This article is cited in 13 scientific papers (total in 13 papers)
Communications
Discrimination of enzyme–substrate complexes by reactivity using the electron density analysis: peptide bond hydrolysis by the matrix metalloproteinase-2
Abstract:
The results of quantum mechanics/molecular mechanics calculations of electron density changes upon oligopeptide hydrolysis by the matrix metalloproteinase-2 are utilized to discriminate between reactive and non-reactive enzyme–substrate complexes. Electron density depletion regions on the carbonyl carbon atom attacked by a catalytic water molecule are found on the 2D maps of electron density Laplacian in the reactive complexes. Also, the computed Fukui function quantitatively describes reactivity of the nucleophilic and electrophilic sites.
Keywords:
metalloenzymes, matrix metalloproteinase-2, QM/MM, Laplacian of electron density, reactivity, nucleophilic addition.
Citation:
M. G. Khrenova, A. V. Nemukhin, V. G. Tsirelson, “Discrimination of enzyme–substrate complexes by reactivity using the electron density analysis: peptide bond hydrolysis by the matrix metalloproteinase-2”, Mendeleev Commun., 30:5 (2020), 583–585
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This publication is cited in the following 13 articles:
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O. S. Borodina, A. E. Masunov, E. V. Bartashevich, “Evolution of Electronic Properties along the Path from a Covalent to a Tetrel Bond in the Synthesis of Tetraphenyl Substituted Compounds”, Moscow Univ. Chem. Bull., 79:4 (2024), 268
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I. V. Ananyev, L. L. Fershtat, “Why pay more? QTAIM descriptors of non-covalent interactions in S22 from promolecular electron density”, Mendeleev Commun., 33:6 (2023), 806–808
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A.M. Kulakova, M.G. Khrenova, A.V. Nemukhin, “Molecular mechanism of chromogenic substrate hydrolysis in the active site of human carboxylesterase-1”, BIOMED KHIM, 67:3 (2021), 300
Maria G. Khrenova, Anna M. Kulakova, Alexander V. Nemukhin, “Light-Induced Change of Arginine Conformation Modulates the Rate of Adenosine Triphosphate to Cyclic Adenosine Monophosphate Conversion in the Optogenetic System Containing Photoactivated Adenylyl Cyclase”, J. Chem. Inf. Model., 61:3 (2021), 1215
A. V. Nelyubin, I. N. Klyukin, A. S. Novikov, A. P. Zhdanov, M. S. Grigoriev, K. Yu. Zhizhin, N. T. Kuznetsov, “Nucleophilic addition of amino acid esters to nitrilium derivatives of closo-decaborate anion”, Mendeleev Commun., 31:2 (2021), 201–203
I. Yu. Titov, V. S. Stroylov, P. V. Rusina, I. Svitanko, “Preliminary modelling as the first stage of targeted organic synthesis”, Russian Chem. Reviews, 90:7 (2021), 831–867