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Article ; Online: Random Coils of Proteins Situated Between a Beta Strand and an Alpha Helix Demonstrate Decreased Solvent Accessibility.

2020 Volume 39, Issue 4, Page(s) 308–317

Abstract: Surface accessibility of different types of the same elements of secondary structure has been studied in 10 non-redundant sets of proteins (total number of three-dimensional structures is 1730) with a help of DSSP (Dictionary of Secondary Structure of ... ...

Abstract	Surface accessibility of different types of the same elements of secondary structure has been studied in 10 non-redundant sets of proteins (total number of three-dimensional structures is 1730) with a help of DSSP (Dictionary of Secondary Structure of Proteins). Random coils (C), beta strands (B), and alpha helices (H) have been classified according to their flanking elements of secondary structure in a polypeptide chain. Thanks to this kind of classification, for the first time it has been shown that random coils situated between a beta strand and an alpha helix (BCH) contain significantly lower fraction of exposed residues compared to other types of random coils; the least accessible beta strands are situated between two alpha helices (HBH), and the least accessible alpha helices are situated between a beta strand and an alpha helix (BHH). Discovered trends are explained as consequences of the natural selection that had been stabilizing the secondary structure of proteins on early steps of their evolution. Acquired differences in amino acid content of different types of random coils, alpha helices, and beta strands led to the formation of partially buried but hydrophilic BCH random coils because of their enrichment by Ser, Thr, and Asp residues. As a result, BCH random coils became prone to bind cations because of their lower hydration and decreased usage of positively charged amino acid residues. The mechanism described above led to the formation of active centers in ancient metalloenzymes. Nowadays one can observe decreased surface accessibility of amino acid residues in BCH random coils, in HBH beta strands, and in BHH alpha helices in proteins possessing hydrophobic cores.
MeSH term(s)	Databases, Protein ; Models, Molecular ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Proteins/chemistry ; Solvents/chemistry
Chemical Substances	Proteins ; Solvents
Language	English
Publishing date	2020-07-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-020-09905-0
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Article ; Online: Consequences of asymmetric mutational pressure for the dynamic of linear B-cell epitopes repertoire of influenza a virus neuraminidase rearrangement.

Khrustalev, Vladislav Victorovich / Stojarov, Aleksander Nicolaevich / Shen, Chenguang / Khrustaleva, Tatyana Aleksandrovna

Bio Systems

2023 Volume 231, Page(s) 104970

Abstract: Full-length nucleotide sequences of avian influenza A virus neuraminidase coding region (20,631 sequences) were analyzed and compared with those isolated from viruses infecting human and swine (63,750 sequences). If in fourfold degenerate sites there is ... ...

Abstract	Full-length nucleotide sequences of avian influenza A virus neuraminidase coding region (20,631 sequences) were analyzed and compared with those isolated from viruses infecting human and swine (63,750 sequences). If in fourfold degenerate sites there is asymmetric A-bias that may be more or less asymmetric depending on the type of neuraminidase and the host, than in twofold degenerate sites from third codon positions there is a strong asymmetric U-bias in coding regions of N4, N5, and N8 isolated from viruses infecting birds, as well as in those of N1 and N2 isolated from viruses infecting human, swine, and birds, while in coding regions of N9 isolated from birds, there is surprisingly strong C-bias, and in sequences of N3, N6, and N7 the usage of C is quite close to the level of U. Revealed stabilization of both U and C in twofold degenerate sites is the evidence of frequent changes in mutational pressure direction. Asymmetric mutational pressure was one of the sources of amino acid replacements that resulted in an equal percentage of sites with appeared and disappeared linear B-cell epitopes in N1, N2, N4, and N5 (33.62-35.33% vs. 32.41-36.45%, respectively), and controlled by the immune pressure it resulted in a stronger tendency to disappear for B-cell epitopes of N3, N6, N7, N8, and N9 of avian viruses (8.74-28.77% vs. 28.96-38.89%). The lack of correlation between nucleotide usages in fourfold and twofold degenerate sites for three nucleotides, except U, is a strong evidence of mutational pressure theory.
MeSH term(s)	Animals ; Humans ; Swine ; Neuraminidase/genetics ; Neuraminidase/chemistry ; Epitopes, B-Lymphocyte/genetics ; Mutation ; Influenza A virus/genetics ; Birds
Chemical Substances	Neuraminidase (EC 3.2.1.18) ; Epitopes, B-Lymphocyte
Language	English
Publishing date	2023-07-11
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	186234-0
ISSN	1872-8324 ; 0303-2647
ISSN (online)	1872-8324
ISSN	0303-2647
DOI	10.1016/j.biosystems.2023.104970
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Article: The PentaFOLD 3.0 algorithm for the selection of stable elements of secondary structure to be included in vaccine peptides

Khrustalev, Vladislav Victorovich

Abstract: AIMS: The aim of this study was to create a new version of the PentaFOLD algorithm and to test its performance experimentally in several proteins and peptides. BACKGROUND: Synthetic vaccines can cause production of neutralizing antibodies only in case if ...

Abstract	AIMS: The aim of this study was to create a new version of the PentaFOLD algorithm and to test its performance experimentally in several proteins and peptides. BACKGROUND: Synthetic vaccines can cause production of neutralizing antibodies only in case if short peptides form the same secondary structure as fragments of full-length proteins. The PentaFOLD 3.0 algorithm was designed to check stability of alpha helices, beta strands, and random coils using several propensity scales obtained during analysis of 1730 3D structures of proteins. OBJECTIVE: The algorithm has been tested in the three peptides known to keep the secondary structure of the corresponding fragments of full-length proteins: the NY25 peptide from the Influenza H1N1 hemagglutinin, the SF23 peptide from the diphtheria toxin, the NQ21 peptide from the HIV1 gp120; as well as in the CC36 peptide from the human major prion protein. METHOD: Affine chromatography for antibodies against peptides accompanied by circular dichroism and fluorescence spectroscopy were used to check the predictions of the algorithm. RESULT: Immunological experiments showed that all abovementioned peptides are more or less immunogenic in rabbits. The fact that antibodies against the NY25, the SF23, and the NQ21 form stable complexes with corresponding full-length proteins has been confirmed by affine chromatography. The surface of SARS CoV-2 spike receptor-binding domain interacting with hACE2 has been shown to be unstable according to the results of the PentaFOLD 3.0. CONCLUSION: The PentaFOLD 3.0 algorithm (http://chemres.bsmu.by/PentaFOLD30.htm) can be used with the aim to design vaccine peptides with stable secondary structure elements.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #918981
Database	COVID19

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Article ; Online: Germline mutations directions are different between introns of the same gene: case study of the gene coding for amyloid-beta precursor protein.

Khrustalev, Vladislav Victorovich / Khrustaleva, Tatyana Aleksandrovna / Popinako, Anna Vladimirovna

Genetica

2022 Volume 151, Issue 1, Page(s) 61–73

Abstract: Amyloid-beta precursor protein (APP) is highly conserved in mammals. This feature allowed us to compare nucleotide usage biases in fourfold degenerated sites along the length of its coding region for 146 species of mammals and birds in search of ... ...

Abstract	Amyloid-beta precursor protein (APP) is highly conserved in mammals. This feature allowed us to compare nucleotide usage biases in fourfold degenerated sites along the length of its coding region for 146 species of mammals and birds in search of fragments with significant deviations. Even though cytosine usage has the highest value in fourfold degenerated sites in APP coding region from all tested placental mammals, in contrast to marsupial mammals with the bias toward thymine usage, the most frequent germline and somatic mutations in human APP coding region are C to T and G to A transitions. The same mutational AT-pressure is characteristic for germline mutations in introns of human APP gene. However, surprisingly, there are several exceptional introns with deviations in germline mutations rates. The most of those introns surround exons with exceptional biases in nucleotide usage in fourfold degenerated sites. Existence of such fragments in exons 4 and 5, as well as in exon 14, can be connected with the presence of lncRNA genes in complementary strand of DNA. Exceptional nucleotide usage bias in exons 16 and 17 that contain a sequence encoding amyloid-beta peptides can be explained either by the presence of yet unmapped lncRNA(s), or by the autonomous expression of a short mRNA that encodes just C-terminal part of the APP providing an alternative source of amyloid-beta peptides. This hypothesis is supported by the increased rate of T to C transitions in introns 16-17 and 17-18 of Human APP gene relatively to other introns.
MeSH term(s)	Pregnancy ; Animals ; Female ; Humans ; Amyloid beta-Protein Precursor/genetics ; Introns ; Germ-Line Mutation ; RNA, Long Noncoding ; Base Sequence ; Placenta ; Mammals/genetics ; Nucleotides ; Peptides/genetics
Chemical Substances	Amyloid beta-Protein Precursor ; RNA, Long Noncoding ; Nucleotides ; Peptides
Language	English
Publishing date	2022-09-21
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2165-9
ISSN	1573-6857 ; 0016-6707
ISSN (online)	1573-6857
ISSN	0016-6707
DOI	10.1007/s10709-022-00166-6
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Article ; Online: Germline mutations directions are different between introns of the same gene: case study of the gene coding for amyloid-beta precursor protein

Khrustalev, Vladislav Victorovich / Khrustaleva, Tatyana Aleksandrovna / Popinako, Anna Vladimirovna

Genetica. 2023 Feb., v. 151, no. 1 p.61-73

2023

Abstract	Amyloid-beta precursor protein (APP) is highly conserved in mammals. This feature allowed us to compare nucleotide usage biases in fourfold degenerated sites along the length of its coding region for 146 species of mammals and birds in search of fragments with significant deviations. Even though cytosine usage has the highest value in fourfold degenerated sites in APP coding region from all tested placental mammals, in contrast to marsupial mammals with the bias toward thymine usage, the most frequent germline and somatic mutations in human APP coding region are C to T and G to A transitions. The same mutational AT-pressure is characteristic for germline mutations in introns of human APP gene. However, surprisingly, there are several exceptional introns with deviations in germline mutations rates. The most of those introns surround exons with exceptional biases in nucleotide usage in fourfold degenerated sites. Existence of such fragments in exons 4 and 5, as well as in exon 14, can be connected with the presence of lncRNA genes in complementary strand of DNA. Exceptional nucleotide usage bias in exons 16 and 17 that contain a sequence encoding amyloid-beta peptides can be explained either by the presence of yet unmapped lncRNA(s), or by the autonomous expression of a short mRNA that encodes just C-terminal part of the APP providing an alternative source of amyloid-beta peptides. This hypothesis is supported by the increased rate of T to C transitions in introns 16–17 and 17–18 of Human APP gene relatively to other introns.
Keywords	DNA ; Metatheria ; case studies ; cytosine ; exons ; germ cells ; humans ; introns ; peptides ; thymine
Language	English
Dates of publication	2023-02
Size	p. 61-73.
Publishing place	Springer International Publishing
Document type	Article ; Online
ZDB-ID	2165-9
ISSN	1573-6857 ; 0016-6707
ISSN (online)	1573-6857
ISSN	0016-6707
DOI	10.1007/s10709-022-00166-6
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Article ; Online: The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins.

Poboinev, Victor Vitoldovich / Khrustalev, Vladislav Victorovich / Khrustaleva, Tatyana Aleksandrovna / Kasko, Tihon Evgenyevich / Popkov, Vadim Dmitrievich

Amino acids

2022 Volume 54, Issue 8, Page(s) 1155–1171

Abstract: Intrinsically disordered proteins are frequently involved in important regulatory processes in the cell thanks to their ability to bind several different targets performing sometimes even opposite functions. The PentUnFOLD algorithm is a physicochemical ... ...

Abstract	Intrinsically disordered proteins are frequently involved in important regulatory processes in the cell thanks to their ability to bind several different targets performing sometimes even opposite functions. The PentUnFOLD algorithm is a physicochemical method that is based on new propensity scales for disordered, nonstable and stable elements of secondary structure and on the counting of stabilizing and destabilizing intraprotein contacts. Unlike other methods, it works with a PDB file, and it can determine not only those fragments of alpha helices, beta strands, and random coils that can turn into disordered state (the "dark" side of the disorder), but also nonstable regions of alpha helices and beta strands which are able to turn into random coils (the "light" side), and vice versa (H ↔ C, E ↔ C). The scales have been obtained from structural data on disordered regions from the middle parts of amino acid sequences only, and not on their expectedly disordered N- and C-termini. Among other tendencies we have found that regions of both alpha helices and beta strands that can turn into the disordered state are relatively enriched in residues of Ala, Met, Asp, and Lys, while regions of both alpha helices and beta strands that can turn into random coil are relatively enriched in hydrophilic residues, and Cys, Pro, and Gly. Moreover, PentUnFOLD has the option to determine the effect of secondary structure transitions on the stability of a given region of a protein. The PentUnFOLD algorithm is freely available at http://3.17.12.213/pent-un-fold and http://chemres.bsmu.by/PentUnFOLD.htm .
MeSH term(s)	Algorithms ; Amino Acid Sequence ; Intrinsically Disordered Proteins ; Protein Conformation, alpha-Helical ; Protein Structure, Secondary
Chemical Substances	Intrinsically Disordered Proteins
Language	English
Publishing date	2022-03-16
Publishing country	Austria
Document type	Journal Article
ZDB-ID	1121341-3
ISSN	1438-2199 ; 0939-4451
ISSN (online)	1438-2199
ISSN	0939-4451
DOI	10.1007/s00726-022-03153-5
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Article ; Online: Peptide Models of the Cytoplasmic Tail of Influenza A/H1N1 Virus Hemagglutinin Expand Understanding its pH-Dependent Modes of Interaction with Matrix Protein M1.

Poboinev, Victor Vitoldovich / Khrustalev, Vladislav Victorovich / Akunevich, Anastasia Aleksandrovna / Shalygo, Nikolai Vladimirovich / Stojarov, Aleksander Nikolaevich / Khrustaleva, Tatyana Aleksandrovna / Kordyukova, Larisa Valentinovna

The protein journal

2023 Volume 42, Issue 4, Page(s) 288–304

Abstract: Influenza A virus hemagglutinin (HA) is a major virus antigen. No cryo-electron microscopy or X-ray data can be obtained for the HA intraviral (cytoplasmic) domain (CT) post-translationally modified with long fatty acid residues bound to three highly ... ...

Abstract	Influenza A virus hemagglutinin (HA) is a major virus antigen. No cryo-electron microscopy or X-ray data can be obtained for the HA intraviral (cytoplasmic) domain (CT) post-translationally modified with long fatty acid residues bound to three highly conserved cysteines. We recently proposed a model of HA CT of Influenza A/H1N1 virus possessing an antiparallel beta structure based on the experimental secondary structure analysis of four 14-15 amino acid long synthetic peptides, corresponding to the HA CT sequence, with free or acetaminomethylated cysteines. To dispel doubts about possible non-specific "amyloid-like" aggregation of those synthetic peptides in phosphate buffer solution, we have determined the order of oligomers based on blue native gel electrophoresis, membrane filtration, fluorescence spectroscopy and molecular modeling approaches. We have found that unmodified peptides form only low molecular weight oligomers, while modified peptides form both oligomers of low order similar to those found for unmodified peptides and high order conglomerates, which however are not of beta-amyloid-like fold. This study confirms that the beta structure previously detected by circular dichroism spectroscopy analysis is more likely the result of intrinsic propensity of the HA CT amino acid sequence than the consequence of aggregation. The structures of low order oligomers of the synthetic peptides were used for in silico experiments on modeling of HA CT interactions with matrix protein M1 at physiological and acidic pH levels and revealed two different areas of binding. Finally, tripeptides capable of blocking interactions between HA CT and M1 were proposed.
MeSH term(s)	Humans ; Influenza A Virus, H1N1 Subtype ; Hemagglutinins ; Influenza, Human ; Peptides/chemistry ; Influenza A virus/metabolism ; Hydrogen-Ion Concentration
Chemical Substances	H1N1 virus hemagglutinin ; Hemagglutinins ; Peptides
Language	English
Publishing date	2023-03-23
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-023-10101-z
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Article ; Online: Spectra of tryptophan fluorescence are the result of co-existence of certain most abundant stabilized excited state and certain most abundant destabilized excited state.

Vladislav Victorovich, Khrustalev / Tatyana Aleksandrovna, Khrustaleva / Victor Vitoldovich, Poboinev / Aleksander Nicolaevich, Stojarov / Larisa Valentinovna, Kordyukova / Anastasia Aleksandrovna, Akunevich

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy

2021 Volume 257, Page(s) 119784

Abstract: Fluorescence spectra of proteins and peptides are traditionally used to get an information on self-association of proteins and peptides, on their tertiary and quaternary structure. In this study it was shown that there are just three peaks of tryptophan ... ...

Abstract	Fluorescence spectra of proteins and peptides are traditionally used to get an information on self-association of proteins and peptides, on their tertiary and quaternary structure. In this study it was shown that there are just three peaks of tryptophan fluorescence (at ∼308, at ∼330, and at ∼360 nm) in rough unsmoothed spectra of fluorescence of pure tryptophan in different solvents that change their heights depending on the polarity of a solvent. Two separate peaks at ∼330 nm and ∼360 nm are especially prominent in the spectrum of human epidermal growth factor. In contrast, in smoothed (either mathematically, or physically) spectra of Trp-containing proteins a single maximum of fluorescence varies between 330 and 360 nm. The theory of tryptophan fluorescence is discussed in light of three discrete peaks existence. A stabilizing hydrogen bond with aromatic system of benzene ring in the excited state is proposed as the cause of emission at ∼360 nm bringing Trp to the destabilized ground state. Emission from the destabilized excited state has a maximum at ∼330 nm if the ground state is destabilized, as well as if both states are stabilized. If the excited state is destabilized, while the ground state is stabilized by purely hydrophobic interactions, emitted light should have a maximum at ∼308 nm. The degree of hydrophilicity of tryptophan microenvironment is proposed to be measured as the ratio between the peak at 360 nm and the peak at 330 nm if the observed shifts are not "horizontal", but "vertical". The process of dissociation of hemagglutinin trimers from pandemic Influenza A(H1N1) virus is described as an example of the advantages of the proposed method.
MeSH term(s)	Fluorescence ; Humans ; Hydrogen Bonding ; Influenza A Virus, H1N1 Subtype ; Proteins ; Spectrometry, Fluorescence ; Tryptophan
Chemical Substances	Proteins ; Tryptophan (8DUH1N11BX)
Language	English
Publishing date	2021-04-08
Publishing country	England
Document type	Journal Article
ZDB-ID	210413-1
ISSN	1873-3557 ; 0370-8322 ; 0584-8539 ; 1386-1425
ISSN (online)	1873-3557
ISSN	0370-8322 ; 0584-8539 ; 1386-1425
DOI	10.1016/j.saa.2021.119784
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Article: The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins

Poboinev, Victor Vitoldovich / Khrustalev, Vladislav Victorovich / Khrustaleva, Tatyana Aleksandrovna / Kasko, Tihon Evgenyevich / Popkov, Vadim Dmitrievich

Amino acids. 2022 Aug., v. 54, no. 8

2022

Abstract	Intrinsically disordered proteins are frequently involved in important regulatory processes in the cell thanks to their ability to bind several different targets performing sometimes even opposite functions. The PentUnFOLD algorithm is a physicochemical method that is based on new propensity scales for disordered, nonstable and stable elements of secondary structure and on the counting of stabilizing and destabilizing intraprotein contacts. Unlike other methods, it works with a PDB file, and it can determine not only those fragments of alpha helices, beta strands, and random coils that can turn into disordered state (the “dark” side of the disorder), but also nonstable regions of alpha helices and beta strands which are able to turn into random coils (the “light” side), and vice versa (H ↔ C, E ↔ C). The scales have been obtained from structural data on disordered regions from the middle parts of amino acid sequences only, and not on their expectedly disordered N- and C-termini. Among other tendencies we have found that regions of both alpha helices and beta strands that can turn into the disordered state are relatively enriched in residues of Ala, Met, Asp, and Lys, while regions of both alpha helices and beta strands that can turn into random coil are relatively enriched in hydrophilic residues, and Cys, Pro, and Gly. Moreover, PentUnFOLD has the option to determine the effect of secondary structure transitions on the stability of a given region of a protein. The PentUnFOLD algorithm is freely available at http://3.17.12.213/pent-un-fold and http://chemres.bsmu.by/PentUnFOLD.htm .
Keywords	algorithms ; amino acids ; hydrophilicity
Language	English
Dates of publication	2022-08
Size	p. 1155-1171.
Publishing place	Springer Vienna
Document type	Article
ZDB-ID	1121341-3
ISSN	1438-2199 ; 0939-4451
ISSN (online)	1438-2199
ISSN	0939-4451
DOI	10.1007/s00726-022-03153-5
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Article ; Online: Magnesium and manganese binding sites on proteins have the same predominant motif of secondary structure.

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

Journal of theoretical biology

2016 Volume 395, Page(s) 174–185

Abstract: Manganese ion (Mn(2+)) can substitute magnesium ion (Mg(2+)) in active sites of numerous enzymes. Binding sites for these two ions have been studied in two sets of protein 3D structures from the Protein Data Bank with the homology level lower than 25%. ... ...

Abstract	Manganese ion (Mn(2+)) can substitute magnesium ion (Mg(2+)) in active sites of numerous enzymes. Binding sites for these two ions have been studied in two sets of protein 3D structures from the Protein Data Bank with the homology level lower than 25%. The structural motif "beta strand - binder - random coil" is predominant in both Mn(2+) and Mg(2+) coordination spheres, especially in functionally relevant ones. That predominant motif works as an active binder of those divalent cations which can then attract additional ligands, such as different phosphate-containing compounds. In contrast, such Mg(2+) and Mn(2+) binding motif as "GK(T/S)T" being the N-terminal part of alpha helices works as an active binder of phosphates which can then attract divalent cations. There are few differences between Mg(2+) and Mn(2+) coordination spheres responsible of the cation specificity. His residues are underrepresented in certain positions around Asp and Glu residues involved in Mg(2+) coordination, while they are overrepresented in certain positions around Asp and Glu residues coordinating Mn(2+). The random coil region in the "beta strand - random coil - alpha helix" motif for Mg(2+) binding is usually shorter than that in the same motif for Mn(2+) coordination. This feature is associated with the lower number of binding amino acids (and lower levels of usage of such "major" binders as Asp and Glu) for Mg(2+) (which is a hard Lewis acid) in comparison with those for Mn(2+) (an intermediate Lewis acid).
MeSH term(s)	Amino Acid Motifs ; Binding Sites ; Databases, Protein ; Magnesium/chemistry ; Metalloproteins/chemistry ; Metalloproteins/genetics
Chemical Substances	Metalloproteins ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2016-04-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2972-5
ISSN	1095-8541 ; 0022-5193
ISSN (online)	1095-8541
ISSN	0022-5193
DOI	10.1016/j.jtbi.2016.02.006
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