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Binding region of alanopine dehydrogenase predicted by unbiased molecular dynamics simulations of ligand diffusion
Holger Gohlke1, Ulrike Hergert, Tatu Meyer
1Institute for Pharmaceutical and Medicinal Chemistry and ‡Institute of Biochemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine-University , 40204 Düsseldorf, Germany.
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.
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