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  1. Article ; Online: Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

    Tatyana Aleksandrovna Khrustaleva

    Advances in Bioinformatics, Vol

    2014  Volume 2014

    Abstract: 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 ... ...

    Abstract 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.
    Keywords Biology (General) ; QH301-705.5 ; Statistics ; HA1-4737
    Language English
    Publishing date 2014-01-01T00:00:00Z
    Publisher Hindawi Publishing Corporation
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. 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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  3. Book ; Online: Table_1_Translation-Associated Mutational U-Pressure in the First ORF of SARS-CoV-2 and Other Coronaviruses.XLSX

    Vladislav Victorovich Khrustalev / Rajanish Giri / Tatyana Aleksandrovna Khrustaleva / Shivani Krishna Kapuganti / Aleksander Nicolaevich Stojarov / Victor Vitoldovich Poboinev

    2020  

    Abstract: Within 4 months of the ongoing COVID-19 pandemic caused by SARS-CoV-2, more than 250 nucleotide mutations have been detected in ORF1ab of the virus isolated from infected persons from different parts of the globe. These observations open up an obvious ... ...

    Abstract Within 4 months of the ongoing COVID-19 pandemic caused by SARS-CoV-2, more than 250 nucleotide mutations have been detected in ORF1ab of the virus isolated from infected persons from different parts of the globe. These observations open up an obvious question about the rate and direction of mutational pressure for further vaccine and therapeutics designing. In this study, we did a comparative analysis of ORF1a and ORF1b by using the first isolate (Wuhan strain) as the parent sequence. We observed that most of the nucleotide mutations are C to U transitions. The rate of synonymous C to U transitions is significantly higher than the rate of non-synonymous ones, indicating negative selection on amino acid substitutions. Further, trends in nucleotide usage bias have been investigated in 49 coronaviruses species. A strong bias in nucleotide usage in fourfold degenerate sites toward uracil residues is seen in ORF1ab of all the studied coronaviruses: both in the ORF1a and in the ORF1b translated thanks to the programmed ribosomal frameshifting that has an efficiency of 14 – 45% in different species. A more substantial mutational U-pressure is observed in ORF1a than in ORF1b perhaps because ORF1a is translated more frequently than ORF1b. Mutational U-pressure is there even in ORFs that are not translated from genomic RNA plus strands, but the bias is weaker than in ORF1ab. Unlike other nucleotide mutations, mutational U-pressure caused by cytosine deamination, mostly occurring during the RNA plus strand replication and also translation, cannot be corrected by the proof-reading machinery of coronaviruses. The knowledge generated on the mutational U-pressure that becomes stronger during translation of viral RNA plus strands has implications for vaccine and nucleoside analog development for treating COVID-19 and other coronavirus infections.
    Keywords Microbiology ; Microbial Genetics ; Microbial Ecology ; Mycology ; COVID-19 ; SARS ; MERS ; mutational pressure ; cytosine deamination ; covid19
    Subject code 590
    Publishing date 2020-09-22T04:08:15Z
    Publishing country uk
    Document type Book ; Online
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  4. Article ; Online: Translation-Associated Mutational U-Pressure in the First ORF of SARS-CoV-2 and Other Coronaviruses

    Vladislav Victorovich Khrustalev / Rajanish Giri / Tatyana Aleksandrovna Khrustaleva / Shivani Krishna Kapuganti / Aleksander Nicolaevich Stojarov / Victor Vitoldovich Poboinev

    Frontiers in Microbiology, Vol

    2020  Volume 11

    Abstract: Within 4 months of the ongoing COVID-19 pandemic caused by SARS-CoV-2, more than 250 nucleotide mutations have been detected in ORF1ab of the virus isolated from infected persons from different parts of the globe. These observations open up an obvious ... ...

    Abstract Within 4 months of the ongoing COVID-19 pandemic caused by SARS-CoV-2, more than 250 nucleotide mutations have been detected in ORF1ab of the virus isolated from infected persons from different parts of the globe. These observations open up an obvious question about the rate and direction of mutational pressure for further vaccine and therapeutics designing. In this study, we did a comparative analysis of ORF1a and ORF1b by using the first isolate (Wuhan strain) as the parent sequence. We observed that most of the nucleotide mutations are C to U transitions. The rate of synonymous C to U transitions is significantly higher than the rate of non-synonymous ones, indicating negative selection on amino acid substitutions. Further, trends in nucleotide usage bias have been investigated in 49 coronaviruses species. A strong bias in nucleotide usage in fourfold degenerate sites toward uracil residues is seen in ORF1ab of all the studied coronaviruses: both in the ORF1a and in the ORF1b translated thanks to the programmed ribosomal frameshifting that has an efficiency of 14 – 45% in different species. A more substantial mutational U-pressure is observed in ORF1a than in ORF1b perhaps because ORF1a is translated more frequently than ORF1b. Mutational U-pressure is there even in ORFs that are not translated from genomic RNA plus strands, but the bias is weaker than in ORF1ab. Unlike other nucleotide mutations, mutational U-pressure caused by cytosine deamination, mostly occurring during the RNA plus strand replication and also translation, cannot be corrected by the proof-reading machinery of coronaviruses. The knowledge generated on the mutational U-pressure that becomes stronger during translation of viral RNA plus strands has implications for vaccine and nucleoside analog development for treating COVID-19 and other coronavirus infections.
    Keywords COVID-19 ; SARS ; MERS ; mutational pressure ; cytosine deamination ; Microbiology ; QR1-502 ; covid19
    Subject code 590
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
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  5. Article: Selection and structural analysis of the NY25 peptide – A vaccine candidate from hemagglutinin of swine-origin Influenza H1N1

    Khrustalev, Vladislav Victorovich / Larisa Valentinovna Kordyukova / Tatyana Aleksandrovna Khrustaleva

    Microbial pathogenesis. 2018 Dec., v. 125

    2018  

    Abstract: The aim of this study was to construct a vaccine peptide candidate against pandemic Influenza H1N1 hemagglutinin and to test its structure. With the help of bioinformatic algorithms we showed that the sequence encoding the second polypeptide of pandemic ... ...

    Abstract The aim of this study was to construct a vaccine peptide candidate against pandemic Influenza H1N1 hemagglutinin and to test its structure. With the help of bioinformatic algorithms we showed that the sequence encoding the second polypeptide of pandemic Influenza H1N1 hemagglutinin (HA2) is protected from nonsynonymous mutations better than the sequence encoding its first polypeptide (HA1). With the help of secondary and ternary structure predicting algorithms we found the fragment of HA2 with the most reproducible secondary structure and synthesized the NY25 peptide corresponding to the residues Asn117 – Tyr141 of HA2. According to the circular dichroism spectra analysis, the peptide has short helix and beta hairpin. According to the analysis of differential fluorescence quenching results, two tyrosine residues are situated on a long distance from each other. These facts taken together with the positive results of affine chromatography with the serum of a person immunized by full-length hemagglutinin confirm that the structure of the fragment of viral full-length protein has been reproduced in the synthetic NY25 peptide. Amino acid sequence of the NY25 peptide (NLYEKVRSQLKNNAKEIGNGCFEFY) is relatively conserved in 18 subtypes of Influenza A virus hemagglutinin.
    Keywords algorithms ; blood serum ; chromatography ; circular dichroism spectroscopy ; fluorescence ; hemagglutinins ; Influenza A virus ; mutation ; polypeptides ; tyrosine ; vaccines
    Language English
    Dates of publication 2018-12
    Size p. 72-83.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 632772-2
    ISSN 1096-1208 ; 0882-4010
    ISSN (online) 1096-1208
    ISSN 0882-4010
    DOI 10.1016/j.micpath.2018.09.004
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  6. Article ; Online: Local Mutational Pressures in Genomes of Zaire Ebolavirus and Marburg Virus

    Vladislav Victorovich Khrustalev / Eugene Victorovich Barkovsky / Tatyana Aleksandrovna Khrustaleva

    Advances in Bioinformatics, Vol

    2015  Volume 2015

    Abstract: Heterogeneities in nucleotide content distribution along the length of Zaire ebolavirus and Marburg virus genomes have been analyzed. Results showed that there is asymmetric mutational A-pressure in the majority of Zaire ebolavirus genes; there is ... ...

    Abstract Heterogeneities in nucleotide content distribution along the length of Zaire ebolavirus and Marburg virus genomes have been analyzed. Results showed that there is asymmetric mutational A-pressure in the majority of Zaire ebolavirus genes; there is mutational AC-pressure in the coding region of the matrix protein VP40, probably, caused by its high expression at the end of the infection process; there is also AC-pressure in the 3′-part of the nucleoprotein (NP) coding gene associated with low amount of secondary structure formed by the 3′-part of its mRNA; in the middle of the glycoprotein (GP) coding gene that kind of mutational bias is linked with the high amount of secondary structure formed by the corresponding fragment of RNA negative (−) strand; there is relatively symmetric mutational AU-pressure in the polymerase (Pol) coding gene caused by its low expression level. In Marburg virus all genes, including C-rich fragment of GP coding region, demonstrate asymmetric mutational A-bias, while the last gene (Pol) demonstrates more symmetric mutational AU-pressure. The hypothesis of a newly synthesized RNA negative (−) strand shielding by complementary fragments of mRNAs has been described in this work: shielded fragments of RNA negative (−) strand should be better protected from oxidative damage and prone to ADAR-editing.
    Keywords Biology (General) ; QH301-705.5 ; Statistics ; HA1-4737
    Language English
    Publishing date 2015-01-01T00:00:00Z
    Publisher Hindawi Limited
    Document type Article ; Online
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  7. Article: Intragenic isochores (intrachores) in the platelet phosphofructokinase gene of Passeriform birds

    Khrustalev, Vladislav Victorovich / Eugene Victorovich Barkovsky / Sergey Vladimirovich Lelevich / Tatyana Aleksandrovna Khrustaleva

    Gene. 2014 Aug. 01, v. 546

    2014  

    Abstract: Total GC-content in the platelet phosphofructokinase gene of Zebra Finch (Taeniopygia guttata) is low (37.53±0.51%), while there are short areas (about 300 nucleotides in length) with increased GC-content overlapping its exon 4 and exon 17. GC-content ... ...

    Abstract Total GC-content in the platelet phosphofructokinase gene of Zebra Finch (Taeniopygia guttata) is low (37.53±0.51%), while there are short areas (about 300 nucleotides in length) with increased GC-content overlapping its exon 4 and exon 17. GC-content in third codon positions (3GC) of those two exons is equal to 88.42 and 80.00%, respectively, while overall 3GC of the coding region is equal to 49.9%. Similar distribution of GC-content has been found in platelet phosphofructokinase genes of other birds from Passeriformes order. According to the results of phylogenetic analysis, formation of those areas with high G+C started from 91.4 to 47.1millionyears ago, since there are no such peaks of GC-content in homologous genes of other birds and reptiles. There are clusters of transcription factor binding sites in those areas with higher GC-content, as well as microRNA precursors conserved in Zebra Finch and Flycatcher genes. According to our hypothesis those intragenic isochores (intrachores) may be consequences of autonomous microRNA precursor transcription at certain period(s) of embryogenesis and gametogenesis, when the platelet phosphofructokinase gene itself is not expressed. Transcription-associated mutational pressure existing during those periods may cause the increase in rates of AT to GC mutations in those genes which are transcribed.
    Keywords binding sites ; birds ; embryogenesis ; exons ; gametogenesis ; genes ; microRNA ; mutation ; nucleotides ; phosphofructokinases ; phylogeny ; reptiles ; Taeniopygia guttata ; transcription (genetics) ; transcription factors
    Language English
    Dates of publication 2014-0801
    Size p. 16-24.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2014.05.045
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    Z 79/715: Show issues

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  8. Article: The alpha helix 1 from the first conserved region of HIV1 gp120 is reconstructed in the short NQ21 peptide

    Khrustalev, Vladislav Victorovich / Alexander Leonidovich Ksenofontov / Alexander Migranovich Arutyunyan / Ekaterina Yurievna Kahanouskaya / Hanna Vitalyevna Bandarenka / Kseniya Victorovna Girel / Larisa Valentinovna Kordyukova / Nadia Vladimirovna Khinevich / Tatyana Aleksandrovna Khrustaleva / Yulia Anatolyevna Rudnichenko

    Archives of biochemistry and biophysics. 2018 Jan. 15, v. 638

    2018  

    Abstract: Investigations of short peptides that can be used in the next phase of synthetic HIV1 vaccine development are an urgent goal, as well as investigations of peptides that can be used in immunological tests with the aim to check the titer of antibodies ... ...

    Abstract Investigations of short peptides that can be used in the next phase of synthetic HIV1 vaccine development are an urgent goal, as well as investigations of peptides that can be used in immunological tests with the aim to check the titer of antibodies against the alpha helix 1 from the first conserved region of HIV1 gp120 that are known to cause antibody-dependent cellular cytotoxicity (ADCC). The aim of this work was to study the structure of the NQ21 peptide corresponding to the less mutable part of the first conserved region of HIV1 gp120 (residues 94–114). The NQ21 peptide and its conjugate with biotin (biotin-NQ21) are absolutely alpha-helical in phosphate buffer solutions at pH = 6.8, 7.4 and 8.0, as well as in the dried form, according to the results of surface-enhanced Raman scattering (SERS) spectroscopy. Results of the native gel electrophoresis and thermal analysis under the control of spectrofluorometer and near UV circular dichroism (CD) showed that the peptide exists in form of octamers and tetramers at pH = 7.4, that is important information for further vaccine development. Strong signal of interacting Trp residues in oligomers in the far UV CD obscures the signal from secondary structure, but becomes less intensive during the heating.
    Keywords antibodies ; biotin ; circular dichroism spectroscopy ; cytotoxicity ; gel electrophoresis ; heat ; immunologic techniques ; peptides ; pH ; phosphates ; Raman spectroscopy ; thermal analysis ; vaccine development
    Language English
    Dates of publication 2018-0115
    Size p. 66-75.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 523-x
    ISSN 1096-0384 ; 0003-9861
    ISSN (online) 1096-0384
    ISSN 0003-9861
    DOI 10.1016/j.abb.2017.12.004
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