Reaction mechanism of matrix metalloproteinases with a catalytically active zinc ion studied by the QM(DFTB)/MM simulations

Abstract

The simulations of oligopeptide hydrolysis by the matrix metalloproteinase MMP-2 using the density functional tight binding (DFTB) quantum chemistry method and the QM/MM methodology partly reproduce the qualitative features of the reaction mechanism but show deviations of the computed patterns from those obtained with the conventional DFT-based approaches.