Molecular modeling of lipase binding to a substrate-water interface.

Methods in molecular biology (Clifton, N.J.) (2012-03-20)
Christian C Gruber, Jürgen Pleiss
ABSTRACT

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.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Glyceryl tributyrate, ≥99%
Sigma-Aldrich
Glyceryl tributyrate, puriss., ≥98.5% (GC)