Molecular Simulations of Enzyme

Molecular modelling and simulation techniques have proved power-ful tools for helping to understand how proteins and other biomacro-molecules function at an atomic level. The study of enzyme reactions is a particularly challenging application of these methods because of the variety of processes of differing length and time scales that can contribute to catalysis. Among these are the bond-breaking and form-ing chemical steps, the diffusion of ligands into and out of the active site and conformational changes in the enzyme's structure. This contribution gives a synopsis of the range of molecular simula-tion techniques that are available for studying enzyme reactions with particular emphasis on methods designed for the investigation of the chemical catalytic steps. The capabilities and limitations of current approaches will be described and possible future developments dis-cussed. Special attention is given to the interface between molecular simulation and systems biology modelling and to how the STRENDA guidelines would need to be adapted to allow the reporting of enzyme data determined from simulation