Random coil structures in bacterial proteins. Relationships of their amino acid compositions to flanking structures and corresponding genic base compositions

Khrustalev, Vladislav Victorovich; Khrustaleva, Tatyana Aleksandrovna; Barkovsky, Eugene Victorovich

doi:10.1016/j.biochi.2013.05.014

Cited by 18 publications

(18 citation statements)

References 31 publications

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“…At first, N-termini of helices are enriched by negatively charged amino acid residues: aspartic and glutamic acids [18]. At second, BCH regions demonstrate decreased usage of positively charged amino acids: lysine and arginine [19]. Because of these reasons, B-BCH-H motifs should frequently carry a total negative charge which should attract positively charged cations, such as Mn 2+ [19].…”

Section: Discussionmentioning

confidence: 99%

“…At second, BCH regions demonstrate decreased usage of positively charged amino acids: lysine and arginine [19]. Because of these reasons, B-BCH-H motifs should frequently carry a total negative charge which should attract positively charged cations, such as Mn 2+ [19]. In contrast, H-HCB-B motifs should usually carry a total positive charge: both C-termini of helices and HCB regions are enriched by lysine and arginine [19].…”

Section: Discussionmentioning

confidence: 99%

“…Indeed, BCB regions are enriched by such major Mn 2+ binder, as Asp [19]. Those regions of coil are flexible because of the enrichment by glycine residues [19]. This feature should play some role in the successful coordination of ions.…”

Section: Discussionmentioning

confidence: 99%

“…This feature should play some role in the successful coordination of ions. Moreover, BCB regions are more hydrophilic than HCH ones [19]. …”

Section: Discussionmentioning

confidence: 99%

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Secondary Structure Preferences of Mn²⁺ Binding Sites in Bacterial Proteins

Khrustaleva

2014

Advances in Bioinformatics

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…This feature should play some role in the successful coordination of ions. Moreover, BCB regions are more hydrophilic than HCH ones [19]. …”

Section: Discussionmentioning

confidence: 99%

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Secondary Structure Preferences of Mn²⁺ Binding Sites in Bacterial Proteins

Khrustaleva

2014

Advances in Bioinformatics

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“…This loop demonstrates a rather low level of hydrophobic amino acid usage, that is not common for random coil structures situated between two alpha helices, when they are not intrinsically disordered regions (Khrustalev et al, 2013). The structure of such a "loop" peptide would be quite unstable: just a small part of peptide molecules in the given moment of time may mimic the real epitope.…”

Section: Introductionmentioning

confidence: 99%

Structural and antigenic features of the synthetic SF23 peptide corresponding to the receptor binding fragment of diphtheria toxin

Khrustaleva

Khrustalev

Barkovsky

et al. 2015

Molecular Immunology

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The part of a long beta hairpin from the scrapie form of the human prion protein is reconstructed in the synthetic CC36 protein

et al. 2016

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Mechanisms of beta sheet formation by the human prion protein are not clear yet. In this work, we clarified the role of the region containing C-half of the second helix and N-half of the third helix of that protein in the process of alpha helix to beta sheet transition. Solid phase automatic synthesis of the original peptide (CC36: Cys179-Cys214) failed because of the beta hairpin formation in the region 206-MERVVEQMC-214 with a high beta strand potential. Using Met206Arg and Val210Arg substitutions, we increased the probability of alpha helix formation by that sequence. After that modification, the complete CC36 peptide with disulfide bond has been synthesized. Modified peptide has been studied by circular dichroism (CD) and fluorescence spectrography. According to the CD spectra analysis, the CC36 peptide contains 37% of residues in beta sheet and just 15% in helix. Thermal analysis under the control of CD shows that the secondary structure content of the peptide is stable from 5°C to 80°C. Dissociation of oligomers of the CC36 peptide finishes at 37°C according to the fluorescence analysis. The CC36 peptide is able to bind Mn(2+) cations, which causes small temperature-associated structural shifts at concentrations of 2 - 10·10(-6) M. Predicted beta hairpin of the CC36 peptide (two beta strands are: 184-IKQHTVT-190 and 197-TETDVKM-205) should be the part of a longer beta hairpin from the scrapie form of the prion protein (PrPSc). Analogs of the CC36 peptide may be considered as antigens for the future development of a vaccine against PrPSc. Proteins 2016; 84:1462-1479. © 2016 Wiley Periodicals, Inc.

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Random coil structures in bacterial proteins. Relationships of their amino acid compositions to flanking structures and corresponding genic base compositions

Cited by 18 publications

References 31 publications

Secondary Structure Preferences of Mn²⁺ Binding Sites in Bacterial Proteins

Secondary Structure Preferences of Mn²⁺ Binding Sites in Bacterial Proteins

Structural and antigenic features of the synthetic SF23 peptide corresponding to the receptor binding fragment of diphtheria toxin

The part of a long beta hairpin from the scrapie form of the human prion protein is reconstructed in the synthetic CC36 protein

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Random coil structures in bacterial proteins. Relationships of their amino acid compositions to flanking structures and corresponding genic base compositions

Cited by 18 publications

References 31 publications

Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

Structural and antigenic features of the synthetic SF23 peptide corresponding to the receptor binding fragment of diphtheria toxin

The part of a long beta hairpin from the scrapie form of the human prion protein is reconstructed in the synthetic CC36 protein

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Secondary Structure Preferences of Mn²⁺ Binding Sites in Bacterial Proteins

Secondary Structure Preferences of Mn²⁺ Binding Sites in Bacterial Proteins