Past Event: Oden Institute Seminar

Atomic analysis of stereospecificity in ketoreductase: a molecular dynamics study

Mauro Mugnai, UT Chemistry Department

Abstract

Understanding the microscopic reasons of enzyme specificity is a fundamental task of protein science and protein engineering. Some enzymes are highly specific and they can distinguish different stereoisomers of the same ligand, as in the case of stereospecific enzymes. Here, we examine one of such enzymes. The enzyme ketoreductase (KR) is capable of differentiating between D orientation and L orientation of a methyl group at the alpha carbon of a diketide: it uses an NADPH to stereospecifically reduce only one of those epimers. Here, we use Molecular Dynamics (MD) to shed light on the microscopic mechanism of selectivity in this enzyme. We use an X-ray structure of the enzyme and a built-in model for the ligand to initiate the simulations. The simulations run in explicit solvent using the MD package MOIL. We consider an enzyme specific for the D enantiomer. We run multiple MD simulations for each of these enzymes, with the correct and the incorrect substrates in the binding pocket of the initial (X-ray) structure of the enzyme. We perform two types of simulations: a) we look at the immediate response of the enzyme to both ligands by running many short runs from the same initial structure but with different velocities; b) we look at the long-time relaxation of the enzymes with fewer longer simulations. The data reproduces important qualitative features of the experiments; the enzyme retains the correct ligand closer to a reactive configuration more frequently than the incorrect ligand. An analysis of the interactions of the substrate with the binding pocket highlights which amino acids are important for the selectivity.