title: A computational approach to enzyme design: predicting ω-aminotransferase catalytic activity using docking and MM-GBSA scoring.
abstract: Enzyme design is an important area of ongoing research with a broad range of applications in protein therapeutics, biocatalysis, bioengineering, and other biomedical areas; however, significant challenges exist in the design of enzymes to catalyze specific reactions of interest. Here, we develop a computational protocol using an approach that combines molecular dynamics, docking, and MM-GBSA scoring to predict the catalytic activity of enzyme variants. Our primary focuses are to understand the molecular basis of substrate recognition and binding in an S-stereoselective ω-aminotransferase (ω-AT), which naturally catalyzes the transamination of pyruvate into alanine, and to predict mutations that enhance the catalytic efficiency of the enzyme. The conversion of (R)-ethyl 5-methyl-3-oxooctanoate to (3S,5R)-ethyl 3-amino-5-methyloctanoate in the context of several ω-AT mutants was evaluated using the computational protocol developed in this work. We correctly identify the mutations that yield the greatest improvements in enzyme activity (20-60-fold improvement over wild type) and confirm that the computationally predicted structure of a highly active mutant reproduces key structural aspects of the variant, including side chain conformational changes, as determined by X-ray crystallography. Overall, the protocol developed here yields encouraging results and suggests that computational approaches can aid in the redesign of enzymes with improved catalytic efficiency.
authors.affiliation: Schrödinger, Inc. , 120 West 45th Street, 29th Floor, New York, New York 10036, United States.
authors.forename: Sarah
authors.initials: S
authors.lastname: Sirin
authors.forename: Rajesh
authors.initials: R
authors.lastname: Kumar
authors.forename: Carlos
authors.initials: C
authors.lastname: Martinez
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Karmilowicz
authors.forename: Preeyantee
authors.initials: P
authors.lastname: Ghosh
authors.forename: Yuriy A
authors.initials: YA
authors.lastname: Abramov
authors.forename: Van
authors.initials: V
authors.lastname: Martin
authors.forename: Woody
authors.initials: W
authors.lastname: Sherman
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000410:Alanine Transaminase / Q000737:chemistry* / Q000235:genetics; D055162:Biocatalysis; D002210:Caprylates / Q000737:chemistry*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D006801:Humans; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011485:Protein Binding; D015202:Protein Engineering / Q000379:methods*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D019289:Pyruvic Acid / Q000737:chemistry*; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D002210:Caprylates; D019289:Pyruvic Acid; D000410:Alanine Transaminase; D000409:Alanine