Calculation of substrate binding affinities for a bacterial GH78 rhamnosidase through molecular dynamics simulations.

ABSTRACT: Ram2 from Pediococcus acidilactici is a rhamnosidase from the glycoside hydrolase family 78. It shows remarkable selectivity for rutinose rather than para-nitrophenyl-alpha-l-rhamnopyranoside (p-NPR). Molecular dynamics simulations were performed using a homology model of this enzyme, in complex with both substrates. Free energy calculations lead to predicted binding affinities of -34.4 and -30.6 kJ mol^-1 respectively, agreeing well with an experimentally estimated relative free energy of 5.4 kJ mol^-1. Further, the most relevant binding poses could be determined. While p-NPR preferably orients its rhamnose moiety toward the active site, rutinose interacts most strongly with its glucose moiety. A detailed hydrogen bond analysis confirms previously implicated res

SUBMITTER: Grandits M 

PROVIDER: S-EPMC3663046 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature