Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking.

ABSTRACT:

Background

Previously, ways to adapt docking programs that were developed for modelling inhibitor-receptor interaction have been explored. Two main issues were discussed. First, when trying to model catalysis a reaction intermediate of the substrate is expected to provide more valid information than the ground state of the substrate. Second, the incorporation of protein flexibility is essential for reliable predictions.

Results

Here we present a predictive and robust method to model substrate specificity and enantioselectivity of lipases and esterases that uses reaction intermediates and incorporates protein flexibility. Substrate-imprinted docking starts with covalent docking of reaction intermediates, followed by geometry optimisation of the resulting enzyme-substrate comp

SUBMITTER: Juhl PB 

PROVIDER: S-EPMC2699341 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature