Molecular modeling of lipase binding to a substrate-water interface

Christian C Gruber; Jürgen Pleiss

doi:10.1007/978-1-61779-600-5_19

Molecular modeling of lipase binding to a substrate-water interface

Methods Mol Biol. 2012:861:313-27. doi: 10.1007/978-1-61779-600-5_19.

Authors

Christian C Gruber¹, Jürgen Pleiss

Affiliation

¹ ACIB Austrian Centre of Industrial Biotechnology, c/o Centre of Molecular Biosciences, University of Graz, Graz, Austria.

PMID: 22426727
DOI: 10.1007/978-1-61779-600-5_19

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Binding Sites
Candida / chemistry*
Candida / enzymology
Fungal Proteins / chemistry*
Hydrophobic and Hydrophilic Interactions
Lipase / chemistry*
Molecular Dynamics Simulation*
Protein Binding
Protein Conformation
Software
Solvents / chemistry
Substrate Specificity
Surface Properties
Triglycerides / chemistry*
Water / chemistry

Substances

Fungal Proteins
Solvents
Triglycerides
Water
Lipase
lipase B, Candida antarctica
tributyrin