nov. 21

Dr Sergey D. Varfolomeev “Supercomputer technologies in biocatalysis – new level of view on molecular mechanisms and applications”

Kolmapäeval, 22. novembril 2017 algusega 10:15 toimub TÜ keemia instituudis (Ravila 14a, Chemicum) aud 1020 loeng-seminar teemal  “Supercomputer technologies in biocatalysis – new level of view on molecular mechanisms and applications”.

Esineb dr Sergey D. Varfolomeev, N.M. Emanuel Institute for Biochemical Physics of RAS, M.V. Lomonossov Moscow State University, Russia.

Diskussioon ja konsultatsioonid FMTDK doktorantide ja juhendajatega 20.11-24.11.17 orgaanilise keemia õppetoolis.

Info: dr Lilli Paama lilli.paama@ut.ee, prof Jaak Järv jaak.jarv@ut.ee

During the late decade, due to the efficient development of supercomputer computational technologies, the essential progress has been reached in the area of modeling the molecular-dynamic processes, including the study of elementary processes in catalysis.
A principally important progress has been obtained in the research of molecular mechanisms of catalysis by enzymes. The methods of molecular mechanics, molecular dynamics, quantum chemistry, turned to be highly prolific in deciphing the elementary processes in the catalytic cycle of protein catalysis. The following problems are analysed in the report:
– Current status of molecular mechanics and molecular dynamics of protein molecules.
– Information of entropy approaches to the analysis of the structure of enzymes with identification of the members of the catalytic process and of the critical positions in the protein structure ensuring the formation of functional active sites,
– Molecular-mechanical approaches to the search for effective interaction ligand-active center, the development and use of dockingprocedures,
– Molecular-dynamic methods of analysis of the interaction of ligand-active center and protein-protein interactions,
– Combination methods of quantum chemistry and molecular mechanics (QM / MM approach) to describe the elementary stages and the complete catalytic cycle,
-Modeling of the complete catalytic cycle, the search for the extrema on the surface of the potential and free energy; identification and visualization of structures of all intermediate compounds and transition states, the assessment of the rate constants of all elementary steps of the catalytic cycle,
– Allosteric interactions in regulating the catalytic activity,
– The problem of the molecular polymorphism of human proteins with the analysis of the influence of the substitution of individual amino acids in the enzyme structure to its catalytic activity.
General approaches are analyzed to study the examples of specific enzymatic reactions, including serine proteases, acetylcholine- and buterylcholineesterases, N-acetylaspartase of human brain. The authors likewise discussed in the report the supercomputing applications in molecular medicine and designing drugs.