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M. G. Khrenova, S. A. Zavyalova, E. Y. Bezsudnova

Molecular mechanism of stereospecificity of transaminase from Desulfohalobium retbaense to D-leucine revealed by molecular dynamics modeling


The paper presents the results of a molecular dynamics study of the molecular mechanism of experimentally observed specificity of transaminase from Desulfohalobium retbaense (Dret) to the D-isomer of leucine. A full-atom 3D model of Dret is constructed based on the primary sequence and crystal structures of related enzymes. Analysis of molecular dynamics trajectories demonstrated that the α-COO-group of D-leucine forms stable hydrogen bonds with the Arg54* in the enzyme-substrate complex, that contributes to the proper orientation of the substrate in the active site. The formation of such complex with the L-isomer of leucine leads to the destruction of these hydrogen bonds and disruption of the structure of the entire active site.
Key words: molecular modeling, molecular dynamics, stereospecificity, D-amino-acid transaminase.
Moscow University Chemistry Bulletin.
2020, Vol. 61, No. 3, P. 208

Copyright (C) Chemistry Dept., Moscow State University, 2002
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