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June 2016 August 2016 September 2016 October 2016 November 2016 December 2016 June 2017

June 2017

On the 7th of June our students successfully defended their diploma theses:
N. Anuchin, ‘Modeling conformational transitions in the reaction of enzymatic hydrolysis of guanosine triphosphate’,
D. Kapusta, ‘Solvation effects in enzymatic hydrolysis reactions’.
Congratulations to our graduate students!


December 2016

16-17th of December, Hyderabad, India: conference Intel HPC DevCon 2016 India
Invited report:
Quantum chemistry code optimization for Intel MIC architecture
Vladimir A. Mironov


November 2016

29th of November – 02th of December: National Supercomputing Forum
Supercomputer modeling of large molecular systems using the example of light-harvesting antenna of photosynthetic apparatus of purple bacterium.
Igor V. Polyakov, Alexander A. Moskovsky, Alexander V. Nemukhin

Deputy director of the laboratory PhD Maria G. Khrenova has successfully defended her Doctoral thesis and has been confered a degree of Doctor of Sciences, which is the highest academic degree in Russia.

Our PhD student Anna M. Kulakova became a winner of a young scientists competition within the framework of XXXIV Russian Symposium of Young Scientists on Chemical Kinetics, which took place on November 14-17.


October 2016

24-26th of October: XVI International Conference For Young Scientists “Biochemical physics” and school “Modern Problems Of Biochemical Physics”.

Our conference reports:

Isomorphism of human carboxylesterase-1
(Anna M. Kulakova)

Modeling absorbtion spectra of bacteriochlorophyll aggregates with modern methods of quantum chemistry
(Igor V. Polyakov)

Differences in structure of acetylcholinesterases of various species and their effect on the kinetics of binding with inhibitors.
(Dana A. Novichkova)

Role of aminoacid residues of the active site of Ras-GAP enzyme complex in electrostatic stabilization of transition state of the GTP hydrolysis reaction.
(Leonora A. Lychko)

Poster session:

Modeling the effect of solvent on catalytic activity of matrix metalloproteinase ММР-2
(Dmitry P. Kapusta)

Investiogation of the process of product release in the reaction of enzymatic hydrolysis of GTP by the Ras-GAP complex.
(Nikolay M. Anuchin)


September 2016

Following reports were presented on the XXVIII Symposium Modern chemical physics:

Quantum chemistry of flavin containing proteins

(Maria G. Khrenova, Alexander V. Nemukhin)

Modeling absorbtion of the light-harvesting antenna Thermochromatium tepidum

(Igor V. Polyakov, Maria G. Khrenova, Alexander V. Nemukhin)

August 11, 2016

Our paper “Analysis of proton wires in the enzyme active site suggests a mechanism of c-di-GMP hydrolysis by the EAL domain phosphodiesterases” by Bella Grigorenko, Marina Knyazeva and Alexander Nemukhin is published on-line  by Proteins: Structure, Function, and Bioinformatics in Wiley Online Library ( DOI: 10.1002/prot.25108.

We report for the first time a hydrolysis mechanism of the cyclic dimeric guanosine monophosphate (c-di-GMP) by the EAL domain phosphodiesterases as revealed by molecular simulations. A model system for the enzyme-substrate complex was prepared on the base of the crystal structure of the EAL domain from the BlrP1 protein complexed with c-di-GMP. The nucleophilic hydroxide generated from the bridging water molecule appeared in a favorable position for attack on the phosphorus atom of c-di-GMP. The most difficult task was to find a pathway for a proton transfer to the O3′ atom of c-di-GMP to promote the O3′-P bond cleavage. We show that the hydrogen bond network extended over the chain of water molecules in the enzyme active site and the Glu359 and Asp303 side chains provide the relevant proton wires. The suggested mechanism is consistent with the structural, mutagenesis and kinetic experimental studies on the EAL domain phosphodiesterases.


Graphical abstract.

More details in Research/Current Projects.

June 27, 2016

An interview with Dr. Vladimir A. Mironov entitled “Modern Quantum Chemistry Research Possible Because of Supercomputers, HPC Software” is published in Scientific Computing