scholarly journals The Influence of Flanking Secondary Structures on Amino Acid Content and Typical Lengths of 3/10 Helices

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Vladislav Victorovich Khrustalev ◽  
Eugene Victorovich Barkovsky ◽  
Tatyana Aleksandrovna Khrustaleva
Keyword(s):  
Amino Acid ◽  
Gc Content ◽  
Amino Acid Content ◽  
Alpha Helix ◽  
Major Elements ◽  
Random Coil ◽  
Amino Acid Residues ◽  
Alpha Helices ◽  
Beta Strand ◽  
Bacterial Proteins

We used 3D structures of a highly redundant set of bacterial proteins encoded by genes of high, average, and low GC-content. Four types of connecting bridges—regions situated between any of two major elements of secondary structure (alpha helices and beta strands)—containing a pure random coil were compared with connecting bridges containing 3/10 helices. We included discovered trends in the original “VVTAK Connecting Bridges” algorithm, which is able to predict more probable conformation for a given connecting bridge. The highest number of significant differences in amino acid usage was found between 3/10 helices containing bridges connecting two beta strands (they have increased Phe, Tyr, Met, Ile, Leu, Val, and His usages but decreased usages of Asp, Asn, Gly, and Pro) and those without 3/10 helices. The typical (most common) length of 3/10 helices situated between two beta strands and between beta strand and alpha helix is equal to 5 amino acid residues. The preferred length of 3/10 helices situated between alpha helix and beta strand is equal to 3 residues. For 3/10 helices situated between two alpha helices, both lengths (3 and 5 amino acid residues) are typical.

scholarly journals Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Tatyana Aleksandrovna Khrustaleva
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Glutamic Acid ◽  
Gc Content ◽  
Alpha Helix ◽  
Random Coil ◽  
Amino Acid Residues ◽  
Alpha Helices ◽  
Beta Strand ◽  
Genomic Gc Content

3D structures of proteins with coordinated Mn2+ ions from bacteria with low, average, and high genomic GC-content have been analyzed (149 PDB files were used). Major Mn2+ binders are aspartic acid (6.82% of Asp residues), histidine (14.76% of His residues), and glutamic acid (3.51% of Glu residues). We found out that the motif of secondary structure “beta strand-major binder-random coil” is overrepresented around all the three major Mn2+ binders. That motif may be followed by either alpha helix or beta strand. Beta strands near Mn2+ binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. In the group of proteins from GC-rich bacteria glutamic acid residues situated in alpha helices frequently coordinate Mn2+ ions, probably, because of the decrease of Lys usage under the influence of mutational GC-pressure. On the other hand, the percentage of Mn2+ sites with at least one amino acid in the “beta strand-major binder-random coil” motif of secondary structure (77.88%) does not depend on genomic GC-content.

scholarly journals Structural transitions in mixed classes of proteins

2019 ◽  
Vol 64 (3) ◽  
pp. 326-337
Author(s):  
V. V. Poboinev ◽  
V. V. Khrustalev ◽  
T. A. Khrustaleva ◽  
A. N. Stojarov
Keyword(s):  
Amino Acid ◽  
Acid Content ◽  
Amino Acid Content ◽  
Alpha Helix ◽  
Complete Disappearance ◽  
Structural Transitions ◽  
Alpha Helices ◽  
Alpha Beta ◽  
Mixed Classes ◽  
Characteristic Features

It was studied the features of amino acid content of protein regions of “alpha + beta” and “alpha/beta” classes, that are prone to structural transitions. The data have been obtained by the way of the comparison of different threedimensional structures of proteins with absolutely identical amino acid sequence. In this study we ignored fragments of proteins in which positions of atoms cannot be determined with the help of X-ray crystallography. Proteins of “alpha + beta” class are less stable than proteins of “alpha/beta” class, since the percent of structurally instable residues in them is higher. Most frequent type of structural transitions is the decrease of length of N-terminal and C-terminal parts of alpha helices and beta strands. Alpha helices and beta strands that can completely disappear (turn to coil) have also been found. The data of their amino acid content is important for the development of the method able to detect fragments of proteins prone to transitions from alpha helix to beta strand. Those fragments should combine characteristic features of amino acid content of both completely disappearing alpha helices and completely disappearing beta strands. The amino acid composition of alpha-helices capable to complete disappearance is significantly different from that for beta-strands capable to complete disappearance: frequencies of alanine, glutamine and glutamic acid usage are increased, frequencies of isoleucine, threonine and glycine usage are reduced.

Research on Structure and Property of Silk Fibroin Modified Viscose Fiber

2011 ◽  
Vol 175-176 ◽  
pp. 176-180
Author(s):  
Hui Ying Wu ◽  
Bao Qi Zuo
Keyword(s):  
Amino Acid ◽  
Silk Fibroin ◽  
Amino Acid Content ◽  
Longitudinal Section ◽  
Decomposition Temperature ◽  
Viscose Fiber ◽  
Random Coil ◽  
Wet Strength ◽  
Structure And Property ◽  
Β Sheet

Silk fibroin modified viscose fiber (SFVF) was a new fiber with silken handling and luster, which was produced via adding silk fibroin (SF) during the viscose process. In this paper, a series of testing had been done to study the structure and properties of SFVF. The amino acid content of SFVF was measured by HITACHI-835-50 amino acid tester. The morphology, structure, thermal and mechanical property of SFVF were characterized by SEM, FTIR, DSC and electronic strength tester. The results indicated that SFVF consisted of many kinds of amino acids compared with pure viscose fiber (VF) yarn. The results of SEM showed more continuous multi fine slots existed in the longitudinal section of SFVF than in that of VF, demonstrating that wet permeability and vapor transmission could be enhanced for the SFVF to certain extent. Results from FTIR indicated that the secondary structure of SFVF was mainly β-sheet and random coil, and its absorption peaks were 1616cm-1 and 1644 cm-1 respectively. The DSC curve shown the thermal decomposition temperature of SFVF was about 328.39°C, which was close to that of VF. It suggested that the SF modification had no obvious influence on thermal stability of VF. At last, the dry-strength and wet-strength of SFVF was close to that of VF. Therefore, the application of VF would be expanded with the SF modification.

Primary Structure and Anticandidal Activity of the Major Histatin from Parotid Secretion of the Subhuman Primate, Macaca fascicularis

1990 ◽  
Vol 69 (11) ◽  
pp. 1717-1723 ◽  
Author(s):  
T. Xu ◽  
E. Telser ◽  
R.F. Troxler ◽  
F.G. Oppenheim
Keyword(s):  
Amino Acid ◽  
High Performance ◽  
Macaca Fascicularis ◽  
Sequence Similarity ◽  
Gel Filtration ◽  
Alpha Helix ◽  
Reversed Phase ◽  
Amino Acid Residues ◽  
Beta Turns ◽  
Anticandidal Activity

A major macaque histatin (M-histatin 1) from the parotid secretion of the subhuman primate, Macaca fascicularis, was isolated by gel filtration on Bio-Gel P-2 and purified to homogeneity by reversed-phase high-performance liquid chromatography on a TSK-ODS C18 column. The complete amino acid sequence of M-histatin 1, determined by automated Edman degradation, is: 1 10 20 Asp-Pse-His-Glu-Glu-Arg-His-His-Gly-Arg-His-Gly-His-His-Lys-Tyr-Gly-Arg-Lys-Phe 21 30 38 His-Glu-Lys-His-His-Ser-His-Arg-Gly-Tyr-Arg-Ser-Asn-Tyr-Leu-Tyr-Asp-Asn M-histatin 1 contains 38 amino acid residues, a phosphoserine at residue 2, has a molecular weight of 4881.8, a calculated pI of 8.5, and histidine forms 26.3% of the mass. The hydropathicity plot of M-histatin 1 predicts that the molecule is entirely hydrophilic, and Chou-Fasman secondary prediction indicates that the polypeptide is devoid of alpha-helix and beta-sheet conformation in aqueous solutions but contains a series of beta turns. M-histatin 1 includes a six-amino-acid insert (residue 10-15) not present in human histatins and, with the introduction of gaps to maximize homology, it displays 89% and 91% sequence similarity with human histatins 1 and 3, respectively. M-histatin 1 exhibited fungicidal and fungistatic effects against the dimorphic pathogen, Candida albicans, in three separate bioassays. Its anticandidal effects were comparable with or greater than those of human histatins 1, 3, and 5. M-histatins 2, 3, and 4 were not sequenced directly because insufficient materials were available, but the amino acid composition of M-histatin 3 was nearly identical to that of the N-terminal 20 amino acid residues of M-histatin 1. There appears to be only one major histatin in macaque parotid secretion in contrast to the family of histatins in human parotid and submandibular secretions, and the significance of this in the context of evolution and mechanism of action in anticandidal assays is discussed.

scholarly journals Open-Bundle Structure as the Unfolding Intermediate of Cytochrome c’ Revealed by Small Angle Neutron Scattering

2021 ◽  
Author(s):  
Takahide Yamaguchi ◽  
Kouhei Akao ◽  
Alexandros Koutsioubas ◽  
Henrich Frielinghaus ◽  
Takamitsu Kohzuma
Keyword(s):  
Cytochrome C ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Alpha Helix ◽  
Random Coil ◽  
Radius Of Gyration ◽  
Alpha Helices ◽  
Cyt C ◽  
Bundle Structure

The open-bundle structure of cytochrome c’ as an unfolding intermediate was determined by small-angle neutron scattering experiment (SANS). The four-α-helix bundle structure of Cyt c’ at neutral pH was transited to an open-bundle structure (at pD ~13), which is a joint-clubs consisting of four clubs (α-helices) connected by short loops. The compactly folded structure of Cyt c’ (radius of gyration, Rg = 18 Å for the Cyt c’ dimer) at neutral or mildly alkaline pD transitioned to a remarkably larger “open-bundle” structure at pD ~13 (Rg = 25 Å for the Cyt c’ monomer). Cyt c’ adopts an unstructured random coil structure at pD = 1.7 (Rg = 25 Å for the Cyt c’ monomer). Numerical partial scattering function analysis (joint-clubs) and ab initio modelling gave structures similar to the “open-bundle”, which retains the α-helices but loses the bundle structure.

scholarly journals In silico prediction of the functional and structural consequences of the non-synonymous single nucleotide polymorphism A122V in bovine CXC chemokine receptor type 1

2020 ◽  
Vol 80 (1) ◽  
pp. 39-46
Author(s):  
A. F. Guzzi ◽  
F. S. L. Oliveira ◽  
M. M. S. Amaro ◽  
P. F. Tavares-Filho ◽  
J. E. Gabriel
Keyword(s):  
Amino Acid ◽  
Chemokine Receptor ◽  
In Silico ◽  
Alpha Helix ◽  
Amino Acid Sequences ◽  
Receptor Type ◽  
Amino Acid Residues ◽  
Causal Polymorphism ◽  
Cxc Chemokine

Abstract The current study aimed to assess whether the A122V causal polymorphism promotes alterations in the functional and structural proprieties of the CXC chemokine receptor type 1 protein (CXCR1) of cattle Bos taurus by in silico analyses. Two amino acid sequences of bovine CXCR1 was selected from database UniProtKB/Swiss-Prot: a) non-polymorphic sequence (A7KWG0) with alanine (A) at position 122, and b) polymorphic sequence harboring the A122V polymorphism, substituting alanine by valine (V) at same position. CXCR1 sequences were submitted as input to different Bioinformatics’ tools to examine the effects of this polymorphism on functional and structural stabilities, to predict eventual alterations in the 3-D structural modeling, and to estimate the quality and accuracy of the predictive models. The A122V polymorphism exerted tolerable and non-deleterious effects on the polymorphic CXCR1, and the predictive structural model for polymorphic CXCR1 revealed an alpha helix spatial structure typical of a receptor transmembrane polypeptide. Although higher variations in the distances between pairs of amino acid residues at target-positions are detected in the polymorphic CXCR1 protein, more than 97% of the amino acid residues in both models were located in favored and allowed conformational regions in Ramachandran plots. Evidences has supported that the A122V polymorphism in the CXCR1 protein is associated with increased clinical mastitis incidence in dairy cows. Thus, the findings described herein prove that the replacement of the alanine by valine amino acids provokes local conformational changes in the A122V-harboring CXCR1 protein, which could directly affect its post-translational folding mechanisms and biological functionality.

scholarly journals Characterization of meprin, a membrane-bound metalloendopeptidase from mouse kidney

1987 ◽  
Vol 241 (1) ◽  
pp. 229-235 ◽  
Author(s):  
P E Butler ◽  
M J McKay ◽  
J S Bond
Keyword(s):  
Amino Acid ◽  
Degradation Products ◽  
Amino Acid Content ◽  
Peptide Bond ◽  
Mouse Kidney ◽  
Amino Acid Residues ◽  
Peptide Bonds ◽  
Membrane Bound ◽  
Terminal Amino

Meprin is an intrinsic protein of the brush border, a specialized plasma membrane, of the mouse kidney. It is a metalloendopeptidase that contains 1 mol of zinc and 3 mol of calcium per mol of the 85,000-Mr subunit. The enzyme is isolated, and active, as a tetramer. The behaviour of the enzyme on SDS/polyacrylamide gels in the presence and absence of beta-mercaptoethanol indicates that the subunits are of the same Mr (approx. 85,000) and held together by intersubunit S–S bridges. Eight S-carboxymethyl-L-cysteine residues were detected after reduction of the enzyme with beta-mercaptoethanol and carboxymethylation with iodoacetate. The enzyme is a glycoprotein and contains approx. 18% carbohydrate. Most of the carbohydrate is removed by endoglycosidase F, indicating that the sugar residues are N-linked. The isoelectric point of the enzyme is between pH 4 and 5, and the purified protein yields a pattern of evenly spaced bands in this range on isoelectric focusing. The peptide-bond specificity of the enzyme has been determined by using the oxidized B-chain of insulin as substrate. In all, 15 peptide degradation products were separated by h.p.l.c. and analysed for their amino acid content and N-terminal amino acid residue. The prevalent peptide-bond cleavages were between Gly20 and Glu21, Phe24 and Phe25 and between Phe25 and Tyr26. Other sites of cleavage were Leu6-Cysteic acid7, Ala14-Leu15, His10-Leu11, Leu17-Val18, Gly8-Ser9, Leu15-Tyr16, His5-Leu6. These results indicate that meprin has a preference for peptide bonds that are flanked by hydrophobic or neutral amino acid residues, but hydrolysis is not limited to these bonds. The ability of meprin to hydrolyse peptide bonds between small neutral and negatively charged amino acid residues distinguishes it from several other metalloendopeptidases.

Amino acid residues in conodont elements

2002 ◽  
Vol 76 (3) ◽  
pp. 518-528 ◽  
Author(s):  
A. Kemp
Keyword(s):  
Organic Matter ◽  
Amino Acid ◽  
Amino Acid Content ◽  
Organic Matrix ◽  
Organic Content ◽  
Amino Acid Residues ◽  
Hard Tissues ◽  
Collagen Molecules ◽  
Biochemical Analyses ◽  
Phylogenetic Affinities

Thermally unaltered conodont elements, brachiopods, and vertebrates were analyzed with reverse phase high profile liquid chromatography to locate and quantify amino acid remnants of the original organic matrix in the fossils. No consistent similarities in amino acid content were found in conodont taxa, and criteria based on organic residues appear to have no taxonomic significance in the fossils tested from these localities. However, hydroxyproline, an amino acid that is found in the collagen molecules of animals, as well as in the glycoproteins in the cell walls and reproductive tissues of certain plants, is represented in most taxa. The organic matter retained in the impermeable crowns of conodont elements might have been derived originally from a form of collagen. Biochemical analyses, correlated with histochemical tests, demonstrate that organic matter is an integral part of the hyaline tissue of the element crown and not the result of surface contamination. Tests of a range of vertebrate and invertebrate fossil hard tissues produced similar results. The analyses indicate that hyaline tissue in the conodont element crown is not a form of vertebrate enamel, which contains no collagen. Albid tissue, with little or no organic content, is not a form of vertebrate bone or dentine, both based on collagen and low in mineral. Although these results do not help to determine the phylogenetic affinities of conodont animals, they indicate that conodont elements do not contain hard tissues characteristic of vertebrate animals.

scholarly journals Conserved Determinants for Membrane Association of Nonstructural Protein 5A fromHepatitis C Virus and Related Viruses

2006 ◽  
Vol 81 (6) ◽  
pp. 2745-2757 ◽  
Author(s):  
Volker Brass ◽  
Zsuzsanna Pal ◽  
Nicolas Sapay ◽  
Gilbert Deléage ◽  
Hubert E. Blum ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nonstructural Protein ◽  
Alpha Helix ◽  
Laser Scanning Microscopy ◽  
Membrane Association ◽  
Alpha Helices ◽  
Replication Complex ◽  
Diarrhea Virus ◽  
Amphipathic Alpha Helix ◽  
Nonstructural Protein 5A

ABSTRACT Nonstructural protein 5A (NS5A) is a membrane-associated essential component of the hepatitis C virus (HCV) replication complex. An N-terminal amphipathic alpha helix mediates in-plane membrane association of HCV NS5A and at the same time is likely involved in specific protein-protein interactions required for the assembly of a functional replication complex. The aim of this study was to identify the determinants for membrane association of NS5A from the related GB viruses and pestiviruses. Although primary amino acid sequences differed considerably, putative membrane anchor domains with amphipathic features were predicted in the N-terminal domains of NS5A proteins from these viruses. Confocal laser scanning microscopy, as well as membrane flotation analyses, demonstrated that NS5As from GB virus B (GBV-B), GBV-C, and bovine viral diarrhea virus, the prototype pestivirus, display membrane association characteristics very similar to those of HCV NS5A. The N-terminal 27 to 33 amino acid residues of these NS5A proteins were sufficient for membrane association. Circular dichroism analyses confirmed the capacity of these segments to fold into alpha helices upon association with lipid-like molecules. Despite structural conservation, only very limited exchanges with sequences from related viruses were tolerated in the context of functional HCV RNA replication, suggesting virus-specific interactions of these segments. In conclusion, membrane association of NS5A by an N-terminal amphipathic alpha helix is a feature shared by HCV and related members of the family Flaviviridae. This observation points to conserved roles of the N-terminal amphipathic alpha helices of NS5A in replication complex formation.

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