Quantum chemical modelling in the research of molecular mechanisms of enzymatic catalysis

The advantages and disadvantages of various methods of theoretical modelling of mechanisms of enzymatic reactions based on quantum theory are discussed. Molecular mechanical, quantum mechanical and hybrid approaches are considered. Detailed analysis is performed in relation to a superfamily of enzymes, serine hydrolases, which include cholinesterases playing a crucial role in higher nervous activity. As another example, the results of modelling of enzymatic hydrolysis of nucleoside phosphates are considered. The bibliography includes 177 references.

[1]  Maria G. Khrenova,et al.  Minimum energy reaction profiles for the hydrolysis reaction of the cyclic guanosine monophosphate in water: Comparison of the results of two QM/MM approaches , 2012 .

[2]  C. Schofield,et al.  Structural studies on human 2-oxoglutarate dependent oxygenases. , 2010, Current opinion in structural biology.

[3]  A. Nemukhin,et al.  Correlation between the substrate structure and the rate of acetylcholinesterase hydrolysis modeled with the combined quantum mechanical/molecular mechanical studies. , 2010, Chemico-biological interactions.

[4]  Hua Zhao,et al.  Myosin-catalyzed ATP hydrolysis elucidated by 31P NMR kinetic studies and 1H PFG-diffusion measurements , 2009, Analytical and bioanalytical chemistry.

[5]  Evgeny Epifanovsky,et al.  Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore: 2. Cis-Trans Isomerization in Water. , 2009, Journal of chemical theory and computation.

[6]  A. Nemukhin,et al.  Quantum chemical justification of the specificity of enzyme catalysis: Correlations between the rate of enzyme catalysis by acetylcholinesterase and substrate structure , 2009 .

[7]  J. Collins,et al.  Mechanism of the chemical step for the guanosine triphosphate (GTP) hydrolysis catalyzed by elongation factor Tu. , 2008, Biochimica et biophysica acta.

[8]  A. Nemukhin,et al.  Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling , 2008, Journal of molecular modeling.

[9]  B. Grigorenko,et al.  Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras‐GAP proteins as rationalized by ab initio QM/MM simulations , 2006, Proteins.

[10]  R. Cachau,et al.  On the nature of oxoiron (IV) intermediate in dioxygen activation by non-heme enzymes , 2006 .

[11]  R. Cachau,et al.  QM/MM modeling the Ras–GAP catalyzed hydrolysis of guanosine triphosphate , 2005, Proteins.

[12]  R. Cachau,et al.  Quantum chemical modeling of the GTP hydrolysis by the RAS-GAP protein complex. , 2004, Biochimica et biophysica acta.

[13]  B. Grigorenko,et al.  Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method , 2004 .

[14]  Vytas K Svedas,et al.  Quantitative characterization of the nucleophile reactivity in penicillin acylase-catalyzed acyl transfer reactions. , 2002, Biochimica et biophysica acta.

[15]  N. Okimoto,et al.  Theoretical studies of the ATP hydrolysis mechanism of myosin. , 2001, Biophysical journal.

[16]  F. Jensen Introduction to Computational Chemistry , 1998 .

[17]  A. Rappé,et al.  Molecular Mechanics Across Chemistry , 1997 .

[18]  B. Grigorenko,et al.  Modeling dioxygen binding to the non‐heme iron‐containing enzymes , 2006 .

[19]  Kwang S. Kim,et al.  Theory and applications of computational chemistry : the first forty years , 2005 .

[20]  P. Wormer,et al.  Theory and Applications of Computational Chemistry The First Forty Years , 2005 .

[21]  A. Shestakov,et al.  A density functional theory study of the preparation and decomposition of the complex [(AuPH3)6(N2)]2+ , 2004 .

[22]  Kohei Oda,et al.  Structural and enzymatic properties of the sedolisin family of serine-carboxyl peptidases. , 2003, Acta biochimica Polonica.