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.

Solvent water interactions within the active site of the membrane type I matrix metalloproteinase

“…The chosen QM/MM setup and protocol have been found to be adequate in a previous QM/MM study of the MMP-2 catalytic cycle. 13…”

“…Indeed the first product intermediate proposed is that of a Zn 2+ complexed with an asymmetric bidentate carboxylate ligand. Theoretical models predict that such a motif is stabilized by: 7,12,13 (1) a hydrogen bond between the a oxygen of the carboxylate and the transiently protonated Glu240 residue;…”

“…[9][10][11] A four-step catalytic mechanism of peptide hydrolysis has been proposed for MMPs. 7,[12][13][14] Upon peptide docking (Fig. 1a, ES, 1) the reaction starts with the nucleophilic attack of the carbonyl carbon of the scissile bond by the catalytic water molecule.…”

“…In addition, computational studies suggest that the loss of the bidentate C-terminus fragment from the Zn 2+ during (Fig. 1a, 4) is the rate limiting step with an estimated barrier of 20 kcal mol À1 ; 13 however this intermediate has yet to be characterized. The large barrier is derived from the negatively charged C-fragment coordinating the positive Zn 2+ ion in a bidentate fashion.…”

ONIOM and FMO‐EDA study of metabotropic glutamate receptor 1: Quantum insights into the allosteric binding site

“…QM/MM methods are especially suitable for studying large biological systems and, to date, have provided molecular‐level insights into many processes, such as the photosensitivity of visual pigments, enzyme catalysis, drug recognition by receptors, and cytotoxic activity mechanisms . It must be stressed that relatively few ONIOM studies have focused on one of the most important groups of biological targets, a family of G protein‐coupled receptors (GPCRs).…”