Loading [MathJax]/jax/output/SVG/config.js
Mendeleev Communications
RUS  ENG    JOURNALS   PEOPLE   ORGANISATIONS   CONFERENCES   SEMINARS   VIDEO LIBRARY   PACKAGE AMSBIB  
General information
Latest issue
Archive

Search papers
Search references

RSS
Latest issue
Current issues
Archive issues
What is RSS



Mendeleev Commun.:
Year:
Volume:
Issue:
Page:
Find






Personal entry:
Login:
Password:
Save password
Enter
Forgotten password?
Register


Mendeleev Communications, 2020, Volume 30, Issue 5, Pages 583–585
DOI: https://doi.org/10.1016/j.mencom.2020.09.010
(Mi mendc1259)
 

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

M. G. Khrenovaab, A. V. Nemukhinbc, V. G. Tsirelsond

a Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, Russian Federation
b Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russian Federation
c N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russian Federation
d D.Mendeleev University of Chemical Technology of Russia, Moscow, Russian Federation
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.
Document Type: Article
Language: English
Supplementary materials:
Supplementary_data_1.pdf (251.6 Kb)


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
Linking options:
  • https://www.mathnet.ru/eng/mendc1259
  • https://www.mathnet.ru/eng/mendc/v30/i5/p583
  • This publication is cited in the following 13 articles:
    1. OLGA S. BORODINA, ARTYOM E. MASUNOV, EKATERINA V. BARTASHEVICH, “EVOLUTION OF ELECTRONIC PROPERTIES ALONG THE PATH FROM COVALENT TO TETREL BOND IN THE SYNTHESIS OF TETRAPHENYL SUBSTITUTED COMPOUNDS”, Lomonosov chemistry journal, 65:№4, 2024 (2024), 319  crossref
    2. Tatiana I. Mulashkina, Anna M. Kulakova, Maria G. Khrenova, “Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study”, J. Chem. Inf. Model., 64:18 (2024), 7035  crossref
    3. 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  crossref
    4. S. D. Varfolomeev, V. Švedas, E. N. Efremenko, A. M. Egorov, M. G. Khrenova, V. I. Tishkov, D. L. Atroshenko, A. A. Pometun, S. S. Savin, N. N. Ugarova, G. Yu. Lomakina, I. V. Gachok, I. V. Lyagin, V. I. Muronetz, A. P. Sinitsyn, O. A. Sinitsyna, A. M. Rojhkova, G. F. Makhaeva, S. O. Bachurin, O. I. Lavrik, D. O. Zharkov, A. V. Yudkina, O. M. Panasenko, A. A. Baykov, P. Masson, T. N. Pashirova, Z. M. Shaihutdinova, E. V. Popova, V. E. Tikhomirova, O. A. Kost, E. V. Kudryashova, N. V. Dobryakova, N. L. Klyachko, M. M. Veselov, A. V. Lopukhov, I. M. Le-Deygen, A. D. Usvaliev, I. V. Chudosai, N. L. Eremeev, M. E. Zvereva, M. Yu. Rubtsova, M. M. Ulyashova, G. V. Presnova, L. V. Sigolaeva, D. V. Pergushov, I. N. Kurochkin, E. G. Evtushenko, I. A. Boginskaya, Yu. Yu. Zvyagina, E. A. Slipchenko, O. V. Kryukova, M. V. Sedova, I. A. Ryzhikov, V. V. Shumyantseva, P. I. Koroleva, T. V. Bulko, L. E. Agafonova, R. A. Masamrekh, T. A. Filippova, A. V. Kuzikov, A. P. Savitsky, M. O. Shleeva, I. , “Biocatalysis: modern problems and applications”, Russian Chem. Reviews, 93:12 (2024), 1–55  mathnet  mathnet  crossref
    5. M. G. Khrenova, T. I. Mulashkina, R. A. Stepanyuk, A. V. Nemukhin, “Modeling of enzyme-catalyzed P–O bond cleavage in the adenosine triphosphate molecule”, Mendeleev Commun., 34:1 (2024), 1–7  mathnet  crossref
    6. 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  mathnet  crossref
    7. Alexandra V. Krivitskaya, Maria G. Khrenova, “Boronic Acids as Prospective Inhibitors of Metallo-β-Lactamases: Efficient Chemical Reaction in the Enzymatic Active Site Revealed by Molecular Modeling”, Molecules, 26:7 (2021), 2026  crossref
    8. Alexandra V. Krivitskaya, Maria G. Khrenova, Alexander V. Nemukhin, “Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase”, Molecules, 26:20 (2021), 6280  crossref
    9. Maria G. Khrenova, Anastasia Yu. Soloveva, Larisa A. Varfolomeeva, Tamara V. Tikhonova, Vladimir O. Popov, “The O to S substitution in urea brings inhibition activity against thiocyanate dehydrogenase”, Mendeleev Communications, 31:3 (2021), 373  crossref
    10. 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  crossref
    11. 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  crossref
    12. 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  mathnet  crossref
    13. 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  mathnet  mathnet  crossref  isi  scopus
    Citing articles in Google Scholar: Russian citations, English citations
    Related articles in Google Scholar: Russian articles, English articles
    Mendeleev Communications
    Statistics & downloads:
    Abstract page:39
    Full-text PDF :7
     
      Contact us:
    math-net2025_04@mi-ras.ru
     Terms of Use  Registration to the website  Logotypes © Steklov Mathematical Institute RAS, 2025