title: Molecular modeling of lipase binding to a substrate-water interface.
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.
authors.affiliation: ACIB Austrian Centre of Industrial Biotechnology, c/o Centre of Molecular Biosciences, University of Graz, Graz, Austria.
authors.forename: Christian C
authors.initials: CC
authors.lastname: Gruber
authors.forename: Jürgen
authors.initials: J
authors.lastname: Pleiss
mesh_terms: D001665:Binding Sites; D002175:Candida / Q000737:chemistry* / Q000201:enzymology; D005656:Fungal Proteins / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D008049:Lipase / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D012984:Software; D012997:Solvents / Q000737:chemistry; D013379:Substrate Specificity; D013499:Surface Properties; D014280:Triglycerides / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D005656:Fungal Proteins; D012997:Solvents; D014280:Triglycerides; D014867:Water; D008049:Lipase; C431349:lipase B, Candida antarctica; C005830:tributyrin