Binding region of alanopine dehydrogenase predicted by unbiased molecular dynamics simulations of ligand diffusion
| Autor: | Daniel Mulnaes, Tatu Meyer, Lutz Schmitt, Sander H. J. Smits, Manfred K. Grieshaber, Ulrike Hergert, Holger Gohlke |
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| Rok vydání: | 2013 |
| Předmět: |
Alanopine dehydrogenase
General Chemical Engineering Opine Library and Information Sciences Biology Molecular Dynamics Simulation medicine.disease_cause Ligands Homology (biology) Protein Structure Secondary Substrate Specificity Diffusion Molecular dynamics Pyruvic Acid medicine Animals Homology modeling chemistry.chemical_classification Mutation Oxidoreductases Acting on CH-NH Group Donors Alanine Binding Sites Polychaeta General Chemistry Helminth Proteins Ligand (biochemistry) Recombinant Proteins Computer Science Applications Protein Structure Tertiary Kinetics Enzyme chemistry Biochemistry Amino Acid Substitution Structural Homology Protein Protein Binding |
| Zdroj: | Journal of chemical information and modeling. 53(10) |
| ISSN: | 1549-960X |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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