International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”

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molecular dynamics

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Genomics, transcriptomics, bioinformatics symposiumMolecular basis of phosphoryl guanidine oligonucleotides elongation by Taq DNA polymerase

Molecular basis of phosphoryl guanidine oligonucleotides elongation by Taq DNA polymerase

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Alexander Lomzov1
1ICBFM SB RAS, lomzov@niboch.nsc.ru

Phosphoryl guanidine oligonucleotides (PGO) become essential tools for basic research in molecular biology, molecular diagnostics and perspective for the therapeutics. To determine molecular basis of the observed effects of PG modification on elongation efficiency we performed molecular dynamics simulation of Taq polymerase / PGO complexes. The data obtained shows most important points for the analysis of protein / PGO interaction and gives useful information for development of improved PCR analysis.

Structural сomputational Biology sectioneasyAmber: a step away from inefficient ”static” approaches towards a deeper understanding of protein dynamics

easyAmber: a step away from inefficient ”static” approaches towards a deeper understanding of protein dynamics

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Dmitry Suplatov1, Yana Sharapova2, Vytas Е vedas3
1Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia, d.a.suplatov@belozersky.msu.ru
2Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia, sharapova@belozersky.msu.ru
3Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia, vytas@belozersky.msu.ru

Molecular dynamics (MD) can improve the success rate of in silico tools for drug discovery and protein engineering by accounting for protein structure flexibility/plasticity and predicting the time-dependent behavior of a molecular system, but requires specialized training and skills, what impedes practical use by many investigators. We have developed easyAmber – a comprehensive toolbox to automate the MD routines implemented in the Amber package, freely available at https://biokinet.belozersky.msu.ru/easyAmber.

Structural сomputational Biology sectionBeta-Bends As An Example Of Conformationally Predetermined Segments Of Protein. Conditions Of Stabilization Of The Structure And Role Of Context

Beta-Bends As An Example Of Conformationally Predetermined Segments Of Protein. Conditions Of Stabilization Of The Structure And Role Of Context

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/509.pdf”]
Anastasia A. Anashkina1, Vladimir O. Chekhov2, Ivan Yu. Torshin3, Leonid A. Uroshlev4, Natalia G. Esipova5, Vladimir G. Tumanyan6
1EIMB RAS, Moscow, Russia, nastya@eimb.ru
2EIMB RAS, Moscow, Russia, bock@eimb.ru
3FIC IU RAS, Moscow, Russia, tiy135@yahoo.com
4IGG RAS, Moscow, Russia, leoniduroshlev@gmail.com
5EIMB RAS, Moscow, Russia, nge@eimb.ru
6EIMB RAS, Moscow, Russia, tuman@eimb.ru

Conformations of the local protein structures is determined by the balance of their own energy characteristics and the context (flanking regions). The conformation of a given fragment becomes predetermined if the contribution of the context is clearly defined. Beta bends were chosen as the object of the study due to availability of formalised classification of this structure, small number of variables that determine the conformation of a segment, as well as the beta bends high prevalence in the three-dimensional structures of proteins. Using the PDB data, a complete cluster analysis of the conformationally predetermined beta-bend segments of the four main types was performed. Statistical data on the conformational parameters, amino acid composition and the amino acid sequences in beta-bends and their flanking regions were summarized. Factors have been established that stabilize the beta bend (additional hydrogen bonds between the residues involved in the bend) and the beta hairpin, flanking the bend (presence of a conformationally stable peptide). The existence of such stabilizing hydrogen bonds is confirmed by quantum chemical calculations of the energy of the fragment including bending. Stabilization of the hairpin neck is achieved by a conformationally stable hexapeptide in the conformation of the beta strand that is included in the structure, which is also confirmed by the method of denaturing molecular dynamics.