title: Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling.
abstract: 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.
authors.affiliation: Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Vasilevskaya
authors.affiliation: Chemistry Department, Lomonosov Moscow State University, Moscow, Russia.|A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Maria G
authors.initials: MG
authors.lastname: Khrenova
authors.affiliation: Chemistry Department, Lomonosov Moscow State University, Moscow, Russia.|Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Nemukhin
authors.affiliation: Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
authors.forename: Walter
authors.initials: W
authors.lastname: Thiel
mesh_terms: D020134:Catalytic Domain; D006801:Humans; D020778:Matrix Metalloproteinase 2 / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D059748:Proteolysis; D011789:Quantum Theory
chemical_list: D009842:Oligopeptides; D020778:Matrix Metalloproteinase 2
keywords: matrix metalloproteinases; proteolysis reaction; quantum mechanics/molecular mechanics