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

作者:Gohlke Holger*; Hergert Ulrike; Meyer Tatu; Mulnaes Daniel; Grieshaber Manfred K; Smits Sander H J; Schmitt Lutz
来源:Journal of Chemical Information and Modeling, 2013, 53(10): 2493-2498.
DOI:10.1021/ci400370y

摘要

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.

  • 出版日期2013-10