Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling

Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling

© 2015 Wiley Periodicals, Inc.

Bibliographische Detailangaben
Veröffentlicht in:Journal of computational chemistry. - 1984. - 36(2015), 21 vom: 05. Aug., Seite 1621-30
1. Verfasser: Vasilevskaya, Tatiana (VerfasserIn)
Weitere Verfasser: Khrenova, Maria G, Nemukhin, Alexander V, Thiel, Walter
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2015
Zugriff auf das übergeordnete Werk:Journal of computational chemistry
Schlagworte:Journal Article Research Support, Non-U.S. Gov't matrix metalloproteinases proteolysis reaction quantum mechanics/molecular mechanics Oligopeptides Matrix Metalloproteinase 2 EC 3.4.24.24
Beschreibung
Zusammenfassung:© 2015 Wiley Periodicals, Inc.
The mechanism of enzymatic peptide hydrolysis in matrix metalloproteinase-2 (MMP-2) was studied at atomic resolution through quantum mechanics/molecular mechanics (QM/MM) simulations. An all-atom three-dimensional molecular model was constructed on the basis of a crystal structure from the Protein Data Bank (ID: 1QIB), and the oligopeptide Ace-Gln-Gly∼Ile-Ala-Gly-Nme was considered as the substrate. Two QM/MM software packages and several computational protocols were employed to calculate QM/MM energy profiles for a four-step mechanism involving an initial nucleophilic attack followed by hydrogen bond rearrangement, proton transfer, and C-N bond cleavage. These QM/MM calculations consistently yield rather low overall barriers for the chemical steps, in the range of 5-10 kcal/mol, for diverse QM treatments (PBE0, B3LYP, and BB1K density functionals as well as local coupled cluster treatments) and two MM force fields (CHARMM and AMBER). It, thus, seems likely that product release is the rate-limiting step in MMP-2 catalysis. This is supported by an exploration of various release channels through QM/MM reaction path calculations and steered molecular dynamics simulations
Beschreibung:Date Completed 11.01.2016
Date Revised 16.07.2015
published: Print-Electronic
Citation Status MEDLINE
ISSN:1096-987X
DOI:10.1002/jcc.23977