scholarly journals Characterization of Hidden Chirality: Two-Fold Helicity in β-Strands

Symmetry ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 499 ◽  
Author(s):  
Toshiyuki Sasaki ◽  
Mikiji Miyata
Keyword(s):  
Hydrogen Bonds ◽  
Polypeptide Chain ◽  
Structural Motif ◽  
High Dimensional ◽  
Point Approximation ◽  
Β Sheets ◽  
Α Helix ◽  
Β Sheet

A β-strand is a component of a β-sheet and is an important structural motif in biomolecules. An α-helix has clear helicity, while chirality of a β-strand had been discussed on the basis of molecular twists generated by forming hydrogen bonds in parallel or non-parallel β-sheets. Herein we describe handedness determination of two-fold helicity in a zig-zag β-strand structure. Left- (M) and right-handedness (P) of the two-fold helicity was defined by application of two concepts: tilt-chirality and multi-point approximation. We call the two-fold helicity in a β-strand, whose handedness has been unrecognized and unclarified, as hidden chirality. Such hidden chirality enables us to clarify precise chiral characteristics of biopolymers. It is also noteworthy that characterization of chirality of high dimensional structures like a β-strand and α-helix, referred to as high dimensional chirality (HDC) in the present study, will contribute to elucidation of the possible origins of chirality and homochirality in nature because such HDC originates from not only asymmetric centers but also conformations in a polypeptide chain.

Influence of Post-Treatment with Methanol Vapor on the Properties of SF/P(LLA-CL) Nanofibrous Scaffolds

2011 ◽  
Vol 236-238 ◽  
pp. 2221-2224
Author(s):  
Kui Hua Zhang ◽  
Xiu Mei Mo
Keyword(s):  
Electrospun Nanofibers ◽  
Random Coil ◽  
Methanol Vapor ◽  
Nanofibrous Scaffolds ◽  
Nanofibrous Structure ◽  
Α Helix ◽  
Β Sheet ◽  
Ideal Method ◽  
C Nmr

In order to improve water-resistant ability silk fibroin (SF) and SF/P(LLA-CL) blended nanofibrous scaffolds for tissue engineering applications, methanol vapor were used to treat electrospun nanofibers. SEM indicated SF and SF/ P(LLA-CL) scaffolds maintained nanofibrous structure after treated with methanol vapor and possessed good water-resistant ability. Characterization of 13C NMR clarified methanol vapor induced SF conformation from random coil or α- helix to β-sheet. Moreover, treated SF/ P (LLA-CL) nanofibrous scaffolds still kept good mechanical properties. Methanol vapor could be ideal method to treat SF and SF/ P(LLA-CL) nanofibrous scaffolds for biomedical applications.

Das sterische Verhalten der Alpha-Helix / The steric Behaviour of the Alpha-Helix

1969 ◽  
Vol 24 (6) ◽  
pp. 672-690 ◽  
Author(s):  
R. Jarosch
Keyword(s):  
Hydrogen Bonds ◽  
Polypeptide Chain ◽  
Enzymatic Catalysis ◽  
Alpha Helix ◽  
Side Chains ◽  
Tertiary Structures ◽  
General Variation ◽  
Coiling Direction ◽  
Α Helix ◽  
Molecule Model

The steric behaviour of the α-Helix has been investigated using an elastic molecule-model made of solid rubber balls and steel pins. Shortening of the hydrogen-bonds, which is possible at least in the range from 2.91 to 2.67 A in real α-Helices, has the following effects:1. The α-Helix contracts proportionally to the length of the hydrogen-bonds (figs. 3, 4).2. A torsional force arises leading in the case of longer α-Helices to torsional revolutions of the free ends of the helix (figs. 3 a. 4 a).3. Tertiary structures (superhelices. flattened superhelices. planar wavy lines, planar arcs) superpose the α-Helix if only specific hydrogen-bonds (e. g. indicated by arrows in fig. 5) will be shortened and if the distance between them is repeated in the sequence of the polypeptide chain (Tab. I). Some of the sequence-distances show similar tertiary structures and the same pitches of the superhelices (Tab. II). A general variation in the length of the hydrogen-bonds causes alterations in the superstructure and can also change the coiling direction of the superhelix.4. The Cα— Cβ; bonds incline slightly to the axis of the helix (fig. 11) through which the α-Helix with side chains becomes a little thinner. Because of the torsion (see item 2) the distance between the side chains changes also (fig. 12). The distances increase between specific positions of the side chains and decrease between others (Tab. III).Possible reasons for the shortening of the hydrogen-bonds are briefly discussed. The importance of the described behaviour for biological movements, enzymatic catalysis (“allosteric effect”) and active transport is emphasized.

Structural Characterization of β-Lactoglobulin in Solution Using Two-Dimensional FT Mid-Infrared and FT Near-Infrared Correlation Spectroscopy

1997 ◽  
Vol 51 (4) ◽  
pp. 536-540 ◽  
Author(s):  
Nelson L. Sefara ◽  
Noel P. Magtoto ◽  
Hugh H. Richardson
Keyword(s):  
Near Infrared ◽  
Spectral Response ◽  
Correlation Spectroscopy ◽  
Two Dimensional ◽  
Helical Structures ◽  
Β Sheets ◽  
Α Helix ◽  
Combination Bands ◽  
Β Lactoglobulin ◽  
Β Sheet

Two-dimensional (2D) FT-IR correlation analysis was applied to both the mid-IR (MIR) and near-IR (NIR) regions to investigate changes in the secondary structures of β-lactoglobulin in D2O (or H2O) solvent systems consisting of varying concentrations of bromoethanol. Mid-IR correlation spectra indicate that the amide I bands corresponding to different structures (i.e., α-helical structures at 1650 cm−1, aggregated β-strands at 1620 cm−1, and β-sheet at 1636 cm−1) exhibit apparently different spectral response towards varying concentrations of bromoethanol. We propose that the mechanism for the conversion of the β-sheet into α-helix occurs in terms of two parallel pathways, i.e., (1) β-sheets → aggregated β-strands →α-helix, and (2) β-sheets →α-helix. Although the amide B/amide II combination bands give no spectral features relating to the secondary structure, changes were found in the C–H combination bands that suggest an interaction between the solvent and the protein.

scholarly journals A novel decrystallizing protein CxEXL22 from Arthrobotrys sp. CX1 capable of synergistically hydrolyzing cellulose with cellulases

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Rong Li ◽  
Yunze Sun ◽  
Yihao Zhou ◽  
Jiawei Gai ◽  
Linlu You ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Hydrophobic Surface ◽  
Crystalline Cellulose ◽  
Crystalline Region ◽  
Strong Activity ◽  
Hydrophobic Residues ◽  
Cellulose Accessibility ◽  
Hydrolysis Of ◽  
Β Sheet

AbstractA novel expansin-like protein (CxEXL22) has been identified and characterized from newly isolated Arthrobotrys sp. CX1 that can cause cellulose decrystallization. Unlike previously reported expansin-like proteins from microbes, CxEXL22 has a parallel β-sheet domain at the N terminal, containing many hydrophobic residues to form the hydrophobic surface as part of the groove. The direct phylogenetic relationship implied the genetic transfers occurred from nematode to nematicidal fungal Arthrobotrys sp. CX1. CxEXL22 showed strong activity for the hydrolysis of hydrogen bonds between cellulose molecules, especially when highly crystalline cellulose was used as substrate. The hydrolysis efficiency of Avicel was increased 7.9-fold after pretreating with CxEXL22. The rupture characterization of crystalline region indicated that CxEXL22 strongly binds cellulose and breaks up hydrogen bonds in the crystalline regions of cellulose to split cellulose chains, causing significant depolymerization to expose much more microfibrils and enhances cellulose accessibility.

scholarly journals Prion Interaction with Normal Protein in Topological Changing Secondary Structure to Aggregation

2020 ◽  
Vol 9 (2) ◽  
pp. 53
Author(s):  
Yao Yao
Keyword(s):  
Hydrogen Bond ◽  
Secondary Structure ◽  
Amyloid Fibril ◽  
Double Helix ◽  
Β Amyloid ◽  
Structural Analogy ◽  
Β Sheets ◽  
Α Helix ◽  
Dna Double Helix ◽  
Β Sheet

<p>Prion is a protein smaller than virus and it infects host in the absence of nucleic acid. The secondary structure of protein folds incorrectly from α-helices to β-sheets through breaking and re-formation of hydrogen bond. Structural analogy of α-helix and DNA double helix and comparing differences between α-helix and β-sheet show prion's infectivity and propagation. Aggregates of dimers and polymers generate β-amyloid fibril in Alzheimer's disease.</p>

scholarly journals The β-link motif in protein architecture

2021 ◽  
Vol 77 (8) ◽  
Author(s):  
David P. Leader ◽  
E. James Milner-White
Keyword(s):  
Serine Proteases ◽  
Polypeptide Chain ◽  
Cysteine Proteases ◽  
Type Ii ◽  
Terminal Portion ◽  
Structural Classification ◽  
Protein Motif ◽  
Protein Architecture ◽  
Α Helix ◽  
Β Sheet

The β-link is a composite protein motif consisting of a G1β β-bulge and a type II β-turn, and is generally found at the end of two adjacent strands of antiparallel β-sheet. The 1,2-positions of the β-bulge are also the 3,4-positions of the β-turn, with the result that the N-terminal portion of the polypeptide chain is orientated at right angles to the β-sheet. Here, it is reported that the β-link is frequently found in certain protein folds of the SCOPe structural classification at specific locations where it connects a β-sheet to another area of a protein. It is found at locations where it connects one β-sheet to another in the β-sandwich and related structures, and in small (four-, five- or six-stranded) β-barrels, where it connects two β-strands through the polypeptide chain that crosses an open end of the barrel. It is not found in larger (eight-stranded or more) β-barrels that are straightforward β-meanders. In some cases it initiates a connection between a single β-sheet and an α-helix. The β-link also provides a framework for catalysis in serine proteases, where the catalytic serine is part of a conserved β-link, and in cysteine proteases, including Mpro of human SARS-CoV-2, in which two residues of the active site are located in a conserved β-link.

SHEEP: A TOOL FOR DESCRIPTION OF β-SHEETS IN PROTEIN 3D STRUCTURES

2012 ◽  
Vol 10 (02) ◽  
pp. 1241003 ◽  
Author(s):  
EVGENIY AKSIANOV ◽  
ANDREI ALEXEEVSKI
Keyword(s):  
Protein Structure ◽  
Three Dimensional ◽  
Structural Features ◽  
Protein Domain ◽  
Structural Units ◽  
Protein Structure Classification ◽  
Β Sheets ◽  
Β Sheet ◽  
Explicit Determination

The description of a protein fold is a hard problem due to significant variability of main structural units, β-sheets and α-helixes, and their mutual arrangements. An adequate description of the structural units is an important step in objective protein structure classification, which to date is based on expert judgment in a number of cases. Explicit determination and description of structural units is more complicated for β-sheets than for α-helixes due to β-sheets variability both in composition and geometry. We have developed an algorithm that can significantly modify β-sheets detected by commonly used DSSP and Stride algorithms and represent the result as a “β-sheet map,” a table describing certain β-sheet features. In our approach, β-sheets (rather than β-strands) are considered as holistic objects. Both hydrogen bonds and geometrical restrains are explored for the determination of β-sheets. The algorithm is implemented in SheeP program. It was tested for prediction architectures of domains from 93 well-defined all-β and α/β SCOP protein domain families, and showed 93% of correct results. The Web-service http://mouse.belozersky.msu.ru/sheep allows to detect β-sheets in a given protein structure, visualize β-sheet maps, as well as input three-dimensional structures with highlighted β-sheets and their structural features.

Cloning and Characterization of Three Genes Encoding LMW-GSs from Triticum aestivum, Cultival Cheyenne

2012 ◽  
Vol 554-556 ◽  
pp. 1116-1120 ◽  
Author(s):  
Mei Rong Chen ◽  
Xing Shen ◽  
Lin Li ◽  
Song Qing Hu
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Amino Acid Residues ◽  
Repetitive Domain ◽  
Genebank Accession ◽  
Genes Encoding ◽  
Α Helix ◽  
Β Sheet

Three low molecular weight subunit genes, named LMW-CND1 (GeneBank accession JQ780048), LMW-CND2 (GeneBank accession JQ779840), LMW-CND3 (GeneBank accession JQ779841), with a ORF of 1053 bp, 903 bp, 969 bp, respectively, were isolated from cv. Cheyenne and characterized detailed in molecular level. The proteins encoded by the genes, with 350, 300, 322 amino acid residues respectively, differ only in repetitive domain of sequences due to insertion or deletion of repeats in this domain. Highly similarity in amino-acid sequence between these three subunits and other published LMW-GSs was also observed, showing that all three genes published here are typical LMW-GS genes and closely related to the genes on chromosome 1D. Besides, secondary structure prediction of proteins indicated that, in the three LMW-GSs, random loop accounts for no less than 70 %, α-helix amounts to 26 %, average, and only 1.4 %~1.7 % is β-sheet.

Molecular Basis of Biomechanics of Hemostasis and Thrombosis: Structural Molecular Transitions Underlying Deformation of Fibrin Clots and Thrombi.

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2217-2217
Author(s):  
Rustem I. Litvinov ◽  
Dzhigangir A. Faizullin ◽  
Yuriy F. Zuev ◽  
Artyom Zhmurov ◽  
Olga Kononova ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Structural Changes ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Linear Regime ◽  
Force Extension ◽  
Β Sheets ◽  
Α Helix ◽  
Dynamics Simulations ◽  
Β Sheet

Abstract Abstract 2217 A new field of biomedical research, biomechanics of hemostasis and thrombosis, has been quickly developing over the past few years. The mechanical properties of fibrin are essential in vivo for the ability of clots to stop bleeding in flowing blood but also determine the likelihood of obstructive thrombi that cause heart attack and stroke. Despite such critical importance, the structural basis of clot mechanics is not well understood. The structural changes underlying deformation of fibrin polymer occur at different spatial scales from macroscopic to submolecular, including molecular unfolding, about which relatively little is known. In this work, fibrin mechanics was studied with respect to molecular structural changes during fibrin deformation. The results of atomic force microscopy-induced unfolding of fibrinogen monomers and oligomers were correlated with force-extension curves obtained using Molecular Dynamics simulations. The mechanical unraveling of fibrin(ogen) was shown to be determined by molecular transitions that couple reversible extension-contraction of the α-helical coiled-coil regions with unfolding of the terminal γ-nodules. The coiled-coils act as molecular springs to buffer external mechanical perturbations, transmitting and distributing force as the γ-nodules unfold. Unfolding of the γ-nodules, stabilized by strong inter-domain interactions with the neighboring β-nodules, was characterized by an average force of ∼90 pN and peak-to-peak distance of ∼25 nm. All-atom Molecular Dynamics simulations further showed a transition from α-helix to β-sheet at higher extensions. To reveal the force-induced α-helix to β-sheet transition in fibrin experimentally, we used Fourier Transform infrared spectroscopy of hydrated fibrin clots made from human blood plasma. When extended or compressed, fibrin showed a shift of absorbance intensity mainly in the amide I band but also in the amide II and III bands, demonstrating an increase of the β-sheets and a corresponding reduction of the α-helices. These structural conversions correlated directly with the strain or pressure and were partially reversible at the conditions applied. The spectra characteristic of the nascent inter-chain β-sheets were consistent with protein aggregation and fiber bundling during clot deformation observed using scanning electron microscopy. Additional information on the mechanically induced α-helix to β-sheet transition in fibrin was obtained from computational studies of the forced elongation of the entire fibrin molecule and its α-helical coiled-coil portions. We found that upon force application, the coiled-coils undergo ∼5–50 nm extension and 360-degree unwinding. The force-extension curves for the coiled-coils showed three distinct regimes: the linear elastic regime, the constant-force plastic regime, and the non-linear regime. In the linear regime, the coiled-coils unwind but not unfold. In the plastic regime, the triple α-helical segments rewind and re-unwind while undergoing a non-cooperative phase transition to form parallel β-sheets. We conclude that under extension and/or compression an α-helix to β-sheet conversion of the coiled-coils occurs in the fibrin clot as a part of forced protein unfolding. These regimes of forced elongation of fibrin provide important qualitative and quantitative characteristics of the molecular mechanisms underlying fibrin mechanical properties at the microscopic and macroscopic scales. Furthermore, these structural characteristics of the dynamic mechanical behavior of fibrin at the nanometer scale determine whether or not clots have the strength to stanch bleeding and if thrombi become obstructive or embolize. Finally, this knowledge of the functional significance of different domains of fibrin(ogen) suggests new approaches for modulation of these properties as potential therapeutic interventions. Disclosures: No relevant conflicts of interest to declare.

Film Formation and Structural Characterization of Silk of the Hornet Vespa simillima xanthoptera Cameron

2005 ◽  
Vol 60 (11-12) ◽  
pp. 906-914 ◽  
Author(s):  
Tsunenori Kameda ◽  
Katsura Kojima ◽  
Mitsuhiro Miyazawa ◽  
Seita Fujiwara
Keyword(s):  
Film Formation ◽  
Pure Water ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Molecular Weights ◽  
Sds Page ◽  
Ft Ir ◽  
Α Helix ◽  
Β Sheet

We extracted silk produced by the larva of the hornet Vespa simillima xanthoptera Cameron from its nest. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the extracted hornet silk showed four major components with molecular weights between 35 and 60 kDa. The main amino acid components of the hornet silk protein were Ala (33.5%), Ser (16.9%), Asp (8.5%) and Glu (8.1%). The hornet silk could be dissolved in hexafluoroisopropyl alcohol (HFIP) at 25 °C without incurring molecular degradation. A transparent film of hornet silk was obtained readily by the formation of a cast upon drying of the hornet silk in the HFIP solution. Residual HFIP solvent was removed from the film by extraction with pure water. Solid-state 13C NMR and FT-IR measurements revealed that the secondary structures of hornet silk proteins in the native state consisted of coexisting α-helix and β-sheet conformations. The β-sheet to α-helix ratio, which was changed by processing, was mainly responsible for the silk’s thermostability.

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