Molecular Modeling of Lipase Binding to a SubstrateWater Interface

Interactions of lipases with hydrophobic substrate–water interfaces are of great interest to design improved lipase variants and engineer reaction conditions. This chapter describes the necessary steps to carry out molecular dynamics simulations of Candida antarctica lipase B at tributyrin–water interface using the GROMACS simulation software. Special attention is drawn to the preparation of the protein and the substrate–water interface and to the analysis of the obtained trajectory.