Binding Region of Alanopine Dehydrogenase Predicted by Unbiased Molecular Dynamics Simulations of Ligand Diffusion

Abstract

Opine dehydrogenases catalyze the reductive condensation of pyruvate with L-amino acids. Biochemical characterization of alanopine dehydrogenase from Arenicola marina revealed that this enzyme is highly specific for L-alanine. Unbiased molecular dynamics simulations with a homology model of alanopine dehydrogenase captured the binding of L-alanine diffusing from solvent to a putative binding region near a distinct helix-kink-helix motif. These results and sequence comparisons reveal how mutations and insertions within this motif dictate the L-amino acid specificity.