Publications of Professor Barkovsky's Reseach Group

1. Khrustalev, V. V. An in-silico study of alphaherpesviruses ICP0 genes: Positive selection or strong mutational GC-pressure? / V. V. Khrustalev, E. V. Barkovsky // IUBMB Life. – 2008. – Vol.60. – Issue 7. – P. 456-460.

2. Khrustalev, V. V. Mutational Pressure in Genomes of Human Alpha-Herpesviruses / V. V. Khrustalev, E. V. Barkovsky // Molecular Genetics, Microbiology and Virology. – 2008. – Vol.23. – No.2. – P. 94-100.

3. Barkovsky, E. V. Inverse Correlation between the GC Content of Bacterial Genomes and Their Level of Preterminal Codon Usage / E. V. Barkovsky, V. V. Khrustalev // Molecular Genetics, Microbiology and Virology. – 2009. – Vol.24. – No.1. – P. 17-23.

4. Khrustalev, V. V. Can mutational GC-Pressure create new linear B-cell epitopes in Herpes Simplex virus type 1 glycoprotein B? / V. V. Khrustalev // Immunological Investigations. – 2009. – Vol.38. – Issue 7. – P. 613-623.

5. Khrustalev, V. V. HIV1 V3 loop hypermutability is enhanced by the guanine usage bias in the part of env gene coding for it / V. V. Khrustalev // In Silico Biology. – 2009. – Vol.9. – Number 4. – P. 255-269.

6. Khrustalev, V. V. Main Pathways of Proteome Simplification in Alphaherpesviruses Under the Influence of the Strong Mutational GC-pressure / V. V. Khrustalev, E. V. Barkovsky // Journal of Proteomics and Bioinformatics – 2009. – Vol. 2. – Issue 2. – P. 88-96.

7. Khrustalev, V. V. Mutational pressure is a cause of inter- and intragenomic differences in GC-content of simplex and varicello viruses / V. V. Khrustalev, E. V. Barkovsky // Computational Biology and Chemistry. – 2009. – Vol.33. – Issue 4. – P. 295-302.

8. Khrustalev, V. V. Mutational pressure makes HIV1 gp120 linear B-cell epitopes shorter and may lead to their disappearance / V. V. Khrustalev // Molecular Immunology. – 2010. – Vol.47. – Issues 7-8. – P. 1635-1639.

9. Khrustalev, V. V. Study of completed archaeal genomes and proteomes: hypothesis of strong mutational AT pressure existed in their common predecessor / V. V. Khrustalev, E. V. Barkovsky // Genomics, Proteomics and Bioinformatics. – 2010. – Vol.8. – Issue 1. – P. 22-32.

10. Khrustalev, V. V. The level of cytosine is usually much higher than the level of guanine in two-fold degenerated sites from third codon positions of genes from Simplex- and Varicelloviruses with G+C higher than 50% / V. V. Khrustalev, E. V. Barkovsky // Journal of Theoretical Biology. – 2010. – Vol.266. – Issue 1. – P. 88-98.

11. Khrustalev, V. V. The probability of nonsense mutation caused by replication-associated mutational pressure is much higher for bacterial genes from lagging than from leading strands / V. V. Khrustalev, E. V. Barkovsky // Genomics. – 2010. – Vol.96. – Issue 3. – P. 173-180.

12. Khrustalev, V. V. Levels of HIV1 gp120 3D B-cell epitopes mutability and variability: searching for possible vaccine epitopes / V. V. Khrustalev // Immunological Investigations. – 2010. – Vol.39. – Issue 6. – P. 551-569.

13. Khrustalev, V. V. Unusual nucleotide content of Rubella virus genome as a consequence of biased RNA-editing: comparison with Alphaviruses / V. V. Khrustalev, E. V. Barkovsky // International Journal of Bioinformatics Research and Applications – 2011. – Vol.7. – Issue 1. – P. 82-100.

14. Khrustalev, V. V. Percent of highly immunogenic amino acid residues forming B-cell epitopes is higher in homologous proteins encoded by GC-rich genes / V. V. Khrustalev, E. V. Barkovsky // Journal of Theoretical Biology – 2011. – Vol.282. – P. 71-79.

15. Khrustalev, V. V. “Protoisochores” in certain archaeal species are formed by replication-associated mutational pressure / V. V. Khrustalev, E. V. Barkovsky // Biochimie. – 2011. – Vol.93. – Issue 2. – P. 160-167.

16. Khrustalev, V. V. A method for estimation of immunogenic determinants mutability: case studies of HIV1 gp120 and diphtheria toxin / V. V. Khrustalev, E. V. Barkovsky, A. E. Vasilevskaya, S. M. Skripko, V. L. Kolodkina, G. M. Ignatyev, A. P. Semizon // Journal of Integrated OMICS. – 2011. – Vol.1. – P. 236-252.

17. Khrustalev V. V. A blueprint for a mutationist theory of replicative strand asymmetries formation / V. V. Khrustalev, E. V. Barkovsky // Current Genomics – 2012. – Vol.13. – Issue 1. – P. 55-64.

18. Khrustalev V. V. In silico directed mutagenesis using software for glycosylation sites prediction as a new step in antigen design / V. V. Khrustalev, E. V. Barkovsky // Journal of Integrated OMICS. – 2012. – Vol.2. – P. 31-36.

19. Khrustalev V. V. Low rates of synonymous mutations in sequences of Mycobacterium tuberculosis GyrA and KatG genes / V. V. Khrustalev, M. Arjomandzandegan, E. V. Barkovsky, L. P. Titov // Tuberculosis. – 2012. – Vol.92. – P. 333-344.

20. Khrustalev V. V. Stabilization of secondary structure elements by specific combinations of hydrophilic and hydrophobic amino acid residues is more important for proteins encoded by GC-poor genes / V. V. Khrustalev, E. V. Barkovsky // Biochimie – 2012. – Vol.94. – Issue 12. – P. 2706-2715.

21. The influence of ethanol on pyruvate kinases activity in vivo, in vitro, in silico / S. V. Lelevich, V. V. Khrustalev, E. V. Barkovsky, T. A. Shedogubova // American Journal of Medical and Biological Research. – 2013. – Vol.1. – No.1. – P. 6-15.

22. Khrustalev V. V. Random coil structures in bacterial proteins. Relationships of their amino acid compositions to flanking structures and corresponding genic base compositions / V. V. Khrustalev, T. A. Khrustaleva, E. V. Barkovsky // Biochimie – 2013. – Vol.95. – Issue 9. – P. 1745 -1754.

23. Short repeats in the spa gene of Staphylococcus aureus are prone to nonsense mutations: stop codons can be found in strains isolated from patients with generalized infection / V. V. Khrustalev, E. Ghaznavi-Rad, V. Neela, M. Shamsudin, A. Amouzandeh-Nobaveh, E. V. Barkovsky // Research in Microbiology. – 2013. – Vol.164. – Issue 9. – P. 913 – 922.

24. Khrustalev V. V. Zebra Finch glucokinase containing two homologous halves is an in silico chimera / V. V. Khrustalev, S. V. Lelevich, E. V. Barkovsky // ISRN Computational Biology. – 2013. – Vol.2013. – N. 790240. – P. 1 – 6.

25. Lelevich S. V. Inhibition of rat muscle and liver phosphofructokinases by high doses of ethanol / S. V. Lelevich, V. V. Khrustalev, E. V. Barkovsky // Biochemistry Research International. – 2013. – Vol.2013. – N. 495135. – P. 1 – 8.

26. Intragenic isochores (intrachores) in the platelet phosphofructokinase gene of Passeriform birds / V. V. Khrustalev, E. V. Barkovsky, T. A. Khrustaleva, S. V. Lelevich // Gene. – 2014. – Vol.546. – Issue 1. – P. 16 – 24.

27. Khrustalev V. V. The influence of flanking secondary structures on amino acid content and typical lengths of 3/10 helices / V. V. Khrustalev, E. V. Barkovsky, T. A. Khrustaleva // International Journal of Proteomics. – 2014. – Vol. 2014. – N. 360230. – P. 1 – 13.

28. Khrustaleva T. A. Secondary structure preferences of Mn2+ binding sites in bacterial proteins / T. A. Khrustaleva // Advances in Bioinformatics. – 2014. – Vol.1. – №. 1. – P. 1-14.

29. Khrustaleva T. A. Structural and antigenic features of the synthetic SF23 peptide corresponding to the receptor binding fragment of diphtheria toxin / T. A. Khrustaleva, V. V. Khrustalev, E. V. Barkovsky, V. L. Kolodkina, A. A. Astapov // Molecular Immunology. – 2015. – Vol. 63. – iss. 2. – P. 235 – 244.

30. Khrustalev V.V. Opposite nucleotide usage biases in different parts of the Corynebacterium diphtheriae spaC gene / V. V. Khrustalev, E. V. Barkovsky, V. L. Kolodkina, T. A. Khrustaleva // International Journal of Bioinformatics Research and Applications – 2015. – Vol.11. – Issue 4. – P. 347-365.

31. Khrustalev V.V. Local mutational pressures in genomes of Zaire ebolavirus and Marburg virus / V. V. Khrustalev, E. V. Barkovsky, V. T. A. Khrustaleva // Advances in Bioinformatics – 2015. – Vol.2015. – N678587 – P. 1-14.

32. Khrustalev V.V. Magnesium and manganese binding sites on proteins have the same predominant motif of secondary structure / V. V. Khrustalev, E. V. Barkovsky, V. T. A. Khrustaleva // Journal of Theoretical Biology – 2016. – Vol. 395. – P. 174-185.

33. Khrustalev V.V. The part of a long beta hairpin from the scrapie form of the human prion protein is reconstructed in the synthetic CC36 protein / V. V. Khrustalev, T. A. Khrustaleva, K. Szpotkowski, V. V. Poboinev, K. Y. Kakhanouskaya // Proteins: Structure, Function, and Bioinformatics. – 2016. – Vol. 84. - P. 1462-1479.

34. Khrustalev V. V. In silico study of morphine-like effects of ethanol intake: docking of acetaldehyde conjugates with monoamines to the mu-opioid receptor / V. V. Khrustalev, S. V. Lelevich, T. A. Khrustaleva, M. V. Skorobogatiy, E. A. Demenchuck // MOJ Proteomics and Bioinformatics. – 2016. – Vol. 4. – N. 00124. – P. 1 – 10.

35. Khrustalev V.V. Mutational pressure in Zika virus: Local ADAR-editing areas associated with pauses in translation and replication / V. V. Khrustalev, T. A. Khrustaleva, N. Sharma, R. Giri // Frontiers in Cellular and Molecular Microbiology. – 2017. – Vol.7. – N.44 –P. 1 – 17.

36. Khrustalev V.V. Transcription-associated mutational pressure in the Parvovirus B19 genome: Reactivated genomes contribute to the variability of viral populations / V. V. Khrustalev, M. A. Ermalovich, J. M. Hubschen, T. A. Khrustaleva // Journal of Theoretical Biology. – 2017. – Vol.435. – P. 199 – 207.

37. Khrustalev V.V. Ethanol binding sites on proteins / V. V. Khrustalev, T. A. Khrustaleva, S. V. Lelevich // Journal of Molecular Graphics and Modelling. – 2017. – Vol.78. – P. 187 – 194.

38. Khrustalev V.V. The alpha helix 1 from the first conserved region of HIV1 gp120 is reconstructed in the short NQ21 peptide / V. V. Khrustalev, T. A. Khrustaleva, E. Y. Kahanouskaya, Y. A. Rudnichenko, H. V. Bandarenka, A. M. Arutyunyan, K. V. Girel, N. V. Khinevich, A. L. Ksenofontov, L. V. Kordyukova // Archives of Biochemistry and Biophysics. – 2018. – Vol. 638. – P. 66 – 75.

39. Khrustalev V.V. Amino acid content of beta strands and alpha helices depends on their flanking secondary structure elements / V. V. Khrustalev, T. A. Khrustaleva, V. V. Poboinev // Biosystems. – 2018. – 168. – P. 45 - 54.

40. Khrustalev V. V. Selection and structural analysis of the NY25 peptide – A vaccine candidate from hemagglutinin of swine-origin Influenza H1N1 / V. V. Khrustalev, T. A. Khrustaleva, L. V. Kordyukova // Microbial Pathogenesis. – 2018. – 125. – P. 72 - 83.

41. Khrustalev V. V. Mutational pressure and natural selection in epidermal growth factor receptor gene during germline and somatic mutagenesis in cancer cells / V. V. Khrustalev, T. A. Khrustaleva, V. V. Poboinev, K. V. Yurchenko // Mutation Research. – 2019. – 815. – P. 1 - 9.

42. Khrustalev V. V. Microenvironment of tryptophan residues in proteins of four structural classes: applications for fluorescence and circular dichroism spectroscopy / V. V. Khrustalev, V. V. Poboinev, A. N. Stojarov, T. A. Khrustaleva // European Biophysics Journal. – 2019. – 48. – P. 523 - 537.

43. Khrustalev V. V. Cobalt(ii) cation binding by proteins / V. V. Khrustalev, T. A. Khrustaleva, V. V. Poboinev, C. I. Karchevskaya, E. A. Shablovskaya, T. G. Terechova // Metallomics. - 2019. - 11. - P. 1743 - 1752.

44. Khrustalev V. V. The history of mutational pressure changes during the evolution of adeno-associated viruses: A message to gene therapy and DNA-vaccine vectors designers / V. V. Khrustalev, T. A. Khrustaleva, A. N. Stojarov, N. Sharma, B. Bhaskar, R. Giri // Infection, Genetics and Evolution. - 2020. - 77. - N.104100.

45. Khrustalev V. V. Random coils of proteins situated between a beta strand and an alpha helix demonstrate decreased solvent accessibility / V. V. Khrustalev // The Protein Journal. - 2020. - 39. - P. 308 – 317.

46. Khrustalev V. V. Translation-associated mutational U-pressure in the first ORF of SARS-CoV-2 and other coronaviruses / V. V. Khrustalev, R. Giri, T. A. Khrustaleva, S. K. Kapuganti, A. N. Stojarov, V. V. Poboinev // Frontiers in Microbiology. - 2020. - 11. - 559165.

47. Khrustalev V. V. The PentaFOLD 3.0 algorithm for the selection of stable elements of secondary structure to be included in vaccine peptides / V. V. Khrustalev // Protein and Peptide Letters. – 2021. – Vol. 28. – no. 5. – P. 573 – 588.

48. Khrustalev V. V. Spectra of tryptophan fluorescence are the result of co-existence of certain most abundant stabilized excited state and certain most abundant destabilized excited state / V. V. Khrustalev, T. A. Khrustaleva, V. V. Poboinev, A. N. Stojarov, L. V. Kordyukova, A. A. Akunevich // Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. – 2021. – Vol. 257. – N. 119784. – P. 1 – 13.

49. Khrustalev V. V. The cytoplasmic tail of influenza A/H1N1 virus hemagglutinin is β-structural / V. V. Khrustalev, L. V. Kordyukova, A. M. Arutyunyan, V. V. Poboinev, T. A. Khrustaleva, A. N. Stojarov, L. A. Baratova, A. S. Sapon, V. G. Lugin // Journal of Biomolecular Structure and Dynamics. – 2022. – Vol. 40. – P. 4642-4661.

50. Poboinev V. V. The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins / V. V. Poboinev, V. V. Khrustalev, T. A. Khrustaleva, T. E. Kasko, V. D. Popkov // Amino Acids. – 2022. – Vol. 54. – P. 1155-1171.

51. Akunevich A. A. Equilibrium between dimeric and monomeric forms of human epidermal growth factor is shifted towards dimers in a solution / A. A. Akunevich, V. V. Khrustalev, T. A. Khrustaleva, V. V. Poboinev, N. V. Shalygo, A. N. Stojarov, A. M. Arutyunyan, L. V. Kordyukova, Y. G. Sapon // The Protein Journal. – 2022. – Vol. 41. – P. 245-259.