Cd2+, and Ni2+. Metal binding to the synthesized peptides was evaluated using breakthrough curves from a packed microcolumn and flame atomic absorption spectrophotometry (FAAS) detection. The metal capacities reached values of 590, 2160, and 3710 mumol of metal/g of resin for the 6-mer, 20-mer, and 30-mer, respectively, and this resulted in 2-3 residues per metal for all peptides and metals tested. Surprisingly, the concentrated environment of the resin along with the spatial distribution of attachment groups allowed for most residues to participate in metal binding regardless of the peptide length. Conditional stability constants calculated using single metal binding isotherms indicated that binding strength decreased as the chain length increased on the resin. Raman microscopy on single beads was used to determine PLAsp secondary structure, and all peptides were of a mixed conformation (i.e., beta-sheets, alpha-helices, random chain, etc.) during neutral conditioning and metal binding. Uniquely, the longer 20-mer and 30-mer peptides showed a distinct change from a mixed conformation to beta-sheets and alpha-helices during metal release with acid. This study confirms that metal release by longer immobilized peptides is often assisted by a conformational change, which easily spoils the binding cavity, while shorter peptides may release metal primarily by H+ displacement.

A Logical OR Redundancy within the Asx-Pro-Asx-Gly Type 1 {Beta}-Turn Motif

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

Lee, Jihun; Dubey, Vikash Kumar; Longo, Lian M.

2008-04-19

Turn secondary structure is essential to the formation of globular protein architecture. Turn structures are, however, much more complex than either {alpha}-helix or {beta}-sheet, and the thermodynamics and folding kinetics are poorly understood. Type I {beta}-turns are the most common type of reverse turn, and they exhibit a statistical consensus sequence of Asx-Pro-Asx-Gly (where Asx is Asp or Asn). A comprehensive series of individual and combined Asx mutations has been constructed within three separate type I 3:5 G1 bulge {beta}-turns in human fibroblast growth factor-1, and their effects on structure, stability, and folding have been determined. The results show amore » fundamental logical OR relationship between the Asx residues in the motif, involving H-bond interactions with main-chain amides within the turn. These interactions can be modulated by additional interactions with residues adjacent to the turn at positions i + 4 and i + 6. The results show that the Asx residues in the turn motif make a substantial contribution to the overall stability of the protein, and the Asx logical OR relationship defines a redundant system that can compensate for deleterious point mutations. The results also show that the stability of the turn is unlikely to be the prime determinant of formation of turn structure in the folding transition state.« less

Molecular architecture of human prion protein amyloid: a parallel, in-register beta-structure.

PubMed

Cobb, Nathan J; Sönnichsen, Frank D; McHaourab, Hassane; Surewicz, Witold K

2007-11-27

Transmissible spongiform encephalopathies (TSEs) represent a group of fatal neurodegenerative diseases that are associated with conformational conversion of the normally monomeric and alpha-helical prion protein, PrP(C), to the beta-sheet-rich PrP(Sc). This latter conformer is believed to constitute the main component of the infectious TSE agent. In contrast to high-resolution data for the PrP(C) monomer, structures of the pathogenic PrP(Sc) or synthetic PrP(Sc)-like aggregates remain elusive. Here we have used site-directed spin labeling and EPR spectroscopy to probe the molecular architecture of the recombinant PrP amyloid, a misfolded form recently reported to induce transmissible disease in mice overexpressing an N-terminally truncated form of PrP(C). Our data show that, in contrast to earlier, largely theoretical models, the con formational conversion of PrP(C) involves major refolding of the C-terminal alpha-helical region. The core of the amyloid maps to C-terminal residues from approximately 160-220, and these residues form single-molecule layers that stack on top of one another with parallel, in-register alignment of beta-strands. This structural insight has important implications for understanding the molecular basis of prion propagation, as well as hereditary prion diseases, most of which are associated with point mutations in the region found to undergo a refolding to beta-structure.

A dynamic early East Antarctic Ice Sheet suggested by ice-covered fjord landscapes.

PubMed

Young, Duncan A; Wright, Andrew P; Roberts, Jason L; Warner, Roland C; Young, Neal W; Greenbaum, Jamin S; Schroeder, Dustin M; Holt, John W; Sugden, David E; Blankenship, Donald D; van Ommen, Tas D; Siegert, Martin J

2011-06-02

The first Cenozoic ice sheets initiated in Antarctica from the Gamburtsev Subglacial Mountains and other highlands as a result of rapid global cooling ∼34 million years ago. In the subsequent 20 million years, at a time of declining atmospheric carbon dioxide concentrations and an evolving Antarctic circumpolar current, sedimentary sequence interpretation and numerical modelling suggest that cyclical periods of ice-sheet expansion to the continental margin, followed by retreat to the subglacial highlands, occurred up to thirty times. These fluctuations were paced by orbital changes and were a major influence on global sea levels. Ice-sheet models show that the nature of such oscillations is critically dependent on the pattern and extent of Antarctic topographic lowlands. Here we show that the basal topography of the Aurora Subglacial Basin of East Antarctica, at present overlain by 2-4.5 km of ice, is characterized by a series of well-defined topographic channels within a mountain block landscape. The identification of this fjord landscape, based on new data from ice-penetrating radar, provides an improved understanding of the topography of the Aurora Subglacial Basin and its surroundings, and reveals a complex surface sculpted by a succession of ice-sheet configurations substantially different from today's. At different stages during its fluctuations, the edge of the East Antarctic Ice Sheet lay pinned along the margins of the Aurora Subglacial Basin, the upland boundaries of which are currently above sea level and the deepest parts of which are more than 1 km below sea level. Although the timing of the channel incision remains uncertain, our results suggest that the fjord landscape was carved by at least two iceflow regimes of different scales and directions, each of which would have over-deepened existing topographic depressions, reversing valley floor slopes.

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

Wang Shumin; Tian Hongwei; Pei Yanhui

A novel hedgehog-like core/shell structure, consisting of a high density of vertically aligned graphene sheets and a thin graphene shell/a copper core (VGs-GS/CC), has been synthesized via a simple one-step synthesis route using radio-frequency plasma-enhanced chemical vapor deposition (RF-PECVD). Scanning and transmission electron microscopy investigations show that the morphology of this core/shell material could be controlled by deposition time. For a short deposition time, only multilayer graphene shell tightly surrounds the copper particle, while as the deposition time is relative long, graphene sheets extend from the surface of GS/CC. The GS can protect CC particles from oxidation. The growth mechanismmore » for the obtained GS/CC and VGs-GS/CC has been revealed. Compared to VGs, VGs-GS/CC material exhibits a better electron field emission property. This investigation opens a possibility for designing a core/shell structure of different carbon-metal hybrid materials for a wide variety of practical applications. - Graphical abstract: With increasing deposition time, graphene sheets extend from the surface of GS/CC, causing the multilayer graphene encapsulated copper to be converted into vertically aligned graphene sheets-graphene shell/copper core structure. Highlights: Black-Right-Pointing-Pointer A novel hedgehog-like core/shell structure has been synthesized. Black-Right-Pointing-Pointer The structure consists of vertical graphene sheets-graphene shell and copper core. Black-Right-Pointing-Pointer The morphology of VGs-GS/CC can be controlled by choosing a proper deposition time. Black-Right-Pointing-Pointer With increasing deposition time, graphene sheets extend from the surface of GS/CC. Black-Right-Pointing-Pointer VGs-GS/CC exhibits a better electron field emission property as compared with VGs.« less

MTR WING, TRA604. PRECAST CONCRETE PANELS AND DIMENSIONS. TYPES A, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

MTR WING, TRA-604. PRECAST CONCRETE PANELS AND DIMENSIONS. TYPES A, B, C, D, E, AND F; AND HOW THEY ARE CONNECTED. TYPES C AND D ARE ON WEST SIDE WHERE GLASS BLOCKS SURROUND ENTRY DOOR. BLAW-KNOX 3150-804-20, SHEET #1, 11/1950. INL INDEX NO. 531-0604-62-098-100644, REV. 0. - Idaho National Engineering Laboratory, Test Reactor Area, Materials & Engineering Test Reactors, Scoville, Butte County, ID

Identification of pH-sensitive regions in the mouse prion by the cysteine-scanning spin-labeling ESR technique

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

Watanabe, Yasuko; Inanami, Osamu; Horiuchi, Motohiro

2006-11-24

We analyzed the pH-induced mobility changes in moPrP{sup C} {alpha}-helix and {beta}-sheets by cysteine-scanning site-directed spin labeling (SDSL) with ESR. Nine amino acid residues of {alpha}-helix1 (H1, codon 143-151), four amino acid residues of {beta}-sheet1 (S1, codon 127-130), and four amino acid residues of {beta}-sheet2 (S2, codon 160-163) were substituted for by cysteine residues. These recombinant mouse PrP{sup C} (moPrP{sup C}) mutants were reacted with a methane thiosulfonate sulfhydryl-specific spin labeling reagent (MTSSL). The 1/{delta}H of the central ({sup 14}N hyperfine) component (M{sub I} = 0) in the ESR spectrum of spin-labeled moPrP{sup C} was measured as a mobility parametermore » of nitroxide residues (R1). The mobilities of E145R1 and Y149R1 at pH 7.4, which was identified as a tertiary contact site by a previous NMR study of moPrP, were lower than those of D143R1, R147R1, and R150R1 reported on the helix surface. Thus, the mobility in the H1 region in the neutral solution was observed with the periodicity associated with a helical structure. On the other hand, the values in the S2 region, known to be located in the buried side, were lower than those in the S1 region located in the surface side. These results indicated that the mobility parameter of the nitroxide label was well correlated with the 3D structure of moPrP. Furthermore, the present study clearly demonstrated three pH-sensitive sites in moPrP, i.e. (1) the N-terminal tertiary contact site of H1 (2) the C-terminal end of H1, and (3) the S2 region. In particular, among these pH-sensitive sites, the N-terminal tertiary contact region of H1 was found to be the most pH-sensitive one and was easily converted to a flexible structure by a slight decrease of pH in the solution. These data provided molecular evidence to explain the cellular mechanism for conversion from PrP{sup C} to PrP{sup Sc} in acidic organelles such as the endosome.« less

A rare cause of hypertension in children: intrathoracic pheochromocytoma.

PubMed

Singh, Jaswinder; Rana, Sandeep Singh; Sharma, Rajeshwar; Ghai, Babita; Puri, G D

2008-07-01

Mediastinal pheochromocytomas account for only a small fraction of mediastinal tumors. Most commonly, these tumors are located in posterior mediastinum. Increasing number of cases of pheochromocytomas is being reported from middle mediastinum. Excision of mediastinal paraganglioma is often hazardous because of its rich blood supply and tendency to involve surrounding structures. It can be a big challenge to manage asymptomatic cases of pheochromocytoma intraoperatively. It is imperative that these patients receive adequate alpha adrenergic and if necessary beta adrenergic blockade. Adequate preoperative preparation with alpha and beta blockers may not prevent serious intraoperative hypertension. We report a case of posterior mediastinal pheochromocytoma which was biochemically active preoperatively. We review the presentation, diagnosis and management of intrathoracic pheochromocytomas including cardiac pheochromocytomas.

Molecular Gas Clumps from the Destruction of Icy Bodies in the beta Pictoris Debris Disk

NASA Technical Reports Server (NTRS)

Dent, W. R. F.; Wyatt, M. C.; Roberge, A.; Augereau, J. -C.; Casassus, S.; Corder, S.; Greaves, J. S.; DeGregorio-Monsalvo, I.; Hales, A.; Jackson, A. P.;

The MAJORANA DEMONSTRATOR Neutrinoless Double-Beta Decay Experiment

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

Abgrall, N.; Aguayo, Estanislao; Avignone, Frank T.

2014-06-01

The MAJORANA DEMONSTRATOR will search for the neutrinoless double-beta (ββ(0ν)) decay of the isotope 76Ge with a mixed array of enriched and natural germanium detectors. The observation of this rare decay would indicate that the neutrino is its own antiparticle, demonstrate that lepton number is not conserved, and provide information on the absolute mass scale of the neutrino. The DEMONSTRATOR is being assembled at the 4850-foot level of the Sanford Underground Research Facility in Lead, South Dakota. The array will be situated in a low-background environment and surrounded by passive and active shielding. Here we describe the science goals ofmore » the DEMONSTRATOR and the details of its design.« less

The MAJORANA DEMONSTRATOR Neutrinoless Double-Beta Decay Experiment

DOE PAGES

Abgrall, N.; Aguayo, E.; Avignone, F. T.; ...

2014-01-29

Tmore » he M ajorana D emonstrator will search for the neutrinoless double-beta ( β β 0 ν ) decay of the isotope Ge with a mixed array of enriched and natural germanium detectors. he observation of this rare decay would indicate that the neutrino is its own antiparticle, demonstrate that lepton number is not conserved, and provide information on the absolute mass scale of the neutrino. he D emonstrator is being assembled at the 4850-foot level of the Sanford Underground Research Facility in Lead, South Dakota. he array will be situated in a low-background environment and surrounded by passive and active shielding. Here we describe the science goals of the D emonstrator and the details of its design.« less

The Antarctic Ice Sheet, Sea Ice, and the Ozone Hole: Satellite Observations of how they are Changing

NASA Technical Reports Server (NTRS)

Parkinson, Claire L.

2012-01-01

Antarctica is the Earth's coldest and highest continent and has major impacts on the climate and life of the south polar vicinity. It is covered almost entirely by the Earth's largest ice sheet by far, with a volume of ice so great that if all the Antarctic ice were to go into the ocean (as ice or liquid water), this would produce a global sea level rise of about 60 meters (197 feet). The continent is surrounded by sea ice that in the wintertime is even more expansive than the continent itself and in the summertime reduces to only about a sixth of its wintertime extent. Like the continent, the expansive sea ice cover has major impacts, reflecting the sun's radiation back to space, blocking exchanges between the ocean and the atmosphere, and providing a platform for some animal species while impeding other species. Far above the continent, the Antarctic ozone hole is a major atmospheric phenomenon recognized as human-caused and potentially quite serious to many different life forms. Satellites are providing us with remarkable information about the ice sheet, the sea ice, and the ozone hole. Satellite visible and radar imagery are providing views of the large scale structure of the ice sheet never seen before; satellite laser altimetry has produced detailed maps of the topography of the ice sheet; and an innovative gravity-measuring two-part satellite has allowed mapping of regions of mass loss and mass gain on the ice sheet. The surrounding sea ice cover has a satellite record that goes back to the 1970s, allowing trend studies that show a decreasing sea ice presence in the region of the Bellingshausen and Amundsen seas, to the west of the prominent Antarctic Peninsula, but increasing sea ice presence around much of the rest of the continent. Overall, sea ice extent around Antarctica has increased at an average rate of about 17,000 square kilometers per year since the late 1970s, as determined from satellite microwave data that can be collected under both light and dark conditions and irrespective of whether clouds are in the way between the surface and the satellite. In contrast, the highest quality satellite measurements of the ozone hole use ultraviolet light, which requires daylight conditions. Still, satellite ultraviolet measurements of the ozone hole have also been made since the late 1970s, and these show a marked increase in the area and depth of the ozone hole in the 1980s and early 1990s, followed by a welcome leveling off of both measures since the mid-1990s.

Topology of membrane proteins-predictions, limitations and variations.

PubMed

Tsirigos, Konstantinos D; Govindarajan, Sudha; Bassot, Claudio; Västermark, Åke; Lamb, John; Shu, Nanjiang; Elofsson, Arne

2017-10-26

Transmembrane proteins perform a variety of important biological functions necessary for the survival and growth of the cells. Membrane proteins are built up by transmembrane segments that span the lipid bilayer. The segments can either be in the form of hydrophobic alpha-helices or beta-sheets which create a barrel. A fundamental aspect of the structure of transmembrane proteins is the membrane topology, that is, the number of transmembrane segments, their position in the protein sequence and their orientation in the membrane. Along these lines, many predictive algorithms for the prediction of the topology of alpha-helical and beta-barrel transmembrane proteins exist. The newest algorithms obtain an accuracy close to 80% both for alpha-helical and beta-barrel transmembrane proteins. However, lately it has been shown that the simplified picture presented when describing a protein family by its topology is limited. To demonstrate this, we highlight examples where the topology is either not conserved in a protein superfamily or where the structure cannot be described solely by the topology of a protein. The prediction of these non-standard features from sequence alone was not successful until the recent revolutionary progress in 3D-structure prediction of proteins. Copyright © 2017 Elsevier Ltd. All rights reserved.

Adsorption of fibrinogen on a biomedical-grade stainless steel 316LVM surface: a PM-IRRAS study of the adsorption thermodynamics, kinetics and secondary structure changes.

PubMed

Desroches, Marie-Josee; Omanovic, Sasha

2008-05-14

Polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS) was employed to investigate the interaction of serum protein fibrinogen with a biomedical-grade 316LVM stainless steel surface, in terms of the adsorption thermodynamics, kinetics and secondary structure changes of the protein. Apparent Gibbs energy of adsorption values indicated a highly spontaneous and strong adsorption of fibrinogen onto the surface. The kinetics of fibrinogen adsorption were successfully modeled using a pseudo first-order kinetic model. Deconvolution of the amide I bands indicated that the adsorption of fibrinogen on 316LVM results in significant changes in the protein's secondary structure that occur predominantly within the first minute of adsorption. Among the investigated structures, the alpha-helix structure undergoes the smallest changes, while the beta-sheet and beta-turns structures undergo significant changes. It was shown that lateral interactions between the adsorbed molecules do not play a role in controlling the secondary structure changes. An increase in temperature induced changes in the secondary structure of the protein, characterized by a loss of the alpha-helical content and its transformation into the beta-turns structure.

3D 14N/1H Double Quantum/1H Single Quantum Correlation Solid-State NMR for Probing Parallel and Anti-Parallel Beta-Sheet Arrangement of Oligo-Peptides at Natural Abundance.

PubMed

Hong, You-Lee; Asakura, Tetsuo; Nishiyama, Yusuke

2018-05-08

β-sheet structure of oligo- and poly-peptides can be formed in anti-parallel (AP)- and parallel (P)-structure, which is the important feature to understand the structures. In principle, P- and AP-β-sheet structures can be identified by the presence (AP) and absence (P) of the interstrand 1HNH/1HNH correlations on a diagonal in 2D 1H double quantum (DQ)/1H single quantum (SQ) spectrum due to the different interstrand 1HNH/1HNH distances between these two arrangements. However, the 1HNH/1HNH peaks overlap to the 1HNH3+/1HNH3+ peaks, which always give cross peaks regardless of the β-sheet arrangement. The 1HNH3+/1HNH3+ peaks disturb the observation of the presence/absence of 1HNH/1HNH correlations and the assignment of 1HNH and 1HNH3+ is not always available. Here, 3D 14N/1H DQ/1H SQ correlation solid-state NMR experiments at fast magic angle spinning (70 kHz) are introduced to distinguish AP and P β-sheet structure. The 14N dimension allows the separate observation of 1HNH/1HNH peaks from 1HNH3+/1HNH3+ peaks with clear assignment of 1HNH and 1HNH3+. In addition, the high natural abundance of 1H and 14N enables 3D 14N/1H DQ/1H SQ experiments of oligo-alanines (Ala3-6) in four hours without any isotope labelling. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sea-level projections representing the deeply uncertain contribution of the West Antarctic ice sheet.

PubMed

Bakker, Alexander M R; Wong, Tony E; Ruckert, Kelsey L; Keller, Klaus

2017-06-20

There is a growing awareness that uncertainties surrounding future sea-level projections may be much larger than typically perceived. Recently published projections appear widely divergent and highly sensitive to non-trivial model choices . Moreover, the West Antarctic ice sheet (WAIS) may be much less stable than previous believed, enabling a rapid disintegration. Here, we present a set of probabilistic sea-level projections that approximates the deeply uncertain WAIS contributions. The projections aim to inform robust decisions by clarifying the sensitivity to non-trivial or controversial assumptions. We show that the deeply uncertain WAIS contribution can dominate other uncertainties within decades. These deep uncertainties call for the development of robust adaptive strategies. These decision-making needs, in turn, require mission-oriented basic science, for example about potential signposts and the maximum rate of WAIS-induced sea-level changes.

Effectiveness of Rotation-free Triangular and Quadrilateral Shell Elements in Sheet-metal Forming Simulations

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

Brunet, M.; Sabourin, F.

2005-08-05

This paper is concerned with the effectiveness of triangular 3-node shell element without rotational d.o.f. and the extension to a new 4-node quadrilateral shell element called S4 with only 3 translational degrees of freedom per node and one-point integration. The curvatures are computed resorting to the surrounding elements. Extension from rotation-free triangular element to a quadrilateral element requires internal curvatures in order to avoid singular bending stiffness. Two numerical examples with regular and irregular meshes are performed to show the convergence and accuracy. Deep-drawing of a box, spring-back analysis of a U-shape strip sheet and the crash simulation of amore » beam-box complete the demonstration of the bending capabilities of the proposed rotation-free triangular and quadrilateral elements.« less

The effect of convective boundary condition on MHD mixed convection boundary layer flow over an exponentially stretching vertical sheet

NASA Astrophysics Data System (ADS)

Isa, Siti Suzilliana Putri Mohamed; Arifin, Norihan Md.; Nazar, Roslinda; Bachok, Norfifah; Ali, Fadzilah Md

2017-12-01

A theoretical study that describes the magnetohydrodynamic mixed convection boundary layer flow with heat transfer over an exponentially stretching sheet with an exponential temperature distribution has been presented herein. This study is conducted in the presence of convective heat exchange at the surface and its surroundings. The system is controlled by viscous dissipation and internal heat generation effects. The governing nonlinear partial differential equations are converted into ordinary differential equations by a similarity transformation. The converted equations are then solved numerically using the shooting method. The results related to skin friction coefficient, local Nusselt number, velocity and temperature profiles are presented for several sets of values of the parameters. The effects of the governing parameters on the features of the flow and heat transfer are examined in detail in this study.

Bimodal electric tissue ablation (BETA): a study on ablation size when the anode is placed on the peritoneum and the liver.

PubMed

Tiong, Leong U; Finnie, John W; Field, John B; Maddern, Guy J

2012-07-01

In bimodal electric tissue ablation (BETA), the cathode of the DC circuit is attached to the radiofrequency (RF) electrode to increase the surrounding tissue hydration. This will delay tissue desiccation and allowing the ablation process to continue for a longer period of time before "roll-off" occurs, resulting in larger ablations compared with standard radiofrequency ablation (RFA). Previous research showed that attaching the anode to the skin using electrosurgical grounding pads would reduce the efficacy of BETA because of the high electrical resistivity of the skin. This study investigated the ablation size produced when the anode was attached to the peritoneum (BETA-peritoneum) and the liver (BETA-liver) respectively. The anode of the DC circuit in BETA was attached to the peritoneum and the liver in a pig model using ECG dots. In BETA, 9 V of DC was provided for 10 min, after which the radiofrequency generator were switched on and both electrical circuits allowed to run concurrently until "roll-off." The size of ablations produced was compared to when the anode attached to the skin (BETA-skin) and standard RFA, respectively. The sites of anode placement were examined for local tissue injury. The transverse diameters in BETA-peritoneum and BETA-liver were significantly larger compared with BETA-skin and standard RFA, respectively (P < 0.001). The axial diameter in the BETA-peritoneum and BETA-liver groups were also larger compared with the BETA-skin and RFA groups, although the differences did not reach statistical significance (P = 0.09). Hematoxylin and eosin (H and E) examination of the peritoneum and the liver where the anode was attached showed coagulation necrosis involving the superficial epithelium and the liver capsule, respectively. BETA can be used to treat larger liver tumors more effectively and may reduce the tumor recurrence rates compared with standard RFA. The efficacy of BETA depends on ensuring good electrical conductivity between the cathode and the anode of the DC circuit. Research so far has shown that BETA works best when the anode is placed deep to the skin as the stratum corneum consisted of a layer of a-nucleated cells, which have high electrical resistivity. The liver could be the ideal location to place the anode as it has excellent electrical conductivity, therefore ensuring maximum tissue hydration around the cathode to produce the largest ablations possible. Copyright © 2012 Elsevier Inc. All rights reserved.

Simulation of the Greenland Ice Sheet over two glacial-interglacial cycles: investigating a sub-ice-shelf melt parameterization and relative sea level forcing in an ice-sheet-ice-shelf model

NASA Astrophysics Data System (ADS)

Bradley, Sarah L.; Reerink, Thomas J.; van de Wal, Roderik S. W.; Helsen, Michiel M.

2018-05-01

Observational evidence, including offshore moraines and sediment cores, confirm that at the Last Glacial Maximum (LGM) the Greenland ice sheet (GrIS) expanded to a significantly larger spatial extent than seen at present, grounding into Baffin Bay and out onto the continental shelf break. Given this larger spatial extent and its close proximity to the neighbouring Laurentide Ice Sheet (LIS) and Innuitian Ice Sheet (IIS), it is likely these ice sheets will have had a strong non-local influence on the spatial and temporal behaviour of the GrIS. Most previous paleo ice-sheet modelling simulations recreated an ice sheet that either did not extend out onto the continental shelf or utilized a simplified marine ice parameterization which did not fully include the effect of ice shelves or neglected the sensitivity of the GrIS to this non-local bedrock signal from the surrounding ice sheets. In this paper, we investigated the evolution of the GrIS over the two most recent glacial-interglacial cycles (240 ka BP to the present day) using the ice-sheet-ice-shelf model IMAU-ICE. We investigated the solid earth influence of the LIS and IIS via an offline relative sea level (RSL) forcing generated by a glacial isostatic adjustment (GIA) model. The RSL forcing governed the spatial and temporal pattern of sub-ice-shelf melting via changes in the water depth below the ice shelves. In the ensemble of simulations, at the glacial maximums, the GrIS coalesced with the IIS to the north and expanded to the continental shelf break to the southwest but remained too restricted to the northeast. In terms of the global mean sea level contribution, at the Last Interglacial (LIG) and LGM the ice sheet added 1.46 and -2.59 m, respectively. This LGM contribution by the GrIS is considerably higher (˜ 1.26 m) than most previous studies whereas the contribution to the LIG highstand is lower (˜ 0.7 m). The spatial and temporal behaviour of the northern margin was highly variable in all simulations, controlled by the sub-ice-shelf melting which was dictated by the RSL forcing and the glacial history of the IIS and LIS. In contrast, the southwestern part of the ice sheet was insensitive to these forcings, with a uniform response in all simulations controlled by the surface air temperature, derived from ice cores.

Evidence for Intramolecular Antiparallel Beta-Sheet Structure in Alpha-Synuclein Fibrils from a Combination of Two-Dimensional Infrared Spectroscopy and Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Roeters, Steven J.; Iyer, Aditya; Pletikapić, Galja; Kogan, Vladimir; Subramaniam, Vinod; Woutersen, Sander

2017-01-01

The aggregation of the intrinsically disordered protein alpha-synuclein (αS) into amyloid fibrils is thought to play a central role in the pathology of Parkinson’s disease. Using a combination of techniques (AFM, UV-CD, XRD, and amide-I 1D- and 2D-IR spectroscopy) we show that the structure of αS fibrils varies as a function of ionic strength: fibrils aggregated in low ionic-strength buffers ([NaCl] ≤ 25 mM) have a significantly different structure than fibrils grown in higher ionic-strength buffers. The observations for fibrils aggregated in low-salt buffers are consistent with an extended conformation of αS molecules, forming hydrogen-bonded intermolecular β-sheets that are loosely packed in a parallel fashion. For fibrils aggregated in high-salt buffers (including those prepared in buffers with a physiological salt concentration) the measurements are consistent with αS molecules in a more tightly-packed, antiparallel intramolecular conformation, and suggest a structure characterized by two twisting stacks of approximately five hydrogen-bonded intermolecular β-sheets each. We find evidence that the high-frequency peak in the amide-I spectrum of αS fibrils involves a normal mode that differs fundamentally from the canonical high-frequency antiparallel β-sheet mode. The high sensitivity of the fibril structure to the ionic strength might form the basis of differences in αS-related pathologies.

Evidence for Intramolecular Antiparallel Beta-Sheet Structure in Alpha-Synuclein Fibrils from a Combination of Two-Dimensional Infrared Spectroscopy and Atomic Force Microscopy

PubMed Central

Roeters, Steven J.; Iyer, Aditya; Pletikapić, Galja; Kogan, Vladimir; Subramaniam, Vinod; Woutersen, Sander

2017-01-01

The aggregation of the intrinsically disordered protein alpha-synuclein (αS) into amyloid fibrils is thought to play a central role in the pathology of Parkinson’s disease. Using a combination of techniques (AFM, UV-CD, XRD, and amide-I 1D- and 2D-IR spectroscopy) we show that the structure of αS fibrils varies as a function of ionic strength: fibrils aggregated in low ionic-strength buffers ([NaCl] ≤ 25 mM) have a significantly different structure than fibrils grown in higher ionic-strength buffers. The observations for fibrils aggregated in low-salt buffers are consistent with an extended conformation of αS molecules, forming hydrogen-bonded intermolecular β-sheets that are loosely packed in a parallel fashion. For fibrils aggregated in high-salt buffers (including those prepared in buffers with a physiological salt concentration) the measurements are consistent with αS molecules in a more tightly-packed, antiparallel intramolecular conformation, and suggest a structure characterized by two twisting stacks of approximately five hydrogen-bonded intermolecular β-sheets each. We find evidence that the high-frequency peak in the amide-I spectrum of αS fibrils involves a normal mode that differs fundamentally from the canonical high-frequency antiparallel β-sheet mode. The high sensitivity of the fibril structure to the ionic strength might form the basis of differences in αS-related pathologies. PMID:28112214

A new research project on the interaction of the solid Earth and the Antarctic Ice Sheet

NASA Astrophysics Data System (ADS)

Fukuda, Y.; Nishijima, J.; Kazama, T.; Nakamura, K.; Doi, K.; Suganuma, Y.; Okuno, J.; Araya, A.; Kaneda, H.; Aoyama, Y.

2017-12-01

A new research project of "Grant-in-Aid for Scientific Research on Innovative Areas" funded by JSPS (Japan Society for the Promotion of Science) has recently been launched. The title of the project is "Giant reservoirs of heat/water/material: Global environmental changes driven by Southern Ocean and Antarctic Ice Sheet", and as a five years project, is aiming to establish a new research area for Antarctic environmental system science. The project consists of 7 research topics, including Antarctic ice sheet and Southern ocean sciences, new observation methodology, modeling and other interdisciplinary topics, and we are involved in the topic A02-2, "Interaction of the solid Earth and the Antarctic Ice Sheet". The Antarctic ice sheet, which relates to the global climate changes through the sea level rise and ocean circulation, is an essential element of the Earth system for predicting the future environment changes. Thus many studies of the ice sheet changes have been conducted by means of geomorphological, geological, geodetic surveys, as well as satellite gravimetry and satellite altimetry. For these studies, one of the largest uncertainties is the effects of GIA. Therefore, GIA as a key to investigate the interaction between the solid Earth and the ice sheet changes, we plan to conduct geomorphological, geological and geodetic surveys in the inland mountain areas and the coastal areas including the surrounding areas of a Japanese station Syowa in East Antarctica, where the in-situ data for constraining GIA models are very few. Combining these new observations with other in-site data, various satellite data and numerical modeling, we aim to estimating a precise GIA model, constructing a reliable ice melting history after the last glacial maximum and obtaining the viscoelastic structure of the Earth's interior. In the presentation, we also show the five years research plans as well. This study was partially supported by JSPS KAKENHI Grant No. 17H06321.

Wave propagation of carbon nanotubes embedded in an elastic medium

NASA Astrophysics Data System (ADS)

Natsuki, Toshiaki; Hayashi, Takuya; Endo, Morinobu

2005-02-01

This paper presents analytical models of wave propagation in single- and double-walled carbon nanotubes, as well as nanotubes embedded in an elastic matrix. The nanotube structures are treated within the multilayer thin shell approximation with the elastic properties taken to be those of the graphene sheet. The double-walled nanotubes are coupled together through the van der Waals force between the inner and outer nanotubes. For carbon nanotubes embedded in an elastic matrix, the surrounding elastic medium can be described by a Winkler model. Tube wave propagation of both symmetrical and asymmetrical modes can be analyzed based on the present elastic continuum model. It is found that the asymmetrical wave behavior of single- and double-walled nanotubes is significantly different. The behavior is also different from that in the surrounding elastic medium.

Hsp70 and antifibrillogenic peptides promote degradation and inhibit intracellular aggregation of amyloidogenic light chains.

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

Dul, J. L.; Davis, D. P.; Williamson, E. K.

2001-02-19

In light chain (LC) amyloidosis an immunoglobulin LC assembles into fibrils that are deposited in various tissues. Little is known about how these fibrils form in vivo. We previously showed that a known amyloidogenic LC, SMA, can give rise to amyloid fibrils in vitro when a segment of one of its {beta} sheets undergoes a conformational change, exposing an Hsp70 binding site. To examine SMA aggregation in vivo, we expressed it and its wild-type counterpart, LEN, in COS cells. While LEN is rapidly oxidized and subsequently secreted, newly synthesized SMA remains in the reduced state. Most SMA molecules are dislocatedmore » out of the ER into the cytosol, where they are ubiquitinylated and degraded by proteasomes. A parallel pathway for molecules that are not degraded is condensation into perinuclear aggresomes that are surrounded by vimentin-containing intermediate filaments and are dependent upon intact microtubules. Inhibition of proteasome activity shifts the balance toward aggresome formation. Intracellular aggregation is decreased and targeting to proteasomes improved by overexpression of the cytosolic chaperone Hsp70. Importantly, transduction into the cell of an Hsp70 target peptide, derived from the LC sequence, also reduces aggresome formation and increases SMA degradation. These results demonstrate that an amyloidogenic LC can aggregate intracellularly despite the common presentation of extracellular aggregates, and that a similar molecular surface mediates both in vitro fibril formation and in vivo aggregation. Furthermore, rationally designed peptides can be used to suppress this aggregation and may provide a feasible therapeutic approach.« less

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.

Folding-unfolding transitions of Rv3221c on the pressure-temperature plane

NASA Astrophysics Data System (ADS)

Somkuti, Judit; Jain, Sriyans; Ramachandran, Srinivasan; ászló Smeller, L.

2013-06-01

Rv3221c is a biotin-binding protein found in Mycobacterium tuberculosis. It has been reported that an elevated temperature is needed for it to adopt a folded conformation. We determined the complete pressure-temperature phase diagram, and determined the thermodynamical parameters of the denaturation. The phase diagram follows well the Hawley theory. The secondary structure of the protein was found to contain predominantly beta sheet. The pressure unfolding was partially reversible, resulting in pressure-sensitive aggregates, besides the correctly refolded and biotin-bound fraction of proteins.

Beta cell chromogranin B is partially segregated in distinct granules and can be released separately from insulin in response to stimulation.

PubMed

Giordano, T; Brigatti, C; Podini, P; Bonifacio, E; Meldolesi, J; Malosio, M L

2008-06-01

We investigated, in three beta cell lines (INS-1E, RIN-5AH, betaTC3) and in human and rodent primary beta cells, the storage and release of chromogranin B, a secretory protein expressed in beta cells and postulated to play an autocrine role. We asked whether chromogranin B is stored together with and discharged in constant ratio to insulin upon various stimuli. The intracellular distribution of insulin and chromogranin B was revealed by immunofluorescence followed by three-dimensional image reconstruction and by immunoelectron microscopy; their stimulated discharge was measured by ELISA and immunoblot analysis of homogenates and incubation media. Insulin and chromogranin B, co-localised in the Golgi complex/trans-Golgi network, appeared largely segregated from each other in the secretory granule compartment. In INS-1E cells, the percentage of granules positive only for insulin or chromogranin B and of those positive for both was 66, 7 and 27%, respectively. In resting cells, both insulin and chromogranin B were concentrated in the granule cores; upon stimulation, chromogranin B (but not insulin) was largely redistributed to the core periphery and the surrounding halo. Strong stimulation with a secretagogue mixture induced parallel release of insulin and chromogranin B, whereas with 3-isobutyl-1-methylxantine and forskolin +/- high glucose release of chromogranin B predominated. Weak, Ca(2+)-dependent stimulation with ionomycin or carbachol induced exclusive release of chromogranin B, suggesting a higher Ca(2+) sensitivity of the specific granules. The unexpected complexity of the beta cell granule population in terms of heterogeneity, molecular plasticity and the differential discharge, could play an important role in physiological control of insulin release and possibly also in beta cell pathology.

New Way of Characterizing the State of the Ring Current

NASA Astrophysics Data System (ADS)

Wolf, R.; Bao, S.; Gkioulidou, M.; Yang, J.; Toffoletto, F.

2017-12-01

The flux tube entropy S is invariant in ideal MHD and is a good way to characterize the degree to which a closed flux tube is loaded with particle energy. Flux tube entropy generally increases with increasing geocentric distance. A flux tube that is injected from the plasma sheet into the ring current tends to be a bubble that has a lower S value than typical plasma sheet flux tubes, and it tends to penetrate to a position where the surroundings matches its S. From this point of view, a good way to characterize the state of the ring current is through the function dF/dS, which specifies how much magnetic flux is occupied by tubes with different degrees of loading. By displaying dF/dS curves before and during storm main phases simulated with the RCM-E code, we determine that, in the model, the injection of the stormtime ring current consists of replacing pre-storm low-S flux tubes with tubes from the plasma sheet that have a certain limited range of S, which is well below typical plasma-sheet values. We also display dF/dS curves for passes by the Van Allen Probes before and during storm main phases, and compare with the RCM-E-derived curves, to gain insight into the nature of the flux tubes that are injected to form the real storm-time ring current.

Effluent Limit Exceedances Search (beta) | ECHO | US EPA

EPA Pesticide Factsheets

ECHO, Enforcement and Compliance History Online, provides compliance and enforcement information for approximately 800,000 EPA-regulated facilities nationwide. ECHO includes permit, inspection, violation, enforcement action, and penalty information about facilities regulated under the Clean Air Act (CAA) Stationary Source Program, Clean Water Act (CWA) National Pollutant Elimination Discharge System (NPDES), and/or Resource Conservation and Recovery Act (RCRA). Information also is provided on surrounding demographics when available.

Implications of possible shuttle charging. [prediction analysis techniques for insulation and electrical grounding against ionospheric conductivity

NASA Technical Reports Server (NTRS)

Taylor, W. W. L.

1979-01-01

Shuttle charging is discussed and two analyses of shuttle charging are performed. The first predicts the effective collecting area of a wire grid, biased with the respect to the potential of the magnetoplasma surrounding it. The second predicts the intensity of broadband electromagnetic noise that is emitted when surface electrostatic discharges occur between the beta cloth and the wire grid sewn on it.

Adenovirus E1A functions as a cofactor for retinoic acid receptor beta (RAR beta) through direct interaction with RAR beta.

PubMed

Folkers, G E; van der Saag, P T

1995-11-01

Transcription regulation by DNA-bound activators is thought to be mediated by a direct interaction between these proteins and TATA-binding protein (TBP), TFIIB, or TBP-associated factors, although occasionally cofactors or adapters are required. For ligand-induced activation by the retinoic acid receptor-retinoid X receptor (RAR-RXR) heterodimer, the RAR beta 2 promoter is dependent on the presence of E1A or E1A-like activity, since this promoter is activated by retinoic acid only in cells expressing such proteins. The mechanism underlying this E1A requirement is largely unknown. We now show that direct interaction between RAR and E1A is a requirement for retinoic acid-induced RAR beta 2 activation. The activity of the hormone-dependent activation function 2 (AF-2) of RAR beta is upregulated by E1A, and an interaction between this region and E1A was observed, but not with AF-1 or AF-2 of RXR alpha. This interaction is dependent on conserved region III (CRIII), the 13S mRNA-specific region of E1A. Deletion analysis within this region indicated that the complete CRIII is needed for activation. The putative zinc finger region is crucial, probably as a consequence of interaction with TBP. Furthermore, the region surrounding amino acid 178, partially overlapping with the TBP binding region, is involved in both binding to and activation by AF-2. We propose that E1A functions as a cofactor by interacting with both TBP and RAR, thereby stabilizing the preinitiation complex.

Open Boundary Particle-in-Cell Simulation of Dipolarization Front Propagation

NASA Technical Reports Server (NTRS)

Klimas, Alex; Hwang, Kyoung-Joo; Vinas, Adolfo F.; Goldstein, Melvyn L.

2014-01-01

First results are presented from an ongoing open boundary 2-1/2D particle-in-cell simulation study of dipolarization front (DF) propagation in Earth's magnetotail. At this stage, this study is focused on the compression, or pileup, region preceding the DF current sheet. We find that the earthward acceleration of the plasma in this region is in general agreement with a recent DF force balance model. A gyrophase bunched reflected ion population at the leading edge of the pileup region is reflected by a normal electric field in the pileup region itself, rather than through an interaction with the current sheet. We discuss plasma wave activity at the leading edge of the pileup region that may be driven by gradients, or by reflected ions, or both; the mode has not been identified. The waves oscillate near but above the ion cyclotron frequency with wavelength several ion inertial lengths. We show that the waves oscillate primarily in the perpendicular magnetic field components, do not propagate along the background magnetic field, are right handed elliptically (close to circularly) polarized, exist in a region of high electron and ion beta, and are stationary in the plasma frame moving earthward. We discuss the possibility that the waves are present in plasma sheet data, but have not, thus far, been discovered.

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

Influence and timing of arrival of murine neural crest on pancreatic beta cell development and maturation.

PubMed

Plank, Jennifer L; Mundell, Nathan A; Frist, Audrey Y; LeGrone, Alison W; Kim, Thomas; Musser, Melissa A; Walter, Teagan J; Labosky, Patricia A

2011-01-15

Interactions between cells from the ectoderm and mesoderm influence development of the endodermally-derived pancreas. While much is known about how mesoderm regulates pancreatic development, relatively little is understood about how and when the ectodermally-derived neural crest regulates pancreatic development and specifically, beta cell maturation. A previous study demonstrated that signals from the neural crest regulate beta cell proliferation and ultimately, beta cell mass. Here, we expand on that work to describe timing of neural crest arrival at the developing pancreatic bud and extend our knowledge of the non-cell autonomous role for neural crest derivatives in the process of beta cell maturation. We demonstrated that murine neural crest entered the pancreatic mesenchyme between the 26 and 27 somite stages (approximately 10.0 dpc) and became intermingled with pancreatic progenitors as the epithelium branched into the surrounding mesenchyme. Using a neural crest-specific deletion of the Forkhead transcription factor Foxd3, we ablated neural crest cells that migrate to the pancreatic primordium. Consistent with previous data, in the absence of Foxd3, and therefore the absence of neural crest cells, proliferation of insulin-expressing cells and insulin-positive area are increased. Analysis of endocrine cell gene expression in the absence of neural crest demonstrated that, although the number of insulin-expressing cells was increased, beta cell maturation was significantly impaired. Decreased MafA and Pdx1 expression illustrated the defect in beta cell maturation; we discovered that without neural crest, there was a reduction in the percentage of insulin-positive cells that co-expressed Glut2 and Pdx1 compared to controls. In addition, transmission electron microscopy analyses revealed decreased numbers of characteristic insulin granules and the presence of abnormal granules in insulin-expressing cells from mutant embryos. Together, these data demonstrate that the neural crest is a critical regulator of beta cell development on two levels: by negatively regulating beta cell proliferation and by promoting beta cell maturation. Copyright © 2010 Elsevier Inc. All rights reserved.

Differentiating Amino Acid Residues and Side Chain Orientations in Peptides Using Scanning Tunneling Microscopy

PubMed Central

Claridge, Shelley A.; Thomas, John C.; Silverman, Miles A.; Schwartz, Jeffrey J.; Yang, Yanlian; Wang, Chen; Weiss, Paul S.

2014-01-01

Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structure at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer’s and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level. PMID:24219245

Impact of different cultivation and induction regimes on the structure of cytosolic inclusion bodies of TEM1-beta-lactamase.

PubMed

Margreiter, Gerd; Schwanninger, Manfred; Bayer, Karl; Obinger, Christian

2008-10-01

The enzyme TEM1-beta-lactamase has been used as a model to study the impact of different cultivation and induction regimes on the structure of cytosolic inclusion bodies (IBs). The protein has been heterologously expressed in Escherichia coli in fed-batch cultivations at different temperatures (30, 37, and 40 degrees C) as well as induction regimes that guaranteed distinct product formation rates and ratios of soluble to aggregated protein. Additionally, shake flask cultivations at 20, 30, and 37 degrees C were performed. IBs were sampled during the whole bioprocess and structural analysis was performed by attenuated total reflectance Fourier transform infrared (ATR-FT-IR) spectroscopy. This work clearly demonstrates that the tested production regimes and rates had no impact on the IB structure, which was characterized by decreased alpha-helical and increased and modified beta-sheet contents compared to the native protein. Moreover, aggregates formed during refolding of IBs by solubilization and simple dilution showed very similar FT-IR spectra suggesting (i) the existence of only one critical folding step from which either aggregation (IB formation) or native folding branches off, and (ii) underlining the important role of the specific amino acid sequence in aggregation. The findings are discussed with respect to the known structure of TEM1-beta-lactamase and the reported kinetics of its (un)folding as well as contradictory data on the effect of cultivation regimes on IB structure(s) of other proteins.

Microstructure evolution and tensile properties of Zr-2.5 wt.% Nb pressure tubes processed from billets with different microstructures

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

Kapoor, K.; Saratchandran, N.; Muralidharan, K.

1999-02-01

Pressurized heavy water reactors (PHWR) use zirconium-base alloys for their low neutron-absorption cross section, good mechanical strength, low irradiation creep, and high corrosion resistance in reactor atmospheres. Starting with identical ingots, billets having different microstructures were obtained by three different processing methods for fabrication of Zr-2.5 wt%Nb pressure tubes., The billets were further processed by hot extrusion and cold Pilger tube reducing to the finished product. Microstructural characterization was done at each stage of processing. The effects of the initial billet microstructure on the intermediate and final microstructure and mechanical property results were determined. It was found that the structuremore » at each stage and the final mechanical properties depend strongly on the initial billet microstructure. The structure at the final stage consists of elongated alpha zirconium grains with a network of metastable beta zirconium phase. Some of this metastable phase transforms into stable beta niobium during thermomechanical processing. Billets with quenched structure resulted in less beta niobium at the final stage. The air cooled billets resulted in a large amount of beta niobium. The tensile properties, especially the percentage elongation, were found to vary for the different methods. Higher percentage elongation was observed for billets having quenched structure. Extrusion and forging did not produce any characteristic differences in the properties. The results were used to select a process flow sheet which yields the desired mechanical properties with suitable microstructure in the final product.« less

Molecular organization of amyloid protofilament-like assembly of betabellin 15D: helical array of beta-sandwiches.

PubMed Central

Inouye, Hideyo; Bond, Jeremy E; Deverin, Sean P; Lim, Amareth; Costello, Catherine E; Kirschner, Daniel A

2002-01-01

Betabellin is a 32-residue peptide engineered to fold into a four-stranded antiparallel beta-sheet protein. Upon air oxidation, the betabellin peptides can fold and assemble into a disulfide-bridged homodimer, or beta-sandwich, of 64 residues. Recent biophysical and ultrastructural studies indicate that betabellin 15D (B15D) (a homodimer of HSLTAKIpkLTFSIAphTYTCAVpkYTAKVSH, where p = DPro, k = DLys, and h = DHis) forms unbranched, 35-A wide assemblies that resemble the protofilaments of amyloid fibers. In the present study, we have analyzed in detail the X-ray diffraction patterns of B15D prepared from acetonitrile. The fiber diffraction analysis indicated that the B15D fibril was composed of a double helix defined by the selection rule l = n + 7m (where l is even, and n and m are any integers), and having a 199-A period and pitch, 28-A rise per unit, and 10-A radius. This helical model is equivalent to a reverse-handed, single helix with half the period and defined by the selection rule l = -3n + 7m (where l is any integer). The asymmetric unit is the single B15D beta-sandwich molecule. These results suggest that the betabellin assembly that models the protofilaments of amyloid fibers is made up of discrete subunits on a helical array. Multiple intersheet hydrogen bonds in the axial direction and intersandwich polar interactions in the lateral direction stabilize the array. PMID:12202394

Crystal Structure of the Bovine lactadherin C2 Domain, a Membrane Binding Motif, Shows Similarity to the C2 Domains of Factor V and Factor VIII

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

Lin,L.

2007-01-01

Lactadherin, a glycoprotein secreted by a variety of cell types, contains two EGF domains and two C domains with sequence homology to the C domains of blood coagulation proteins factor V and factor VIII. Like these proteins, lactadherin binds to phosphatidylserine (PS)-containing membranes with high affinity. We determined the crystal structure of the bovine lactadherin C2 domain (residues 1 to 158) at 2.4 {angstrom}. The lactadherin C2 structure is similar to the C2 domains of factors V and VIII (rmsd of C{sub {alpha}} atoms of 0.9 {angstrom} and 1.2 {angstrom}, and sequence identities of 43% and 38%, respectively). The lactadherinmore » C2 domain has a discoidin-like fold containing two {beta}-sheets of five and three antiparallel {beta}-strands packed against one another. The N and C termini are linked by a disulfide bridge between Cys1 and Cys158. One {beta}-turn and two loops containing solvent-exposed hydrophobic residues extend from the C2 domain {beta}-sandwich core. In analogy with the C2 domains of factors V and VIII, some or all of these solvent-exposed hydrophobic residues, Trp26, Leu28, Phe31, and Phe81, likely participate in membrane binding. The C2 domain of lactadherin may serve as a marker of cell surface phosphatidylserine exposure and may have potential as a unique anti-thrombotic agent.« less

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

1H and 15N NMR resonance assignments and secondary structure of titin type I domains.

PubMed

Muhle-Goll, C; Nilges, M; Pastore, A

1997-01-01

Titin/connectin is a giant muscle protein with a highly modular architecture consisting of multiple repeats of two sequence motifs, named type I and type II. Type I modules have been suggested to be intracellular members of the fibronectin type III (Fn3) domain family. Along the titin sequence they are exclusively present in the region of the molecule located in the sarcomere A-band. This region has been shown to interact with myosin and C-protein. One of the most noticeable features of type I modules is that they are particularly rich in semiconserved prolines, since these residues account for about 8% of their sequence. We have determined the secondary structure of a representative type I domain (A71) by 15N and 1H NMR. We show that the type I domains of titin have the Fn3 fold as proposed, consisting of a three- and a four-stranded beta-sheet. When the two sheets are placed on top of each other to form the beta-sandwich characteristic of the Fn3 fold, 8 out of 10 prolines are found on the same side of the molecule and form an exposed hydrophobic patch. This suggests that the semiconserved prolines might be relevant for the function of type I modules, providing a surface for binding to other A-band proteins. The secondary structure of A71 was structurally aligned to other extracellular Fn3 modules of known 3D structure. The alignment shows that titin type I modules have closest similarity to the first Fn3 domain of Drosophila neuroglian.

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

Alred, Erik J.; Scheele, Emily G.; Berhanu, Workalemahu M.

Recent experiments indicate a connection between the structure of amyloid aggregates and their cytotoxicity as related to neurodegenerative diseases. Of particular interest is the Iowa Mutant, which causes early-onset of Alzheimer's disease. While wild-type Amyloid β-peptides form only parallel beta-sheet aggregates, the mutant also forms meta-stable antiparallel beta sheets. Since these structural variations may cause the difference in the pathological effects of the two Aβ-peptides, we have studied in silico the relative stability of the wild type and Iowa mutant in both parallel and antiparallel forms. We compare regular molecular dynamics simulations with such where the viscosity of the samplesmore » is reduced, which, we show, leads to higher sampling efficiency. By analyzing and comparing these four sets of all-atom molecular dynamics simulations, we probe the role of the various factors that could lead to the structural differences. Our analysis indicates that the parallel forms of both wild type and Iowa mutant aggregates are stable, while the antiparallel aggregates are meta-stable for the Iowa mutant and not stable for the wild type. The differences result from the direct alignment of hydrophobic interactions in the in-register parallel oligomers, making them more stable than the antiparallel aggregates. The slightly higher thermodynamic stability of the Iowa mutant fibril-like oligomers in its parallel organization over that in antiparallel form is supported by previous experimental measurements showing slow inter-conversion of antiparallel aggregates into parallel ones. Knowledge of the mechanism that selects between parallel and antiparallel conformations and determines their relative stability may open new avenues for the development of therapies targeting familial forms of early-onset Alzheimer's disease.« less

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.

The molecular architecture of human N-acetylgalactosamine kinase.

PubMed

Thoden, James B; Holden, Hazel M

2005-09-23

Galactokinase plays a key role in normal galactose metabolism by catalyzing the conversion of alpha-d-galactose to galactose 1-phosphate. Within recent years, the three-dimensional structures of human galactokinase and two bacterial forms of the enzyme have been determined. Originally, the gene encoding galactokinase in humans was mapped to chromosome 17. An additional gene, encoding a protein with sequence similarity to galactokinase, was subsequently mapped to chromosome 15. Recent reports have shown that this second gene (GALK2) encodes an enzyme with greater activity against GalNAc than galactose. This enzyme, GalNAc kinase, has been implicated in a salvage pathway for the reutilization of free GalNAc derived from the degradation of complex carbohydrates. Here we report the first structural analysis of a GalNAc kinase. The structure of the human enzyme was solved in the presence of MnAMPPNP and GalNAc or MgATP and GalNAc (which resulted in bound products in the active site). The enzyme displays a distinctly bilobal appearance with its active site wedged between the two domains. The N-terminal region is dominated by a seven-stranded mixed beta-sheet, whereas the C-terminal motif contains two layers of anti-parallel beta-sheet. The overall topology displayed by GalNAc kinase places it into the GHMP superfamily of enzymes, which generally function as small molecule kinases. From this investigation, the geometry of the GalNAc kinase active site before and after catalysis has been revealed, and the determinants of substrate specificity have been defined on a molecular level.

Graphene plasmons embedded in a gain medium: layer and ribbon plasmons

NASA Astrophysics Data System (ADS)

Altares Menendez, Galaad; Rosolen, Gilles; Maes, Bjorn

2016-12-01

Graphene plasmonics has attracted much attention due to its remarkable properties such as tunable conductivity and extreme confinement. However, losses remain one of the major drawbacks to developing more efficient devices based on graphene plasmons. Here we show that when a gain medium is introduced around a 1D graphene sheet, lossless propagation can be achieved for a critical gain value. Both numerics and analytics are employed; and with the Drude approximation the analytical expression for this critical gain becomes remarkably simple. Furthermore, we examine a single 2D graphene nanoribbon within a gain environment. We report that the plasmonic resonant modes exhibit a spasing effect for a specific value of the surrounding gain. This feature is indicated by an absorption cross section that strongly increases and narrows. Finally, we manage to connect the ribbon results to the 1D sheet critical gain, by taking external coupling into account.

Hollow Fiber Spacesuit Water Membrane Evaporator Development and Testing for Advanced Spacesuits

NASA Technical Reports Server (NTRS)

Bue, Grant C.; Trevino, Luis; Tsioulos, Gus; Settles, Joseph; Colunga, Aaron; Vogel, Matthew; Vonau, Walt

2010-01-01

Grant Bue and Matthew Vogel presented the two types of Spacesuit Water Membrane Evaporators (SWME) that were developed based on hydrophobic microporous membranes. One type, the Sheet Membrane (SaM) SWME, is composed of six concentric Teflon sheet membranes fixed on cylindrical-supporting screens to form three concentric annular water channels. Those water channels are surrounded by vacuum passages to draw off the water vapor that passes through the membrane. The other type, the Hollow Fiber (HoFi) SWME, is composed of more than 14,000 tubes. Water flows through the tubes and water vapor passes through the tube wall to the shell side that vents to the vacuum of space. Both SWME types have undergone testing to baseline the performance at predicted operating temperatures and flow rates; the units also have been subjected to contamination testing and other conditions to test resiliency.

Glaciotectonic deformation associated with the Orient Point-Fishers Island moraine, westernmost Block Island Sound: further evidence of readvance of the Laurentide ice sheet

USGS Publications Warehouse

Poppe, Lawrence J.; Oldale, Robert N.; Foster, David S.; Smith, Shepard M.

2012-01-01

High-resolution seismic-reflection profiles collected across pro-glacial outwash deposits adjacent to the circa 18 ka b.p. Orient Point–Fishers Island end moraine segment in westernmost Block Island Sound reveal extensive deformation. A rhythmic seismic facies indicates the host outwash deposits are composed of fine-grained glaciolacustrine sediments. The deformation is variably brittle and ductile, but predominantly compressive in nature. Brittle deformation includes reverse faults and thrust faults that strike parallel to the moraine, and thrust sheets that extend from beneath the moraine. Ductile deformation includes folded sediments that overlie undisturbed deposits, showing that they are not drape features. Other seismic evidence for compression along the ice front consists of undisturbed glaciolacustrine strata that dip back toward and underneath the moraine, and angular unconformities on the sea floor where deformed sediments extend above the surrounding undisturbed correlative strata. Together, these ice-marginal glaciotectonic features indicate that the Orient Point–Fishers Island moraine marks a significant readvance of the Laurentide ice sheet, consistent with existing knowledge for neighboring coeval moraines, and not simply a stillstand as previously reported.

Encoding Gaussian curvature in glassy and elastomeric liquid crystal solids

PubMed Central

Mostajeran, Cyrus; Ware, Taylor H.; White, Timothy J.

2016-01-01

We describe shape transitions of thin, solid nematic sheets with smooth, preprogrammed, in-plane director fields patterned across the surface causing spatially inhomogeneous local deformations. A metric description of the local deformations is used to study the intrinsic geometry of the resulting surfaces upon exposure to stimuli such as light and heat. We highlight specific patterns that encode constant Gaussian curvature of prescribed sign and magnitude. We present the first experimental results for such programmed solids, and they qualitatively support theory for both positive and negative Gaussian curvature morphing from flat sheets on stimulation by light or heat. We review logarithmic spiral patterns that generate cone/anti-cone surfaces, and introduce spiral director fields that encode non-localized positive and negative Gaussian curvature on punctured discs, including spherical caps and spherical spindles. Conditions are derived where these cap-like, photomechanically responsive regions can be anchored in inert substrates by designing solutions that ensure compatibility with the geometric constraints imposed by the surrounding media. This integration of such materials is a precondition for their exploitation in new devices. Finally, we consider the radial extension of such director fields to larger sheets using nematic textures defined on annular domains. PMID:27279777

Geological-morphological description of the Lakshmi planum (photomap of the Venusian surface sheet B-4)

NASA Technical Reports Server (NTRS)

Pronin, A. A.

1987-01-01

The Lakshmi Planum and its surrounding area (together comprising a single structure) are described in morphological terms on the basis of Venera 15 and 16 photomap data. Plume ascent from the planetary interior and subsequent horizontal spreading represent the underlying mechanisms behind structural formation: folding and/or imbricating accompany these processes. In effect, the Laksmi structure can be regarded as a local spreading center. Its structural dimensions attest to the role that asthenospheric currents played in its formation.

Satellite radar altimetry over ice. Volume 1: Processing and corrections of Seasat data over Greenland

NASA Technical Reports Server (NTRS)

Zwally, H. Jay; Brenner, Anita C.; Major, Judith A.; Martin, Thomas V.; Bindschadler, Robert A.

1990-01-01

The data-processing methods and ice data products derived from Seasat radar altimeter measurements over the Greenland ice sheet and surrounding sea ice are documented. The corrections derived and applied to the Seasat radar altimeter data over ice are described in detail, including the editing and retracking algorithm to correct for height errors caused by lags in the automatic range tracking circuit. The methods for radial adjustment of the orbits and estimation of the slope-induced errors are given.

The Center for Astrophysics Redshift Survey - Recent results

NASA Technical Reports Server (NTRS)

Geller, Margaret J.; Huchra, John P.

1989-01-01

Six strips of the CfA redshift survey extension are now complete. The data continue to support a picture in which galaxies are on thin sheets which nearly surround vast low-density voids. The largest structures are comparable with the extent of the survey. Voids like the one in Bootes are a common feature of the large-scale distribution of galaxies. The issue of fair samples of the galaxy distribution is discussed, examining statistical measures of the galaxy distribution including the two-point correlation functions.

Lymphosarcoma associated with Heterobilharzia americana infection in a dog.

PubMed

Stone, Richard H; Frontera-Acevedo, Karelma; Saba, Corey F; Ambrose, Dana; Moorhead, Andrew R; Brown, Cathy A

2011-09-01

Hepatic T-cell lymphosarcoma with involvement of regional lymph nodes and concurrent schistosomiasis were diagnosed in an 11-year-old male neutered mixed-breed dog with a history of chronic weight loss, inappetence, vomiting, and diarrhea. Trematode ova present in the hepatic parenchyma and mesenteric node were surrounded by sheets of neoplastic lymphocytes while those in the intestinal wall were surrounded by large numbers of non-neoplastic lymphocytes. Immunohistochemistry revealed that both the neoplastic and hyperplastic populations were T lymphocytes. The ova were identified by fecal saline sedimentation as Heterobilharzia spp., and fecal ova shedding resolved after praziquantel anthelmintic treatment. The lymphoma progressed despite chemotherapy, and the dog was euthanized after developing neurologic signs and a necropsy was performed. A monomorphic population of neoplastic T cells expanded and replaced normal architecture in the liver and spleen, surrounded nerve roots within the cauda equina, and infiltrated the meninges of the brain. The presence of schistosome ova embedded within neoplastic T-cell infiltrates suggests that, as previously reported in human schistosomiasis, heterobilharziasis may be associated with neoplasia.

Preparation and characterization of calcium phosphate ceramics and composites as bone substitutes

NASA Astrophysics Data System (ADS)

Zhang, Xing

Marine CaCO3 skeletons have tailored architectures created by nature, which give them structural support and other functions. For example, seashells have dense lamellar structures, while coral, cuttlebone and sea urchin spines have interconnected porous structures. In our experiments, seashells, coral and cuttlebone were hydrothermally converted to hydroxyapatite (HAP), and sea urchin spines were converted to Mg-substituted tricalcium phosphate (beta-TCMP), while maintaining their original structures. Partially converted shell samples have mechanical strength, which is close to that of compact human bone. After implantation of converted shell and spine samples in rat femoral defects for 6 weeks, there was newly formed bone growth up to and around the implants. Some new bone was found to migrate through the pores of converted spine samples and grow inward. These results show good bioactivity and osteoconductivity of the implants, indicating the converted shell and spine samples can be used as bone defect fillers. Calcium phosphate powders were prepared through different synthesis methods. Micro-size HAP rods were synthesized by hydrothermal method through a nucleation-growth mechanism. On the other hand, HAP particles, which have good crystallinity, were prepared by wet precipitation with further hydrothermal treatment. beta-TCP or beta-TCMP powders were prepared by a two-step process: wet precipitation of apatitic tricalcium phosphate ('precursor') and calcination of the precursor at 800°C for 3 hours. beta-TCMP or beta-TCP powders were also prepared by solid-state reactions from CaHPO4 and CaCO 3 with/without MgO. Biphasic calcium phosphate, which is mixture of HAP and beta-TCP, can be prepared though mechanical mixing of HAP and beta-TCP powders synthesized as above. Dense beta-TCP and beta-TCMP ceramics can be produced by pressing green bodies at 100MPa and further sintering above 1100°C for 2 hours. beta-TCMP ceramics ˜99.4% relative dense were prepared by this method. Dense beta-TCP ceramics have average strength up to 540MPa. Macroporous beta-TCMP ceramics were produced with sucrose as the porogen following a two-step pressing method. Porous beta-TCMP ceramics were also prepared by replication of polyurethane sponge. beta-TCMP ceramics with porous structures in the center surrounded by dense structures were created. The outside dense structures give the scaffold mechanical strength, while the central porous structures enable cells migration and vascular infiltration, and finally in-growth of new bone into the scaffold.

Purification, physicochemical characterization, saccharide specificity, and chemical modification of a Gal/GalNAc specific lectin from the seeds of Trichosanthes dioica.

PubMed

Sultan, Nabil Ali Mohammed; Kenoth, Roopa; Swamy, Musti J

2004-12-15

A new galactose-specific lectin has been purified from the extracts of Trichosanthes dioica seeds by affinity chromatography on cross-linked guar gum. The purified lectin (T. dioica seed lectin, TDSL) moved as a single symmetrical peak on gel filtration on Superose-12 in the presence of 0.1 M lactose with an M(r) of 55 kDa. In the absence of ligand, the movement was retarded, indicating a possible interaction of the lectin with the column matrix. In SDS-PAGE, in the presence of beta-mercaptoethanol, two non-identical bands of M(r) 24 and 37 kDa were observed, whereas in the absence of beta-mercaptoethanol, the lectin yielded a single band corresponding to approximately 55,000 Da, indicating that the two subunits of TDSL are connected by one or more disulfide bridges. TDSL is a glycoprotein with about 4.9% covalently bound neutral sugar. Analysis of near-UV CD spectrum by three different methods (CDSSTR, CONTINLL, and SELCON3) shows that TDSL contains 13.3% alpha-helix, 36.7% beta-sheet, 19.4% beta-turns, and 31.6% unordered structure. Among a battery of sugars investigated, TDSL was inhibited strongly by beta-d-galactopyranosides, with 4-methylumbelliferyl-beta-d-galactopyranoside being the best ligand. Chemical modification studies indicate that tyrosine residues are important for the carbohydrate-binding and hemagglutinating activities of the lectin. A partial protection was observed when the tyrosine modification was performed in the presence of 0.2 M lactose. The tryptophan residues of TDSL appear to be buried in the protein interior as they could not be modified under native conditions, whereas upon denaturation with 8 M urea two Trp residues could be selectively modified by N-bromosuccinimide. The subunit composition and size, secondary structure, and sugar specificity of this lectin are similar to those of type-2 ribosome inactivating proteins, suggesting that TDSL may belong to this protein family.

Ultrastructure and cytochemistry of cardiac intramitochondrial glycogen.

PubMed

Sótonyi, P; Somogyi, E; Nemes, A; Juhász-Nagy, S

1976-01-01

Authors have observed abnormalities of glycogen localization in cardiac muscle, after normothermic cardiac arrest. The identification of these intramitrochondrial particles as glycogen was confirmed by selective staining with periodic acid-lead citrat, periodic acid-thiosemicarbazide protein methods and by their selective removal from tissue sections by alfa-amylase. The intramitochondrial glycogen particles were of beta-type. Some intramitochondrial particles were surrounded by paired membranes which resulted from protrusion of parts of mitochondrial membrane.

Medium-{beta} free-boundary equilibria of a quasi-isodynamic stellarator

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

Mikhailov, M. I.; Drevlak, M.; Nuehrenberg, J.

Free-boundary MHD equilibria with magnetic surfaces in the vacuum region surrounding the plasma [E. Strumberger, Nucl. Fusion 37, 19 (1997); M. Drevlak, D. Monticello, and A. Reiman, Nucl. Fusion 45, 731 (2005)] are obtained for a quasi-isodynamic stellarator [A. A. Subbotin, M. I. Mikhailov, V. D. Shafranov et al., Nucl. Fusion 46, 921 (2006); M. I. Mikhailov, J. Nuhrenberg, and V. D. Shafranov, Plasma Phys. Rep. 35, 529 (2009)].

AmrZ Beta-Sheet Residues Are Essential for DNA Binding and Transcriptional Control of Pseudomonas aeruginosa Virulence Genes ▿ †

PubMed Central

Waligora, Elizabeth A.; Ramsey, Deborah M.; Pryor, Edward E.; Lu, Haiping; Hollis, Thomas; Sloan, Gina P.; Deora, Rajendar; Wozniak, Daniel J.

2010-01-01

AmrZ is a putative ribbon-helix-helix (RHH) transcriptional regulator. RHH proteins utilize residues within the β-sheet for DNA binding, while the α-helices promote oligomerization. AmrZ is of interest due to its dual roles as a transcriptional activator and as a repressor, regulating genes encoding virulence factors associated with both chronic and acute Pseudomonas aeruginosa infection. In this study, cross-linking revealed that AmrZ forms oligomers in solution but that the amino terminus, containing an unordered region and a β-sheet, were not required for oligomerization. The first 12 unordered residues (extended amino terminus) contributed minimally to DNA binding. Mutagenesis of the AmrZ β-sheet demonstrated that residues 18, 20, and 22 were essential for DNA binding at both activation and repressor sites, suggesting that AmrZ utilizes a similar mechanism for binding to these sites. Mice infected with amrZ mutants exhibited reduced bacterial burden, morbidity, and mortality. Direct in vivo competition assays showed a 5-fold competitive advantage for the wild type over an isogenic amrZ mutant. Finally, the reduced infection phenotype of the amrZ-null strain was similar to that of a strain expressing a DNA-binding-deficient AmrZ variant, indicating that DNA binding and transcriptional regulation by AmrZ is responsible for the in vivo virulence defect. These recent infection data, along with previously identified AmrZ-regulated virulence factors, suggest the necessity of AmrZ transcriptional regulation for optimal virulence during acute infection. PMID:20709902

Analysis and separation of residues important for the chemoattractant and antimicrobial activities of beta-defensin 3.

PubMed

Taylor, Karen; Clarke, David J; McCullough, Bryan; Chin, Wutharath; Seo, Emily; Yang, De; Oppenheim, Joost; Uhrin, Dusan; Govan, John R W; Campopiano, Dominic J; MacMillan, Derek; Barran, Perdita; Dorin, Julia R

2008-03-14

beta-Defensins are important in mammalian immunity displaying both antimicrobial and chemoattractant activities. Three canonical disulfide intramolecular bonds are believed to be dispensable for antimicrobial activity but essential for chemoattractant ability. However, here we show that HBD3 (human beta-defensin 3) alkylated with iodoactemide and devoid of any disulfide bonds is still a potent chemoattractant. Furthermore, when the canonical six cysteine residues are replaced with alanine, the peptide is no longer active as a chemoattractant. These findings are replicated by the murine ortholog Defb14. We restore the chemoattractant activity of Defb14 and HBD3 by introduction of a single cysteine in the fifth position (Cys V) of the beta-defensin six cysteine motif. In contrast, a peptide with a single cysteine at the first position (Cys I) is inactive. Moreover, a range of overlapping linear fragments of Defb14 do not act as chemoattractants, suggesting that the chemotactic activity of this peptide is not dependent solely on an epitope surrounding Cys V. Full-length peptides either with alkylated cysteine residues or with cysteine residues replaced with alanine are still strongly antimicrobial. Defb14 peptide fragments were also tested for antimicrobial activity, and peptides derived from the N-terminal region display potent antimicrobial activity. Thus, the chemoattractant and antimicrobial activities of beta-defensins can be separated, and both of these functions are independent of intramolecular disulfide bonds. These findings are important for further understanding of the mechanism of action of defensins and for therapeutic design.

Interaction of the p85 subunit of PI 3-kinase and its N-terminal SH2 domain with a PDGF receptor phosphorylation site: structural features and analysis of conformational changes.

PubMed Central

Panayotou, G; Bax, B; Gout, I; Federwisch, M; Wroblowski, B; Dhand, R; Fry, M J; Blundell, T L; Wollmer, A; Waterfield, M D

1992-01-01

Circular dichroism and fluorescence spectroscopy were used to investigate the structure of the p85 alpha subunit of the PI 3-kinase, a closely related p85 beta protein, and a recombinant SH2 domain-containing fragment of p85 alpha. Significant spectral changes, indicative of a conformational change, were observed on formation of a complex with a 17 residue peptide containing a phosphorylated tyrosine residue. The sequence of this peptide is identical to the sequence surrounding Tyr751 in the kinase-insert region of the platelet-derived growth factor beta-receptor (beta PDGFR). The rotational correlation times measured by fluorescence anisotropy decay indicated that phosphopeptide binding changed the shape of the SH2 domain-containing fragment. The CD and fluorescence spectroscopy data support the secondary structure prediction based on sequence analysis and provide evidence for flexible linker regions between the various domains of the p85 proteins. The significance of these results for SH2 domain-containing proteins is discussed. Images PMID:1330535

Ion-scale spectral break of solar wind turbulence at high and low beta

PubMed Central

Chen, C H K; Leung, L; Boldyrev, S; Maruca, B A; Bale, S D

2014-01-01

The power spectrum of magnetic fluctuations in the solar wind at 1 AU displays a break between two power laws in the range of spacecraft-frame frequencies 0.1 to 1 Hz. These frequencies correspond to spatial scales in the plasma frame near the proton gyroradius ρi and proton inertial length di. At 1 AU it is difficult to determine which of these is associated with the break, since and the perpendicular ion plasma beta is typically β⊥i∼1. To address this, several exceptional intervals with β⊥i≪1 and β⊥i≫1 were investigated, during which these scales were well separated. It was found that for β⊥i≪1 the break occurs at di and for β⊥i≫1 at ρi, i.e., the larger of the two scales. Possible explanations for these results are discussed, including Alfvén wave dispersion, damping, and current sheets. PMID:26074642

Sequence-specific sup 1 H NMR resonance assignments of Bacillus subtilis HPr: Use of spectra obtained from mutants to resolve spectral overlap

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

Wittekind, M.; Klevit, R.E.; Reizer, J.

1990-08-07

On the basis of an analysis of two-dimensional {sup 1}H NMR spectra, the complete sequence-specific {sup 1}H NMR assignments are presented for the phosphocarrier protein HPr from the Gram-positive bacterium Bacillus subtilis. During the assignment procedure, extensive use was made of spectra obtained from point mutants of HPr in order to resolve spectral overlap and to provide verification of assignments. Regions of regular secondary structure were identified by characteristic patterns of sequential backbone proton NOEs and slowly exchanging amide protons. B subtilis HPr contains four {beta}-strands that form a single antiparallel {beta}-sheet and two well-defined {alpha}-helices. There are two stretchesmore » of extended backbone structure, one of which contains the active site His{sub 15}. The overall fold of the protein is very similar to that of Escherichia coli HPr determined by NMR studies.« less

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

PubMed

Compton, L A; Johnson, W C

1986-05-15

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

Crystal structure of bovine Cu,Zn superoxide dismutase at 3 A resolution: chain tracing and metal ligands.

PubMed Central

Richardson, J; Thomas, K A; Rubin, B H; Richardson, D C

1975-01-01

An electron density map at 3 angstrom resolution has been calculated for Cu2+, Zn2+ superoxide dismutase from bovine erythrocytes, and the course of the main chain has been traced. The dominant structural feature is an 8-stranded barrel of antiparallel beta-pleated sheet. There is one very short helical section and two long loops of non-repetitive structure. The Cu and Zn are bound between the loops and one side of the beta barrel and are about 6 Angstrom apart, with a common histidine ligand. The Cu has four histidine ligands in a somewhat distorted square plane, and the Zn has three histidines and an aspartate in approximately tetrahedral arrangement. The two coppers of a dimer are about 34 Angstrom apart. The two subunits have essentially the same conformation and have an extensive contact area that mainly involves hydrophobic side chain interactions. The overall folding pattern of the polypeptide chain is very similar to that of an immunoglobulin domain. Images PMID:1055410

Large-scale purification and biochemical characterization of crystallization-grade porin protein P from Pseudomonas aeruginosa.

PubMed

Worobec, E A; Martin, N L; McCubbin, W D; Kay, C M; Brayer, G D; Hancock, R E

1988-04-07

A large-scale purification scheme was developed for lipopolysaccharide-free protein P, the phosphate-starvation-inducible outer-membrane porin from Pseudomonas aeruginosa. This highly purified protein P was used to successfully form hexagonal crystals in the presence of n-octyl-beta-glucopyranoside. Amino-acid analysis indicated that protein P had a similar composition to other bacterial outer membrane proteins, containing a high percentage (50%) of hydrophilic residues. The amino-terminal sequence of this protein, although not homologous to either outer membrane protein, PhoE or OmpF, of Escherichia coli, was found to have an analogous protein-folding pattern. Protein P in the native trimer form was capable of maintaining a stable functional trimer after proteinase cleavage. This suggested the existence of a strongly associated tertiary and quaternary structure. Circular dichroism studies confirmed these results in that a large proportion of the protein structure was determined to be beta-sheet and resistant to acid pH and heating in 0.1% sodium dodecyl sulphate.

Ion-scale spectral break of solar wind turbulence at high and low beta

DOE PAGES

Chen, C. H. K.; Leung, L.; Boldyrev, S.; ...

2014-11-25

Here, the power spectrum of magnetic fluctuations in the solar wind at 1 AU displays a break between two power laws in the range of spacecraft-frame frequencies 0.1 to 1 Hz. These frequencies correspond to spatial scales in the plasma frame near the proton gyroradius ρi and proton inertial length di. At 1 AU it is difficult to determine which of these is associated with the break, since d i=ρ i/ √ β ⊥i and the perpendicular ion plasma beta is typically β ⊥i~1. To address this, several exceptional intervals with β ⊥i<<1 and β ⊥i>>1 were investigated, during whichmore » these scales were well separated. It was found that for β⊥i<<1 the break occurs at di and for β ⊥i>>1 at ρi, i.e., the larger of the two scales. Possible explanations for these results are discussed, including Alfvén wave dispersion, damping, and current sheets.« less

A de novo designed 11 kDa polypeptide: model for amyloidogenic intrinsically disordered proteins.

PubMed

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

2010-07-01

A de novo polypeptide GH(6)[(GA)(3)GY(GA)(3)GE](8)GAH(6) (YE8) has a significant number of identical weakly interacting beta-strands with the turns and termini functionalized by charged amino acids to control polypeptide folding and aggregation. YE8 exists in a soluble, disordered form at neutral pH but is responsive to changes in pH and ionic strength. The evolution of YE8 secondary structure has been successfully quantified during all stages of polypeptide fibrillation by deep UV resonance Raman (DUVRR) spectroscopy combined with other morphological, structural, spectral, and tinctorial characterization. The YE8 folding kinetics at pH 3.5 are strongly dependent on polypeptide concentration with a lag phase that can be eliminated by seeding with a solution of folded fibrillar YE8. The lag phase of polypeptide folding is concentration dependent leading to the conclusion that beta-sheet folding of the 11-kDa amyloidogenic polypeptide is completely aggregation driven.

Application of cyclodextrins in antibody microparticles: potentials for antibody protection in spray drying.

PubMed

Ramezani, Vahid; Vatanara, Alireza; Seyedabadi, Mohammad; Nabi Meibodi, Mohsen; Fanaei, Hamed

2017-07-01

Dry powder formulations are extensively used to improve the stability of antibodies. Spray drying is one of important methods for protein drying. This study investigated the effects of trehalose, hydroxypropyl beta cyclodextrin (HPBCD) and beta cyclodextrin (BCD) on the stability and particle properties of spray-dried IgG. D-optimal design was employed for both experimental design and analysis and optimization of the variables. The size and aerodynamic behavior of particles were determined using laser light scattering and glass twin impinger, respectively. In addition, stability, ratio of beta sheets and morphology of antibody were analyzed using size exclusion chromatography, IR spectroscopy and electron microscopy, respectively. Particle properties and antibody stability were significantly improved in the presence of HPBCD. In addition, particle aerodynamic behavior, in terms of fine-particle fraction (FPF), enhanced up to 52.23%. Furthermore, antibody was better preserved not only during spray drying, but also during long-term storage. In contrast, application of BCD resulted in the formation of larger particles. Although trehalose caused inappropriate aerodynamic property, it efficiently decreased antibody aggregation. HPBCD is an efficient excipient for the development of inhalable protein formulations. In this regard, optimal particle property and antibody stability was obtained with proper combination of cyclodextrins and simple sugars, such as trehalose.

Identification and comparative analysis of the epidermal differentiation complex in snakes

PubMed Central

Brigit Holthaus, Karin; Mlitz, Veronika; Strasser, Bettina; Tschachler, Erwin; Alibardi, Lorenzo; Eckhart, Leopold

2017-01-01

The epidermis of snakes efficiently protects against dehydration and mechanical stress. However, only few proteins of the epidermal barrier to the environment have so far been identified in snakes. Here, we determined the organization of the Epidermal Differentiation Complex (EDC), a cluster of genes encoding protein constituents of cornified epidermal structures, in snakes and compared it to the EDCs of other squamates and non-squamate reptiles. The EDC of snakes displays shared synteny with that of the green anole lizard, including the presence of a cluster of corneous beta-protein (CBP)/beta-keratin genes. We found that a unique CBP comprising 4 putative beta-sheets and multiple cysteine-rich EDC proteins are conserved in all snakes and other squamates investigated. Comparative genomics of squamates suggests that the evolution of snakes was associated with a gene duplication generating two isoforms of the S100 fused-type protein, scaffoldin, the origin of distinct snake-specific EDC genes, and the loss of other genes that were present in the EDC of the last common ancestor of snakes and lizards. Taken together, our results provide new insights into the evolution of the skin in squamates and a basis for the characterization of the molecular composition of the epidermis in snakes. PMID:28345630

Folding thermodynamics of model four-strand antiparallel beta-sheet proteins.

PubMed Central

Jang, Hyunbum; Hall, Carol K; Zhou, Yaoqi

2002-01-01

The thermodynamic properties for three different types of off-lattice four-strand antiparallel beta-strand protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed for different sizes of the bias gap g, an artificial measure of a model protein's preference for its native state. The thermodynamic transition temperatures are obtained by calculating the squared radius of gyration R(g)(2), the root-mean-squared pair separation fluctuation Delta(B), the specific heat C(v), the internal energy of the system E, and the Lindemann disorder parameter Delta(L). Despite these models' simplicity, they exhibit a complex set of protein transitions, consistent with those observed in experimental studies on real proteins. Starting from high temperature, these transitions include a collapse transition, a disordered-to-ordered globule transition, a folding transition, and a liquid-to-solid transition. The high temperature transitions, i.e., the collapse transition and the disordered-to-ordered globule transition, exist for all three beta-strand proteins, although the native-state geometry of the three model proteins is different. However the low temperature transitions, i.e., the folding transition and the liquid-to-solid transition, strongly depend on the native-state geometry of the model proteins and the size of the bias gap. PMID:11806908

A free-energy approach for all-atom protein simulation.

PubMed

Verma, Abhinav; Wenzel, Wolfgang

2009-05-06

All-atom free-energy methods offer a promising alternative to kinetic molecular mechanics simulations of protein folding and association. Here we report an accurate, transferable all-atom biophysical force field (PFF02) that stabilizes the native conformation of a wide range of proteins as the global optimum of the free-energy landscape. For 32 proteins of the ROSETTA decoy set and six proteins that we have previously folded with PFF01, we find near-native conformations with an average backbone RMSD of 2.14 A to the native conformation and an average Z-score of -3.46 to the corresponding decoy set. We used nonequilibrium sampling techniques starting from completely extended conformations to exhaustively sample the energy surface of three nonhomologous hairpin-peptides, a three-stranded beta-sheet, the all-helical 40 amino-acid HIV accessory protein, and a zinc-finger beta beta alpha motif, and find near-native conformations for the minimal energy for each protein. Using a massively parallel evolutionary algorithm, we also obtain a near-native low-energy conformation for the 54 amino-acid engrailed homeodomain. Our force field thus stabilized near-native conformations for a total of 20 proteins of all structure classes with an average RMSD of only 3.06 A to their respective experimental conformations.

Laser based spot weld characterization

NASA Astrophysics Data System (ADS)

Jonietz, Florian; Myrach, Philipp; Rethmeier, Michael; Suwala, Hubert; Ziegler, Mathias

2016-02-01

Spot welding is one of the most important joining technologies, especially in the automotive industry. Hitherto, the quality of spot welded joints is tested mainly by random destructive tests. A nondestructive testing technique offers the benefit of cost reduction of the testing procedure and optimization of the fabrication process, because every joint could be examined. This would lead to a reduced number of spot welded joints, as redundancies could be avoided. In the procedure described here, the spot welded joint between two zinc-coated steel sheets (HX340LAD+Z100MB or HC340LA+ZE 50/50) is heated optically on one side. Laser radiation and flash light are used as heat sources. The melted zone, the so called "weld nugget" provides the mechanical stability of the connection, but also constitutes a thermal bridge between the sheets. Due to the better thermal contact, the spot welded joint reveals a thermal behavior different from the surrounding material, where the heat transfer between the two sheets is much lower. The difference in the transient thermal behavior is measured with time resolved thermography. Hence, the size of the thermal contact between the two sheets is determined, which is directly correlated to the size of the weld nugget, indicating the quality of the spot weld. The method performs well in transmission with laser radiation and flash light. With laser radiation, it works even in reflection geometry, thus offering the possibility of testing with just one-sided accessibility. By using heating with collimated laser radiation, not only contact-free, but also remote testing is feasible. A further convenience compared to similar thermographic approaches is the applicability on bare steel sheets without any optical coating for emissivity correction. For this purpose, a proper way of emissivity correction was established.

New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow.

PubMed

Kalgin, Igor V; Caflisch, Amedeo; Chekmarev, Sergei F; Karplus, Martin

2013-05-23

A new analysis of the 20 μs equilibrium folding/unfolding molecular dynamics simulations of the three-stranded antiparallel β-sheet miniprotein (beta3s) in implicit solvent is presented. The conformation space is reduced in dimensionality by introduction of linear combinations of hydrogen bond distances as the collective variables making use of a specially adapted principal component analysis (PCA); i.e., to make structured conformations more pronounced, only the formed bonds are included in determining the principal components. It is shown that a three-dimensional (3D) subspace gives a meaningful representation of the folding behavior. The first component, to which eight native hydrogen bonds make the major contribution (four in each beta hairpin), is found to play the role of the reaction coordinate for the overall folding process, while the second and third components distinguish the structured conformations. The representative points of the trajectory in the 3D space are grouped into conformational clusters that correspond to locally stable conformations of beta3s identified in earlier work. A simplified kinetic network based on the three components is constructed, and it is complemented by a hydrodynamic analysis. The latter, making use of "passive tracers" in 3D space, indicates that the folding flow is much more complex than suggested by the kinetic network. A 2D representation of streamlines shows there are vortices which correspond to repeated local rearrangement, not only around minima of the free energy surface but also in flat regions between minima. The vortices revealed by the hydrodynamic analysis are apparently not evident in folding pathways generated by transition-path sampling. Making use of the fact that the values of the collective hydrogen bond variables are linearly related to the Cartesian coordinate space, the RMSD between clusters is determined. Interestingly, the transition rates show an approximate exponential correlation with distance in the hydrogen bond subspace. Comparison with the many published studies shows good agreement with the present analysis for the parts that can be compared, supporting the robust character of our understanding of this "hydrogen atom" of protein folding.

Beta functions in Chirally deformed supersymmetric sigma models in two dimensions

NASA Astrophysics Data System (ADS)

Vainshtein, Arkady

2016-10-01

We study two-dimensional sigma models where the chiral deformation diminished the original 𝒩 = (2, 2) supersymmetry to the chiral one, 𝒩 = (0, 2). Such heterotic models were discovered previously on the world sheet of non-Abelian stringy solitons supported by certain four-dimensional 𝒩 = 1 theories. We study geometric aspects and holomorphic properties of these models, and derive a number of exact expressions for the β functions in terms of the anomalous dimensions analogous to the NSVZ β function in four-dimensional Yang-Mills. Instanton calculus provides a straightforward method for the derivation.

Beta Functions in Chirally Deformed Supersymmetric Sigma Models in Two Dimensions

NASA Astrophysics Data System (ADS)

Vainshtein, Arkady

We study two-dimensional sigma models where the chiral deformation diminished the original 𝒩 =(2, 2) supersymmetry to the chiral one, 𝒩 =(0, 2). Such heterotic models were discovered previously on the world sheet of non-Abelian stringy solitons supported by certain four-dimensional 𝒩 = 1 theories. We study geometric aspects and holomorphic properties of these models, and derive a number of exact expressions for the β functions in terms of the anomalous dimensions analogous to the NSVZ β function in four-dimensional Yang-Mills. Instanton calculus provides a straightforward method for the derivation.

Treatment Characteristics of Second Order Structure of Proteins Using Low-Pressure Oxygen RF Plasma

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

Hayashi, Nobuya; Nakahigashi, Akari; Kawaguchi, Ryutaro

2010-10-13

Removal of proteins from the surface of medical equipments is attempted using oxygen plasma produced by RF discharge. FTIR spectra indicate that the bonding of C-H and N-H in the casein protein is reduced after irradiation of oxygen plasma. Also, the second order structure of a protein such as {alpha}-helix and {beta}-sheet are modified by the oxygen plasma. Complete removal of casein protein with the concentration of 0.016 mg/cm{sup 2} that is equivalent to remnants on the medical equipment requires two hours avoiding the damage to medical equipments.

Enzymatically-stable oxetane-based dipeptide hydrogels.

PubMed

McDougall, Laura; Draper, Emily R; Beadle, Jonathan D; Shipman, Michael; Raubo, Piotr; Jamieson, Andrew G; Adams, Dave J

2018-02-13

Low molecular weight gelators that are not easily degraded by enzymes have a range of potential applications. Here, we report new Fmoc-protected dipeptides in which the amide carbonyl group has been replaced by an oxetane ring. Remarkably one of these peptidomimetics, but not the corresponding dipeptide, is an effective gelator, forming hydrogels at a concentration of 3 mg mL -1 . On assembly, there is a lack of beta-sheet structure, implying that there is no requirement for this motif in such a gel. Furthermore, the modified dipeptide is also stable to proteolysis compared to the parent dipeptide.

Energetic Particles of keV–MeV Energies Observed near Reconnecting Current Sheets at 1 au

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

Khabarova, Olga V.; Zank, Gary P.

2017-07-01

We provide evidence for particle acceleration up to ∼5 MeV at reconnecting current sheets in the solar wind based on both case studies and a statistical analysis of the energetic ion and electron flux data from the five Advanced Composition Explorer Electron, Proton, and Alpha Monitor (EPAM) detectors. The case study of a typical reconnection exhaust event reveals (i) a small-scale peak of the energetic ion flux observed in the vicinity of the reconnection exhaust and (ii) a long-timescale atypical energetic particle event (AEPE) encompassing the reconnection exhaust. AEPEs associated with reconnecting strong current sheets last for many hours, evenmore » days, as confirmed by statistical studies. The case study shows that time-intensity profiles of the ion flux may vary significantly from one EPAM detector to another partially because of the local topology of magnetic fields, but mainly because of the impact of upstream magnetospheric events; therefore, the occurrence of particle acceleration can be hidden. The finding of significant particle energization within a time interval of ±30 hr around reconnection exhausts is supported by a superposed epoch analysis of 126 reconnection exhaust events. We suggest that energetic particles initially accelerated via prolonged magnetic reconnection are trapped and reaccelerated in small- or medium-scale magnetic islands surrounding the reconnecting current sheet, as predicted by the transport theory of Zank et al. Other mechanisms of initial particle acceleration can contribute also.« less

Metacommunity composition of web-spiders in a fragmented neotropical forest: relative importance of environmental and spatial effects.

PubMed

Baldissera, Ronei; Rodrigues, Everton N L; Hartz, Sandra M

2012-01-01

The distribution of beta diversity is shaped by factors linked to environmental and spatial control. The relative importance of both processes in structuring spider metacommunities has not yet been investigated in the Atlantic Forest. The variance explained by purely environmental, spatially structured environmental, and purely spatial components was compared for a metacommunity of web spiders. The study was carried out in 16 patches of Atlantic Forest in southern Brazil. Field work was done in one landscape mosaic representing a slight gradient of urbanization. Environmental variables encompassed plot- and patch-level measurements and a climatic matrix, while principal coordinates of neighbor matrices (PCNMs) acted as spatial variables. A forward selection procedure was carried out to select environmental and spatial variables influencing web-spider beta diversity. Variation partitioning was used to estimate the contribution of pure environmental and pure spatial effects and their shared influence on beta-diversity patterns, and to estimate the relative importance of selected environmental variables. Three environmental variables (bush density, land use in the surroundings of patches, and shape of patches) and two spatial variables were selected by forward selection procedures. Variation partitioning revealed that 15% of the variation of beta diversity was explained by a combination of environmental and PCNM variables. Most of this variation (12%) corresponded to pure environmental and spatially environmental structure. The data indicated that (1) spatial legacy was not important in explaining the web-spider beta diversity; (2) environmental predictors explained a significant portion of the variation in web-spider composition; (3) one-third of environmental variation was due to a spatial structure that jointly explains variation in species distributions. We were able to detect important factors related to matrix management influencing the web-spider beta-diversity patterns, which are probably linked to historical deforestation events.

Partial deletion of beta9 loop in pancreatic lipase-related protein 2 reduces enzyme activity with a larger effect on long acyl chain substrates.

PubMed

Dridi, Kaouthar; Amara, Sawsan; Bezzine, Sofiane; Rodriguez, Jorge A; Carrière, Frédéric; Gaussier, Hélène

2013-07-01

Structural studies on pancreatic lipase have revealed a complex architecture of surface loops surrounding the enzyme active site and potentially involved in interactions with lipids. Two of them, the lid and beta loop, expose a large hydrophobic surface and are considered as acyl chain binding sites based on their interaction with an alkyl phosphonate inhibitor. While the role of the lid in substrate recognition and selectivity has been extensively studied, the implication of beta9 loop in acyl chain stabilization remained hypothetical. The characterization of an enzyme with a natural deletion of the lid, guinea pig pancreatic lipase-related protein 2 (GPLRP2), suggests however an essential contribution of the beta9 loop in the stabilization of the acyl enzyme intermediate formed during the lipolysis reaction. A GPLRP2 mutant with a seven-residue deletion of beta9 loop (GPLRP2-deltabeta9) was produced and its enzyme activity was measured using various substrates (triglycerides, monoglycerides, galactolipids, phospholipids, vinyl esters) with short, medium and long acyl chains. Whatever the substrate tested, GPLRP2-deltabeta9 activity is drastically reduced compared to that of wild-type GPLRP2 and this effect is more pronounced as the length of substrate acyl chain increases. Changes in relative substrate selectivity and stereoselectivity remained however weak. The deletion within beta9 loop has also a negative effect on the rate of enzyme inhibition by alkyl phosphonates. All these findings indicate that the reduced enzyme turnover observed with GPLRP2-deltabeta9 results from a weaker stabilization of the acyl enzyme intermediate due to a loss of hydrophobic interactions.

Engineering Neprilysin Activity and Specificity to Create a Novel Therapeutic for Alzheimer’s Disease

PubMed Central

Webster, Carl I.; Burrell, Matthew; Olsson, Lise-Lotte; Fowler, Susan B.; Digby, Sarah; Sandercock, Alan; Snijder, Arjan; Tebbe, Jan; Haupts, Ulrich; Grudzinska, Joanna; Jermutus, Lutz; Andersson, Christin

2014-01-01

Neprilysin is a transmembrane zinc metallopeptidase that degrades a wide range of peptide substrates. It has received attention as a potential therapy for Alzheimer’s disease due to its ability to degrade the peptide amyloid beta. However, its broad range of peptide substrates has the potential to limit its therapeutic use due to degradation of additional peptides substrates that tightly regulate many physiological processes. We sought to generate a soluble version of the ectodomain of neprilysin with improved activity and specificity towards amyloid beta as a potential therapeutic for Alzheimer’s disease. Extensive amino acid substitutions were performed at positions surrounding the active site and inner surface of the enzyme and variants screened for activity on amyloid beta 1–40, 1–42 and a variety of other physiologically relevant peptides. We identified several mutations that modulated and improved both enzyme selectivity and intrinsic activity. Neprilysin variant G399V/G714K displayed an approximately 20-fold improved activity on amyloid beta 1–40 and up to a 3,200-fold reduction in activity on other peptides. Along with the altered peptide substrate specificity, the mutant enzyme produced a markedly altered series of amyloid beta cleavage products compared to the wild-type enzyme. Crystallisation of the mutant enzyme revealed that the amino acid substitutions result in alteration of the shape and size of the pocket containing the active site compared to the wild-type enzyme. The mutant enzyme offers the potential for the more efficient degradation of amyloid beta in vivo as a therapeutic for the treatment of Alzheimer’s disease. PMID:25089527

The 1984 eclipse of the symbiotic binary SY Muscae

NASA Technical Reports Server (NTRS)

Kenyon, S. J.; Michalitisianos, A. G.; Lutz, J. H.; Kafatos, M.

1985-01-01

Data from IUE spectra obtained with the 10 x 20-arcsec aperture on May 13, 1984, and optical spectrophotometry obtained with an SIT vidicon on the 1.5-m telescope at CTIO on April 29-May 1, 1984, are reported for the symbiotic binary SY Mus. The data are found to be consistent with a model of a red-giant secondary of 60 solar radii which completely eclipses the hot primary every 627 d but only partially eclipses the 75-solar-radius He(+) region surrounding the primary. The distance to SY Mus is estimated as 1.3 kpc. It is suggested that the large Balmer decrement in eclipse, with (H-alpha)/(H-beta) = 8.3 and (H-beta)/(H-gamma) = 1.5, is associated with an electron density of about 10 to the 10th/cu cm.

Surface polarity of beta-HMX crystal and the related adhesive forces with Estane binder.

PubMed

Yang, Lu

2008-12-02

Here I present the results on the study of surface properties of beta-HMX crystal utilizing molecular dynamics simulations. The surface polarity of three principal crystal surfaces, (011), (010), and (110), is investigated by measuring the water contact angles. The calculated contact angles are in excellent agreement with the values measured by experiment and show that the surface polarity of three crystal surfaces are different. The free energies and forces of detaching an Estane chain (with and without surrounding nitroplasticizer molecules) from the three principal crystal surfaces are also calculated using the umbrella sampling method. I find that the force for Estane detachment increases with the increasing HMX surface polarity. In addition, my results show that the nitroplasticizer also plays an important role in the adhesion between Estane and HMX surfaces.

Modeling of subglacial hydrological development following rapid supraglacial lake drainage.

PubMed

Dow, C F; Kulessa, B; Rutt, I C; Tsai, V C; Pimentel, S; Doyle, S H; van As, D; Lindbäck, K; Pettersson, R; Jones, G A; Hubbard, A

2015-06-01

The rapid drainage of supraglacial lakes injects substantial volumes of water to the bed of the Greenland ice sheet over short timescales. The effect of these water pulses on the development of basal hydrological systems is largely unknown. To address this, we develop a lake drainage model incorporating both (1) a subglacial radial flux element driven by elastic hydraulic jacking and (2) downstream drainage through a linked channelized and distributed system. Here we present the model and examine whether substantial, efficient subglacial channels can form during or following lake drainage events and their effect on the water pressure in the surrounding distributed system. We force the model with field data from a lake drainage site, 70 km from the terminus of Russell Glacier in West Greenland. The model outputs suggest that efficient subglacial channels do not readily form in the vicinity of the lake during rapid drainage and instead water is evacuated primarily by a transient turbulent sheet and the distributed system. Following lake drainage, channels grow but are not large enough to reduce the water pressure in the surrounding distributed system, unless preexisting channels are present throughout the domain. Our results have implications for the analysis of subglacial hydrological systems in regions where rapid lake drainage provides the primary mechanism for surface-to-bed connections. Model for subglacial hydrological analysis of rapid lake drainage eventsLimited subglacial channel growth during and following rapid lake drainagePersistence of distributed drainage in inland areas where channel growth is limited.

Modeling of subglacial hydrological development following rapid supraglacial lake drainage

PubMed Central

Dow, C F; Kulessa, B; Rutt, I C; Tsai, V C; Pimentel, S; Doyle, S H; van As, D; Lindbäck, K; Pettersson, R; Jones, G A; Hubbard, A

2015-01-01

The rapid drainage of supraglacial lakes injects substantial volumes of water to the bed of the Greenland ice sheet over short timescales. The effect of these water pulses on the development of basal hydrological systems is largely unknown. To address this, we develop a lake drainage model incorporating both (1) a subglacial radial flux element driven by elastic hydraulic jacking and (2) downstream drainage through a linked channelized and distributed system. Here we present the model and examine whether substantial, efficient subglacial channels can form during or following lake drainage events and their effect on the water pressure in the surrounding distributed system. We force the model with field data from a lake drainage site, 70 km from the terminus of Russell Glacier in West Greenland. The model outputs suggest that efficient subglacial channels do not readily form in the vicinity of the lake during rapid drainage and instead water is evacuated primarily by a transient turbulent sheet and the distributed system. Following lake drainage, channels grow but are not large enough to reduce the water pressure in the surrounding distributed system, unless preexisting channels are present throughout the domain. Our results have implications for the analysis of subglacial hydrological systems in regions where rapid lake drainage provides the primary mechanism for surface-to-bed connections. Key Points Model for subglacial hydrological analysis of rapid lake drainage events Limited subglacial channel growth during and following rapid lake drainage Persistence of distributed drainage in inland areas where channel growth is limited PMID:26640746

Woven-grid sealed quasi-bipolar lead-acid battery construction and fabricating method

NASA Technical Reports Server (NTRS)

Rippel, Wally E. (Inventor)

1989-01-01

A quasi-bipolar lead-acid battery construction includes a plurality of bipolar cells disposed in side-by-side relation to form a stack, and a pair of monoplanar plates at opposite ends of the stack, the cell stack and monopolar plates being contained within a housing of the battery. Each bipolar cell is loaded with an electrolyte and composed of a bipolar electrode plate and a pair of separator plates disposed on opposite sides of the electrode plate and peripherally sealed thereto. Each bipolar electrode plate is composed of a partition sheet and two bipolar electrode elements folded into a hairpin configuration and applied over opposite edges of the partition sheet so as to cover the opposite surfaces of the opposite halves thereof. Each bipolar electrode element is comprised of a woven grid with a hot-melt strip applied to a central longitudinal region of the grid along which the grid is folded into the hairpin configuration, and layers of negative and positive active material pastes applied to opposite halves of the grid on opposite sides of the central hot-melt strip. The grid is made up of strands of conductive and non-conductive yarns composing the respective transverse and longitudinal weaves of the grid. The conductive yarn has a multi-stranded glass core surrounded and covered by a lead sheath, whereas the non-conductive yarn has a multi-stranded glass core surrounded and covered by a thermally activated sizing.

Differential Velocity between Solar Wind Protons and Alpha Particles in Pressure Balance Structures

NASA Technical Reports Server (NTRS)

Yamauchi, Yohei; Suess, Steven T.; Steinberg, John T.; Sakurai, Takashi

2004-01-01

Pressure balance structures (PBSs) are a common high-plasma beta feature in high-latitude, high-speed solar wind. They have been proposed as remnants of coronal plumes. If true, they should reflect the observation that plumes are rooted in unipolar magnetic flux concentrations in the photosphere and are heated as oppositely directed flux is advected into and reconnects with the flux concentration. A minimum variance analysis (MVA) of magnetic discontinuities in PBSs showed there is a larger proportion of tangential discontinuities than in the surrounding high-speed wind, supporting the hypothesis that plasmoids or extended current sheets are formed during reconnection at the base of plumes. To further evaluate the character of magnetic field discontinuities in PBSs, differential streaming between alpha particles and protons is analyzed here for the same sample of PBSs used in the MVA. Alpha particles in high-speed wind generally have a higher radial flow speed than protons. However, if the magnetic field is folded back on itself, as in a large-amplitude Alfven wave, alpha particles will locally have a radial flow speed less than protons. This characteristic is used here to distinguish between folded back magnetic fields (which would contain rotational discontinuities) and tangential discontinuities using Ulysses high-latitude, high-speed solar wind data. The analysis indicates that almost all reversals in the radial magnetic field in PBSs are folded back field lines. This is found to also be true outside PBSs, supporting existing results for typical high-speed, high-latitude wind. There remains a small number of cases that appear not to be folds in the magnetic field and which may be flux tubes with both ends rooted in the Sun. The distinct difference in MVA results inside and outside PBSs remains unexplained.

Differential Velocity Between Solar Wind Protons and Alpha Particles in Pressure Balance Structures

NASA Technical Reports Server (NTRS)

Yamauchi, Y.; Suess, S. T.; Steinberg, J. T.; Sakurai, T.

2003-01-01

Pressure balance structures (PBSs) are a common high plasma beta feature in high latitude, high speed solar wind. They have been proposed as remnants of coronal plumes. If true, they should reflect the observation that plumes are rooted in unipolar magnetic flux concentrations in the photosphere and are heated as oppositely directed flux is advected into and reconnects with the flux concentration. A minimum variance analysis (MVA) of magnetic discontinuities in PBSs showed there is a larger proportion of tangential discontinuities than in the surrounding high speed wind, supporting the hypothesis that plasmoids or extended current sheets are formed during reconnection at the base of plumes. To further evaluate the character of magnetic field discontinuities in PBSs, differential streaming between alpha particles and protons is analyzed here for the same sample of PBSs used in the MVA. Alpha particles in high speed wind generally have a higher radial flow speed than protons. However, if the magnetic field is folded back on itself, as in a large amplitude Alfven wave, alpha particles will locally have a radial flow speed less than protons. This characteristic is used here to distinguish between folded back magnetic fields (which would contain rotational discontinuities) and tangential discontinuities using Ulysses high latitude, high speed solar wind data. The analysis indicates that almost all reversals in the radial magnetic field in PBSs are folded back field lines. This is found to also be true outside PBSs, supporting existing results for typical high speed, high latitude wind. There remains a small number of cases that appear not to be folds in the magnetic field and which may be flux tubes with both ends rooted in the Sun. The distinct difference in MVA results inside and outside PBSs remains unexplained.

Genetic screening of non-classic CAH females with hyperandrogenemia identifies a novel CYP11B1 gene mutation.

PubMed

Shammas, Christos; Byrou, Stefania; Phelan, Marie M; Toumba, Meropi; Stylianou, Charilaos; Skordis, Nicos; Neocleous, Vassos; Phylactou, Leonidas A

2016-04-01

Congenital adrenal hyperplasia (CAH) is an endocrine autosomal recessive disorder with various symptoms of diverse severity. Mild hyperandrogenemia is the most commonclinical feature in non-classic CAH patients and 95% of the cases are identified by mutations in the CYP21A2 gene. In the present study, the second most common cause for non-classic CAH (NC-CAH), 11β-hydroxylase deficiency due to mutations in the CYP11B1 gene, is investigated. Screening of the CYP21A2 and CYP11B1 genes by direct sequencing was carried out for the detection of possible genetic defects in patients with suspected CAH. It wasobserved that CYP11B1 variants co-exist only in rare cases along with mutations in CYP21A2 in patients clinically diagnosed with CAH. A total of 23 NC-CAH female patients out of 75 were identified with only one mutation in the CYP21A2 gene. The novel CYP11B1 gene mutation, p.Val484Asp, was identified in a patient with CAH in the heterozygous state. The structural characterization of the novel p.Val484Asp was found to likely cause distortion of the surrounding beta sheet and indirect destabilization of the cavity that occurs on the opposite face of the structural elements, leading to partial impairment of the enzymatic activity. CYP21A2 gene mutations are the most frequent genetic defects in cases of NC-CAH even when these patients are in the heterozygous state. These mutations have a diverse phenotype giving rise to a variable extent of cortisol synthesis impairment; it is also clear that CYP11B1 mutants are a rare type of defects causing CAH.

The Merging Galaxy Cluster A520 - A Broken-Up Cool Core, A Dark Subcluster, and an X-Ray Channel

NASA Technical Reports Server (NTRS)

Wang, Qian H.S.; Markevitch, Maxim; Giacintucci, Simona

2016-01-01

We present results from a deep Chandra X-ray observation of a merging galaxy cluster A520. A high-resolution gas temperature map reveals a long trail of dense, cool clumpsapparently the fragments of a cool core that has been stripped from the infalling subcluster by ram pressure. The clumps should still be connected by the stretched magnetic field lines. The observed temperature variations imply that thermal conductivity is suppressed by a factor greater than 100 across the presumed direction of the magnetic field (as found in other clusters), and is also suppressed along the field lines by a factor of several. Two massive clumps in the periphery of A520, visible in the weak-lensing mass map and the X-ray image, have apparently been completely stripped of gas during the merger, but then re-accreted the surrounding high-entropy gas upon exit from the cluster. The mass clump that hosted the stripped cool core is also re-accreting hotter gas. An X-ray hydrostatic mass estimate for the clump that has the simplest geometry agrees with the lensing mass. Its current gas mass to total mass ratio is very low, 1.5 percent to 3 percent, which makes it a "dark subcluster." We also found a curious low X-ray brightness channel (likely a low-density sheet in projection) going across the cluster along the direction of an apparent secondary merger. The channel may be caused by plasma depletion in a region of an amplified magnetic field (with plasma Beta approximately equal to 10-20). The shock in A520 will be studied in a separate paper.

Liquid Crystal Based Sensor to Detect Beta-Sheet Formation of Peptides

NASA Astrophysics Data System (ADS)

Sadati, Monirosadat; Izmitli Apik, Aslin; Abbott, Nicholas L.; de Pablo, Juan J.

2015-03-01

Protein aggregation into amyloid fibrils is involved in the progression of Alzheimer's, typeII diabetes and Huntington's diseases. Although larger aggregates remain important for clinical determination, small oligomers are of great interest due to their potentially toxic nature. It is therefore crucial to develop methods that probe the aggregation process at early stages and in the vicinity of biological membranes. Here, we present a simple method that relies on liquid crystalline materials and a Langmuir monolayer at the aqueous-liquid crystal (LC) interface. The approach is based on the LC's specific response to β-sheet structures, which abound in amyloid fibrils. When the system is observed under polarized light, the fibrils formed by amyloidogenic peptides give rise to the formation of elongated and branched structures in the LCs. Moreover, the PolScope measurements prove that the LCs are predominantly aligned along the fibrils when exposed to a β-sheet forming peptide. In contrast, non-amyloidogenic peptides form ellipsoidal domains of irregularly tilted LCs. This method is capable of reporting aggregation at lipid-aqueous interfaces at nanomolar concentrations of the peptide, and much earlier than commonly used fluorescence-based techniques. We thank Prof. Oleg D. Levrentovich and Young-Ki Kim from the Liquid Crystal Institute of Kent State University for the use of their PolScope instrument. This work was partially supported by the Swiss National Science Foundation (P300P2_151342).

In silico local structure approach: a case study on outer membrane proteins.

PubMed

Martin, Juliette; de Brevern, Alexandre G; Camproux, Anne-Claude

2008-04-01

The detection of Outer Membrane Proteins (OMP) in whole genomes is an actual question, their sequence characteristics have thus been intensively studied. This class of protein displays a common beta-barrel architecture, formed by adjacent antiparallel strands. However, due to the lack of available structures, few structural studies have been made on this class of proteins. Here we propose a novel OMP local structure investigation, based on a structural alphabet approach, i.e., the decomposition of 3D structures using a library of four-residue protein fragments. The optimal decomposition of structures using hidden Markov model results in a specific structural alphabet of 20 fragments, six of them dedicated to the decomposition of beta-strands. This optimal alphabet, called SA20-OMP, is analyzed in details, in terms of local structures and transitions between fragments. It highlights a particular and strong organization of beta-strands as series of regular canonical structural fragments. The comparison with alphabets learned on globular structures indicates that the internal organization of OMP structures is more constrained than in globular structures. The analysis of OMP structures using SA20-OMP reveals some recurrent structural patterns. The preferred location of fragments in the distinct regions of the membrane is investigated. The study of pairwise specificity of fragments reveals that some contacts between structural fragments in beta-sheets are clearly favored whereas others are avoided. This contact specificity is stronger in OMP than in globular structures. Moreover, SA20-OMP also captured sequential information. This can be integrated in a scoring function for structural model ranking with very promising results. (c) 2007 Wiley-Liss, Inc.

Thermomyces lanuginosus: properties of strains and their hemicellulases.

PubMed

Singh, Suren; Madlala, Andreas M; Prior, Bernard A

2003-04-01

The non-cellulolytic Thermomyces lanuginosus is a widespread and frequently isolated thermophilic fungus. Several strains of this fungus have been reported to produce high levels of cellulase-free beta-xylanase both in shake-flask and bioreactor cultivations but intraspecies variability in terms of beta-xylanase production is apparent. Furthermore all strains produce low extracellular levels of other hemicellulases involved in hemicellulose hydrolysis. Crude and purified hemicellulases from this fungus are stable at high temperatures in the range of 50-80 degrees C and over a broad pH range (3-12). Various strains are reported to produce a single xylanase with molecular masses varying between 23 and 29 kDa and pI values between 3.7 and 4.1. The gene encoding the T. lanuginosus xylanase has been cloned and sequenced and is shown to be a member of family 11 glycosyl hydrolases. The crystal structure of the xylanase indicates that the enzyme consists of two beta-sheets and one alpha-helix and forms a rigid complex with the three central sugars of xyloheptaose whereas the peripheral sugars might assume different configurations thereby allowing branched xylan chains to be accepted. The presence of an extra disulfide bridge between the beta-strand and the alpha-helix, as well as to an increase in the density of charged residues throughout the xylanase might contribute to the thermostability. The ability of T. lanuginosus to produce high levels of cellulase-free thermostable xylanase has made the fungus an attractive source of thermostable xylanase with potential as a bleach-boosting agent in the pulp and paper industry and as an additive in the baking industry.

Insights into Strand Exchange in BTB Domain Dimers from the Crystal Structures of FAZF and Miz1

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

Stogios, Peter J.; Cuesta-Seijo, Jose Antonio; Chen, Lu

2010-09-22

The BTB domain is a widely distributed protein-protein interaction motif that is often found at the N-terminus of zinc finger transcription factors. Previous crystal structures of BTB domains have revealed tightly interwound homodimers, with the N-terminus from one chain forming a two-stranded anti-parallel {beta}-sheet with a strand from the other chain. We have solved the crystal structures of the BTB domains from Fanconi anemia zinc finger (FAZF) and Miz1 (Myc-interacting zinc finger 1) to resolutions of 2.0 {angstrom} and 2.6 {angstrom}, respectively. Unlike previous examples of BTB domain structures, the FAZF BTB domain is a nonswapped dimer, with each N-terminalmore » {beta}-strand associated with its own chain. As a result, the dimerization interface in the FAZF BTB domain is about half as large as in the domain-swapped dimers. The Miz1 BTB domain resembles a typical swapped BTB dimer, although it has a shorter N-terminus that is not able to form the interchain sheet. Using cysteine cross-linking, we confirmed that the promyelocytic leukemia zinc finger (PLZF) BTB dimer is strand exchanged in solution, while the FAZF BTB dimer is not. A phylogenic tree of the BTB fold based on both sequence and structural features shows that the common ancestor of the BTB domain in BTB-ZF (bric a brac, tramtrack, broad-complex zinc finger) proteins was a domain-swapped dimer. The differences in the N-termini seen in the FAZF and Miz1 BTB domains appear to be more recent developments in the structural evolution of the domain.« less

Disruption of the HIV-1 protease dimer with interface peptides: structural studies using NMR spectroscopy combined with [2-(13)C]-Trp selective labeling.

PubMed

Frutos, Silvia; Rodriguez-Mias, Ricard A; Madurga, Sergio; Collinet, Bruno; Reboud-Ravaux, Michèle; Ludevid, Dolors; Giralt, Ernest

2007-01-01

HIV-1 protease (HIV-1 PR), which is encoded by retroviruses, is required for the processing of gag and pol polyprotein precursors, hence it is essential for the production of infectious viral particles. In vitro inhibition of the enzyme results in the production of progeny virions that are immature and noninfectious, suggesting its potential as a therapeutic target for AIDS. Although a number of potent protease inhibitor drugs are now available, the onset of resistance to these agents due to mutations in HIV-1 PR has created an urgent need for new means of HIV-1 PR inhibition. Whereas enzymes are usually inactivated by blocking of the active site, the structure of dimeric HIV-1 PR allows an alternative inhibitory mechanism. Since the active site is formed by two half-enzymes, which are connected by a four-stranded antiparallel beta-sheet involving the N- and C- termini of both monomers, enzyme activity can be abolished by reagents targeting the dimer interface in a region relatively free of mutations would interfere with formation or stability of the functional HIV-1 PR dimer. This strategy has been explored by several groups who targeted the four-stranded antiparallel beta-sheet that contributes close to 75% of the dimerization energy. Interface peptides corresponding to native monomer N- or C-termini of several of their mimetics demonstrated, mainly on the basis of kinetic analyses, to act as dimerization inhibitors. However, to the best of our knowledge, neither X-ray crystallography nor NMR structural studies of the enzyme-inhibitor complex have been performed to date. In this article we report a structural study of the dimerization inhibition of HIV-1 PR by NMR using selective Trp side chain labeling.

Curcumin-functionalized silk biomaterials for anti-aging utility.

PubMed

Yang, Lei; Zheng, Zhaozhu; Qian, Cheng; Wu, Jianbing; Liu, Yawen; Guo, Shaozhe; Li, Gang; Liu, Meng; Wang, Xiaoqin; Kaplan, David L

2017-06-15

Curcumin is a natural antioxidant that is isolated from turmeric (Curcuma longa) and exhibits strong free radical scavenging activity, thus functional for anti-aging. However, poor stability and low solubility of curcumin in aqueous conditions limit its biomedical applications. Previous studies have shown that the anti-oxidation activity of curcumin embedded in silk fibroin films could be well preserved, resulting in the promoted adipogenesis from human mesenchymal stem cells (hMSCs) cultured on the surface of the films. In the present study, curcumin was encapsulated in both silk fibroin films (silk/cur films) and nanoparticles (silk/cur NPs), and their anti-aging effects were compared with free curcumin in solution, with an aim to elucidate the mechanism of anti-aging of silk-associated curcumin and to better serve biomedical applications in the future. The morphology and structure of silk/cur film and silk/cur NP were characterized using SEM, FTIR and DSC, indicating characteristic stable beta-sheet structure formation in the materials. Strong binding of curcumin molecules to the beta-sheet domains of silk fibroin resulted in the slow release of curcumin with well-preserved activity from the materials. For cell aging studies, rat bone marrow mesenchymal stem cells (rBMSCs) were cultured in the presence of free curcumin (FC), silk/cur film and silk/cur NP, and cell proliferation and markers of aging (P53, P16, HSP70 gene expression and β-Galactosidase activity) were examined. The results indicated that cell aging was retarded in all FC, silk/cur NP and silk/cur film samples, with the silk-associated curcumin superior to the FC. Copyright © 2017 Elsevier Inc. All rights reserved.

Genetic variability in E6, E7, and L1 genes of human papillomavirus genotype 52 from Southwest China.

PubMed

Zhang, Yiwen; Cao, Man; Wang, Mengting; Ding, Xianping; Jing, Yaling; Chen, Zuyi; Ma, Tengjiao; Chen, Honghan

2016-07-01

Human papillomavirus (HPV) is the major causative agent of cervical cancer, which accounts for the second highest cancer burden in women worldwide. HPV-52, the prevalent subtype in Asia, especially in southwest China, was analyzed in this study. To analyze polymorphisms, intratypic variants, and genetic variability in the E6-E7 (n=26) and L1 (n=53) genes of HPV-52, these genes were sequenced and the sequences were submitted to GenBank. Phylogenetic trees were constructed using the neighbor-joining and Kimura 2-parameters methods, followed by analysis of the diversity of secondary structure. Finally, we estimated the selection pressures acting on the E6-E7 and L1 genes. Fifty-one novel variants of HPV-52 L1, and two novel variants of HPV-52 E6-E7 were identified in this study. Thirty single nucleotide changes were observed in HPV-52 E6-E7 sequences with 19/30 non-synonymous mutations and 11/30 synonymous mutations (five in the alpha helix and five in the beta sheet). Fifty-five single nucleotide changes were observed in HPV-52 L1 sequences with 17/55 non-synonymous mutations (seven in the alpha helix and fourteen in the beta sheet) and 38/55 synonymous mutations. Selective pressure analysis predicted that most of these mutations reflect positive selection. Identifying new variants in HPV-52 may inform the rational design of new vaccines specifically for women in southwest China. Knowledge of genetic variation in HPV may be useful as an epidemiologic correlate of cervical cancer risk, or may even provide critical information for developing diagnostic probes. Copyright © 2016 Elsevier B.V. All rights reserved.

Stability of Iowa mutant and wild type Aβ-peptide aggregates

NASA Astrophysics Data System (ADS)

Alred, Erik J.; Scheele, Emily G.; Berhanu, Workalemahu M.; Hansmann, Ulrich H. E.

2014-11-01

Recent experiments indicate a connection between the structure of amyloid aggregates and their cytotoxicity as related to neurodegenerative diseases. Of particular interest is the Iowa Mutant, which causes early-onset of Alzheimer's disease. While wild-type Amyloid β-peptides form only parallel beta-sheet aggregates, the mutant also forms meta-stable antiparallel beta sheets. Since these structural variations may cause the difference in the pathological effects of the two Aβ-peptides, we have studied in silico the relative stability of the wild type and Iowa mutant in both parallel and antiparallel forms. We compare regular molecular dynamics simulations with such where the viscosity of the samples is reduced, which, we show, leads to higher sampling efficiency. By analyzing and comparing these four sets of all-atom molecular dynamics simulations, we probe the role of the various factors that could lead to the structural differences. Our analysis indicates that the parallel forms of both wild type and Iowa mutant aggregates are stable, while the antiparallel aggregates are meta-stable for the Iowa mutant and not stable for the wild type. The differences result from the direct alignment of hydrophobic interactions in the in-register parallel oligomers, making them more stable than the antiparallel aggregates. The slightly higher thermodynamic stability of the Iowa mutant fibril-like oligomers in its parallel organization over that in antiparallel form is supported by previous experimental measurements showing slow inter-conversion of antiparallel aggregates into parallel ones. Knowledge of the mechanism that selects between parallel and antiparallel conformations and determines their relative stability may open new avenues for the development of therapies targeting familial forms of early-onset Alzheimer's disease.

Phase Behaviour and Miscibility Studies of Collagen/Silk Fibroin Macromolecular System in Dilute Solutions and Solid State.

PubMed

Ghaeli, Ima; de Moraes, Mariana A; Beppu, Marisa M; Lewandowska, Katarzyna; Sionkowska, Alina; Ferreira-da-Silva, Frederico; Ferraz, Maria P; Monteiro, Fernando J

2017-08-18

Miscibility is an important issue in biopolymer blends for analysis of the behavior of polymer pairs through the detection of phase separation and improvement of the mechanical and physical properties of the blend. This study presents the formulation of a stable and one-phase mixture of collagen and regenerated silk fibroin (RSF), with the highest miscibility ratio between these two macromolecules, through inducing electrostatic interactions, using salt ions. For this aim, a ternary phase diagram was experimentally built for the mixtures, based on observations of phase behavior of blend solutions with various ratios. The miscibility behavior of the blend solutions in the miscible zones of the phase diagram was confirmed quantitatively by viscosimetric measurements. Assessing the effects of biopolymer mixing ratio and salt ions, before and after dialysis of blend solutions, revealed the importance of ion-specific interactions in the formation of coacervate-based materials containing collagen and RSF blends that can be used in pharmaceutical, drug delivery, and biomedical applications. Moreover, the conformational change of silk fibroin from random coil to beta sheet, in solution and in the final solid films, was detected by circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR), respectively. Scanning electron microscopy (SEM) exhibited alterations of surface morphology for the biocomposite films with different ratios. Surface contact angle measurement illustrated different hydrophobic properties for the blended film surfaces. Differential scanning calorimetry (DSC) showed that the formation of the beta sheet structure of silk fibroin enhances the thermal stability of the final blend films. Therefore, the novel method presented in this study resulted in the formation of biocomposite films whose physico-chemical properties can be tuned by silk fibroin conformational changes by applying different component mixing ratios.

Two-dimensional sup 1 H nuclear magnetic resonance study of AaH IT, an anti-insect toxin from the scorpion Androctonus australis Hector. Sequential resonance assignments and folding of the polypeptide chain

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

Darbon, H.; Weber, C.; Braun, W.

1991-02-19

Sequence-specific nuclear magnetic resonance assignments for the polypeptide backbone and for most of the amino acid side-chain protons, as well as the general folding of AaH IT, are described. AaH IT is a neurotoxin purified from the venom of the scorpion Androctonus australis Hector and is specifically active on the insect nervous system. The secondary structure and the hydrogen-bonding patterns in the regular secondary structure elements are deduced from nuclear Overhauser effects and the sequence locations of the slowly exchanging amide protons. The backbone folding is determined by distance geometry calculations with the DISMAN program. The regular secondary structure includesmore » two and a half turns of {alpha}-helix running from residues 21 to 30 and a three-stranded antiparallel {beta}-sheet including peptides 3-5, 34-38, and 41-46. Two tight turns are present, one connecting the end of the {alpha}-helix to an external strand of the {beta}-sheet, i.e., turn 31-34, and another connecting this same strand to the central one, i.e., turn 38-41. The differences in the specificity of these related proteins, which are able to discriminate between mammalian and insect voltage-dependent sodium channels of excitable tissues, are most probably brought about by the position of the C-terminal peptide with regard to a hydrophobic surface common to all scorpion toxins examined thus far. Thus, the interaction of a given scorpion toxin with its receptor might well be governed by the presence of this solvent-exposed hydrophobic surface, whereas adjacent areas modulate the specificity of the interaction.« less

Optical spectroscopic methods for probing the conformational stability of immobilised enzymes.

PubMed

Ganesan, Ashok; Moore, Barry D; Kelly, Sharon M; Price, Nicholas C; Rolinski, Olaf J; Birch, David J S; Dunkin, Ian R; Halling, Peter J

2009-07-13

We report the development of biophysical techniques based on circular dichroism (CD), diffuse reflectance infrared Fourier transform (DRIFT) and tryptophan (Trp) fluorescence to investigate in situ the structure of enzymes immobilised on solid particles. Their applicability is demonstrated using subtilisin Carlsberg (SC) immobilised on silica gel and Candida antartica lipase B immobilised on Lewatit VP.OC 1600 (Novozyme 435). SC shows nearly identical secondary structure in solution and in the immobilised state as evident from far UV CD spectra and amide I vibration bands. Increased near UV CD intensity and reduced Trp fluorescence suggest a more rigid tertiary structure on the silica surface. After immobilised SC is inactivated, these techniques reveal: a) almost complete loss of near UV CD signal, suggesting loss of tertiary structure; b) a shift in the amide I vibrational band from 1658 cm(-1) to 1632 cm(-1), indicating a shift from alpha-helical structure to beta-sheet; c) a substantial blue shift and reduced dichroism in the far UV CD, supporting a shift to beta-sheet structure; d) strong increase in Trp fluorescence intensity, which reflects reduced intramolecular quenching with loss of tertiary structure; and e) major change in fluorescence lifetime distribution, confirming a substantial change in Trp environment. DRIFT measurements suggest that pressing KBr discs may perturb protein structure. With the enzyme on organic polymer it was possible to obtain near UV CD spectra free of interference by the carrier material. However, far UV CD, DRIFT and fluorescence measurements showed strong signals from the organic support. In conclusion, the spectroscopic methods described here provide structural information hitherto inaccessible, with their applicability limited by interference from, rather than the particulate nature of, the support material.

Joint SDO and IRIS Observations of a Novel, Hybrid Prominence-Coronal Rain Complex

NASA Astrophysics Data System (ADS)

Liu, Wei; Antolin, Patrick; Sun, Xudong; Gao, Lijia; Vial, Jean-Claude; Gibson, Sarah; Okamoto, Takenori; Berger, Thomas; Uitenbroek, Han; De Pontieu, Bart

2016-10-01

Solar prominences and coronal rain are intimately related phenomena, both involving cool material at chromospheric temperatures within the hot corona and both playing important roles as part of the return flow of the chromosphere-corona mass cycle. At the same time, they exhibit distinct morphologies and dynamics not yet well understood. Quiescent prominences consist of numerous long-lasting, filamentary downflow threads, while coronal rain is more transient and falls comparably faster along well-defined curved paths. We report here a novel, hybrid prominence-coronal rain complex in an arcade-fan geometry observed by SDO/AIA and IRIS, which provides new insights to the underlying physics of such contrasting behaviors. We found that the supra-arcade fan region hosts a prominence sheet consisting of meandering threads with broad line widths. As the prominence material descends to the arcade, it turns into coronal rain sliding down coronal loops with line widths 2-3 times narrower. This contrast suggests that distinct local plasma and magnetic conditions determine the fate of the cool material, a scenario supported by our magnetic field extrapolations from SDO/HMI. Specifically, the supra-arcade fan (similar to those in solar flares; e.g., McKenzie 2013) is likely situated in a current sheet, where the magnetic field is weak and the plasma-beta could be close to unity, thus favoring turbulent flows like those prominence threads. In contrast, the underlying arcade has a stronger magnetic field and most likely a low-beta environment, such that the material is guided along magnetic field lines to appear as coronal rain. We will discuss the physical implications of these observations beyond prominence and coronal rain.

Optimization and characterization of spray-dried IgG formulations: a design of experiment approach.

PubMed

Faghihi, Homa; Najafabadi, Abdolhosein Rouholamini; Vatanara, Alireza

2017-10-24

The purpose of the present study is to optimize a spray-dried formulation as a model antibody regarding stability and aerodynamic property for further aerosol therapy of this group of macromolecules. A three-factor, three-level, Box-Behnken design was employed milligrams of Cysteine (X 1 ), Trehalose (X 2 ), and Tween 20 (X 3 ) as independent variables. The dependent variables were quantified and the optimized formulation was prepared accordingly. SEC-HPLC and FTIR-spectroscopy were conducted to evaluate the molecular and structural status of spray-dried preparations. Particle characterization of optimized sample was performed with the aid of DSC, SEM, and TSI examinations. Experimental responses of a total of 17 formulations resulted in yield values, (Y 1 ), ranging from 21.1 ± 0.2 to 40.2 ± 0.1 (%); beta-sheet content, (Y 2 ), from 66.22 ± 0.19 to 73.78 ± 0.26 (%); amount of aggregation following process, (Y 3 ), ranging from 0.11 ± 0.03 to 0.95 ± 0.03 (%); and amount of aggregation upon storage, (Y 4 ), from 0.81 ± 0.01 to 3.13 ± 0.64 (%) as dependent variables. Results-except for those of the beta sheet content-were fitted to quadratic models describing the inherent relationship between main factors. Co-application of Cysteine and Tween 20 preserved antibody molecules from molecular degradation and improved immediate and accelerated stability of spry-dried antibodies. Validation of the optimization study indicated high degree of prognostic ability of response surface methodology in preparation of stable spray-dried IgG. Graphical abstract Spray drying of IgG in the presence of Trehalose, Cysteine and Tween 20.

The effect of mutations on the structure of insulin fibrils studied by Fourier transform infrared (FTIR) spectroscopy and electron microscopy.

PubMed

Garriques, Liza Nielsen; Frokjaer, Sven; Carpenter, John F; Brange, Jens

2002-12-01

Fibril formation (aggregation) of human and bovine insulin and six human insulin mutants in hydrochloric acid were investigated by visual inspection, Thioflavin T fluorescence spectroscopy, transmission electron microscopy (TEM), and Fourier transform infrared (FTIR) spectroscopy. The fibrillation tendencies of the wild-type insulins and the insulin mutants were (in order of decreasing fibrillation tendencies): Glu(B1) + Glu(B27) = bovine < human < des-(B1,B2)-insulin < Ser(B2) + Asp(B10) < Glu(A13) + Glu(B10) = Gln(B17) < Asp(B10). Transmission electron micrographs showed that the protofibrils of the mutants were similar to those of wild-type insulins and had a diameter of 5-10 nm and lengths varying from 50 nm to several microns. The fibrils of human insulin mutants exhibited varying degrees of lateral aggregation. The Asp(B10) mutant and human insulin had greater tendency to form laterally aggregated fibrils arranged in parallel bundles, whereas fibrils of the other mutants and bovine insulin were mainly arranged in helical filaments. FTIR spectroscopy showed that the native secondary structure of the wild-type insulins and the human insulin mutants in hydrochloric acid were identical, whereas the secondary structure of the fibrils formed by heating at 50 degrees C depended on the amino acid substitution. FTIR spectra of fibrils of the human insulin mutants exhibited different beta-sheet bands at 1,620-1,640 cm(-1), indicating that the beta-sheet interactions in the fibrils depended on variations in the primary structure of insulin. Copyright 2002 Wiley-Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 91:2473-2480, 2002

Studies of the structure of insulin fibrils by Fourier transform infrared (FTIR) spectroscopy and electron microscopy.

PubMed

Nielsen, L; Frokjaer, S; Carpenter, J F; Brange, J

2001-01-01

Fibril formation (aggregation) of insulin was investigated in acid media by visual inspection, transmission electron microscopy (TEM), and Fourier transform infrared (FTIR) spectroscopy. Insulin fibrillated faster in hydrochloric acid than in acetic acid at elevated temperatures, whereas the fibrillation tendencies were reversed at ambient temperatures. Electron micrographs showed that bovine insulin fibrils consisted of long fibers with a diameter of 5 to 10 nm and lengths of several microns. The fibrils appeared either as helical filaments (in hydrochloric acid) or arranged laterally in bundles (in acetic acid, NaCl). Freeze-thawing cycles broke the fibrils into shorter segments. FTIR spectroscopy showed that the native secondary structure of insulin was identical in hydrochloric acid and acetic acid, whereas the secondary structure of fibrils formed in hydrochloric acid was different from that formed in acetic acid. Fibrils of bovine insulin prepared by heating or agitating an acid solution of insulin showed an increased content of beta-sheet (mostly intermolecular) and a decrease in the intensity of the alpha-helix band. In hydrochloric acid, the frequencies of the beta-sheet bands depended on whether the fibrillation was induced by heating or agitation. This difference was not seen in acetic acid. Freeze-thawing cycles of the fibrils in hydrochloric acid caused an increase in the intensity of the band at 1635 cm(-1) concomitant with reduction of the band at 1622 cm(-1). The results showed that the structure of insulin fibrils is highly dependent on the composition of the acid media and on the treatment. Copyright 2001 Wiley-Liss Inc. and the American Pharmaceutical Association J Pharm Sci 90: 29-37, 2001

Evaluation of a Proposed Biodegradable 188Re Source for Brachytherapy Application

PubMed Central

Khorshidi, Abdollah; Ahmadinejad, Marjan; Hamed Hosseini, S.

2015-01-01

Abstract This study aimed to evaluate dosimetric characteristics based on Monte Carlo (MC) simulations for a proposed beta emitter bioglass 188Re seed for internal radiotherapy applications. The bioactive glass seed has been developed using the sol-gel technique. The simulations were performed for the seed using MC radiation transport code to investigate the dosimetric factors recommended by the AAPM Task Group 60 (TG-60). Dose distributions due to the beta and photon radiation were predicted at different radial distances surrounding the source. The dose rate in water at the reference point was calculated to be 7.43 ± 0.5 cGy/h/μCi. The dosimetric factors consisting of the reference point dose rate, D(r0,θ0), the radial dose function, g(r), the 2-dimensional anisotropy function, F(r,θ), the 1-dimensional anisotropy function, φan(r), and the R90 quantity were estimated and compared with several available beta-emitting sources. The element 188Re incorporated in bioactive glasses produced by the sol-gel technique provides a suitable solution for producing new materials for seed implants applied to brachytherapy applications in prostate and liver cancers treatment. Dose distribution of 188Re seed was greater isotropic than other commercially attainable encapsulated seeds, since it has no end weld to attenuate radiation. The beta radiation-emitting 188Re source provides high doses of local radiation to the tumor tissue and the short range of the beta particles limit damage to the adjacent normal tissue. PMID:26181543

Expression of hemidesmosomal and extracellular matrix proteins by normal and malignant human prostate tissue.

PubMed Central

Nagle, R. B.; Hao, J.; Knox, J. D.; Dalkin, B. L.; Clark, V.; Cress, A. E.

1995-01-01

The progression of prostate carcinoma may be influenced by the biochemical nature of the basal lamina surrounding the primary carcinoma cells. As a first step toward understanding this process, the composition and structure of the basal lamina in normal prostate, prostatic intraepithelial neoplasia, and human carcinoma were determined. In addition, a comparison was made between the attachments of the normal basal cell to its underlying basal lamina and those made by primary prostate carcinoma. The normal basal cells form both focal adhesions and hemidesmosomal-like structures as observed by transmission electron microscopy. The normal basal cells exhibited a polarized distribution of hemidesmosomal associated proteins including BP180, BP230, HD1, plectin, laminin-gamma 2(B2t), collagen VII, and the corresponding integrin laminin receptors alpha 6 beta 1 and alpha 6 beta 4. The expression and distribution pattern of these proteins were retained in the prostate intraepithelial neoplasia lesions. In contrast, the carcinoma cells uniformly lacked hemidesmosomal structures, the integrin alpha 6 beta 4, BP180, laminin-gamma 2 (B2t), and collagen VII but did express BP230 (30%), plectin, HD1 (15%), and the integrin laminin receptors alpha 3 beta 1 and alpha 6 beta 1. These results suggest that, although a detectable basal lamina structure is present in carcinoma, its composition and cellular attachments are abnormal. The loss of critical cellular attachments may play a role in influencing the progression potential of prostate carcinoma. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:7778688

Measuring Geophysical Parameters of the Greenland Ice Sheet using Airborne Radar Altimetry

NASA Technical Reports Server (NTRS)

Ferraro, Ellen J.; Swift. Calvin T.

1995-01-01

This paper presents radar-altimeter scattering models for each of the diagenetic zones of the Greenland ice sheet. AAFE radar- altimeter waveforms obtained during the 1991 and 1993 NASA multi-sensor airborne altimetry experiments over Greenland reveal that the Ku-band return pulse changes significantly with the different diagenetic zones. These changes are due to varying amounts of surface and volume scattering in the return waveform. In the ablation and soaked zones, where surface scattering dominates the AAFE return, geophysical parameters such as rms surface height and rms surface slope are obtained by fitting the waveforms to a surface-scattering model. Waveforms from the percolation zone show that the sub-surface ice features have a much more significant effect on the return pulse than the surrounding snowpack. Model percolation waveforms, created using a combined surface- and volume-scattering model and an ice-feature distribution obtained during the 1993 field season, agree well with actual AAFE waveforms taken in the same time period. Using a combined surface- and volume-scattering model for the dry-snow-zone return waveforms, the rms surface height and slope and the attenuation coefficient of the snowpack are obtained. These scattering models not only allow geophysical parameters of the ice sheet to be measured but also help in the understanding of satellite radar-altimeter data.

Robust free-space optical communication for indoor information environment

NASA Astrophysics Data System (ADS)

Nakada, Toyohisa; Itoh, Hideo; Kunifuji, Susumu; Nakashima, Hideyuki

2003-10-01

The purpose of our study is to establish a robust communication, while keeping security and privacy, between a handheld communicator and the surrounding information environment. From the viewpoint of low power consumption, we have been developing a reflectivity modulating communication module composed of a liquid crystal light modulator and a corner-reflecting mirror sheet. We installed a corner-reflecting sheet instead of light scattering sheet in a handheld videogame machine with a display screen with a reflection-type liquid crystal. Infrared (IR) LED illuminator attached next to the IR camera of a base station illuminates all the room, and the terminal send their data to the base station by switching ON and OFF of the reflected IR beam. Intensity of reflected light differs with the position and the direction of the terminal, and sometimes the intensity of OFF signal at a certain condition is brighter than that of ON signal at another condition. To improve the communication quality, use of machine learning technique is a possibility of the solution. In this paper, we compare various machine learning techniques for the purpose of free space optical communication, and propose a new algorithm that improves the robustness of the data link. Evaluation using an actual free-space communication system is also described.

Epithelial Folding Driven by Apical or Basal-Lateral Modulation: Geometric Features, Mechanical Inference, and Boundary Effects.

PubMed

Wen, Fu-Lai; Wang, Yu-Chiun; Shibata, Tatsuo

2017-06-20

During embryonic development, epithelial sheets fold into complex structures required for tissue and organ functions. Although substantial efforts have been devoted to identifying molecular mechanisms underlying epithelial folding, far less is understood about how forces deform individual cells to sculpt the overall sheet morphology. Here we describe a simple and general theoretical model for the autonomous folding of monolayered epithelial sheets. We show that active modulation of intracellular mechanics along the basal-lateral as well as the apical surfaces is capable of inducing fold formation in the absence of buckling instability. Apical modulation sculpts epithelia into shallow and V-shaped folds, whereas basal-lateral modulation generates deep and U-shaped folds. These characteristic tissue shapes remain unchanged when subject to mechanical perturbations from the surroundings, illustrating that the autonomous folding is robust against environmental variabilities. At the cellular scale, how cells change shape depends on their initial aspect ratios and the modulation mechanisms. Such cell deformation characteristics are verified via experimental measurements for a canonical folding process driven by apical modulation, indicating that our theory could be used to infer the underlying folding mechanisms based on experimental data. The mechanical principles revealed in our model could potentially guide future studies on epithelial folding in diverse systems. Copyright © 2017. Published by Elsevier Inc.

The Controversy Surrounding Bone Morphogenetic Proteins in the Spine: A Review of Current Research

PubMed Central

Hustedt, Joshua W.; Blizzard, Daniel J.

2014-01-01

Bone morphogenetic proteins have been in use in spinal surgery since 2002. These proteins are members of the TGF-beta superfamily and guide mesenchymal stem cells to differentiate into osteoblasts to form bone in targeted tissues. Since the first commercial BMP became available in 2002, a host of research has supported BMPs and they have been rapidly incorporated in spinal surgeries in the United States. However, recent controversy has arisen surrounding the ethical conduct of the research supporting the use of BMPs. Yale University Open Data Access (YODA) recently teamed up with Medtronic to offer a meta-analysis of the effectiveness of BMPs in spinal surgery. This review focuses on the history of BMPs and examines the YODA research to guide spine surgeons in their use of BMP in spinal surgery. PMID:25506287

Bioinformatic analysis of neurotropic HIV envelope sequences identifies polymorphisms in the gp120 bridging sheet that increase macrophage-tropism through enhanced interactions with CCR5

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

Mefford, Megan E., E-mail: megan_mefford@hms.harvard.edu; Kunstman, Kevin, E-mail: kunstman@northwestern.edu; Wolinsky, Steven M., E-mail: s-wolinsky@northwestern.edu

Macrophages express low levels of the CD4 receptor compared to T-cells. Macrophage-tropic HIV strains replicating in brain of untreated patients with HIV-associated dementia (HAD) express Envs that are adapted to overcome this restriction through mechanisms that are poorly understood. Here, bioinformatic analysis of env sequence datasets together with functional studies identified polymorphisms in the β3 strand of the HIV gp120 bridging sheet that increase M-tropism. D197, which results in loss of an N-glycan located near the HIV Env trimer apex, was detected in brain in some HAD patients, while position 200 was estimated to be under positive selection. D197 andmore » T/V200 increased fusion and infection of cells expressing low CD4 by enhancing gp120 binding to CCR5. These results identify polymorphisms in the HIV gp120 bridging sheet that overcome the restriction to macrophage infection imposed by low CD4 through enhanced gp120–CCR5 interactions, thereby promoting infection of brain and other macrophage-rich tissues. - Highlights: • We analyze HIV Env sequences and identify amino acids in beta 3 of the gp120 bridging sheet that enhance macrophage tropism. • These amino acids at positions 197 and 200 are present in brain of some patients with HIV-associated dementia. • D197 results in loss of a glycan near the HIV Env trimer apex, which may increase exposure of V3. • These variants may promote infection of macrophages in the brain by enhancing gp120–CCR5 interactions.« less

COLD TRAP

DOEpatents

Milleron, N.

1963-03-12

An improved linear-flow cold trap is designed for highvacuum applications such as mitigating back migration of diffusion pump oil moiecules. A central pot of liquid nitrogen is nested within and supported by a surrounding, vertical, helical coil of metai sheet, all enveloped by a larger, upright, cylindrical, vacuum vessel. The vertical interstices between successive turns of the coil afford lineal, axial, high-vacuum passages between open mouths at top and bottom of said vessel, while the coil, being cold by virtue of thermal contact of its innermost turn with the nitrogen pot, affords expansive proximate condensation surfaces. (AEC)

X-Ray Crystal Structure of the passenger domain of Plasmid encoded toxin(Pet), an Autotransporter Enterotoxin from enteroaggregative Escherichia coli (EAEC)

PubMed Central

Meza-Aguilar, J. Domingo; Fromme, Petra; Torres-Larios, Alfredo; Mendoza-Hernández, Guillermo; Hernandez-Chiñas, Ulises; Monteros, Roberto A. Arreguin-Espinosa de los; Campos, Carlos A. Eslava; Fromme, Raimund

2014-01-01

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 of 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 135-143 compared to the structure of EspP. PMID:24530907