Computational screening of novel thiamine-catalyzed decarboxylation reactions of 2-keto acids.
A molecular modeling strategy to screen the capacity of known enzymes to catalyze the reactions of non-native substrates is presented. The binding of pyruvic acid and non-native ketoacids in the active site of pyruvate ferredoxin oxidoreductase was examined using docking analysis, and our results suggest that enzyme-non-native ketoacid-bound species are feasible. Quantum mechanics/molecular mechanics methods were then used to study the geometry of the covalent intermediate formed from the enzyme and the various ketoacids. Finally, quantum mechanical methods were used to study the decarboxylation reaction of 2-keto acids at the mechanistic level. This hierarchical screening ranked the substrates from those that cannot be accommodated by the enzyme (phenyl pyruvate) to those whose conversion rate would most closely approach that of the native substrate (2-ketobutanoic acid and 2-ketovaleric acid). Most notably, our investigation suggests that novel pathways generated using generalized enzyme actions may be screened using the hierarchical approach employed here.
Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.
Rajeev S
RS
Assary
Linda J
LJ
Broadbelt
D001665:Binding Sites; D002384:Catalysis; D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods*; D003653:Decarboxylation; D007651:Keto Acids / Q000032:analysis* / Q000737:chemistry*; D007700:Kinetics; D008958:Models, Molecular; D015394:Molecular Structure; D050743:Pyruvate Synthase / Q000032:analysis; D019289:Pyruvic Acid / Q000737:chemistry; D011789:Quantum Theory; D013379:Substrate Specificity; D013831:Thiamine / Q000737:chemistry*
D007651:Keto Acids; D019289:Pyruvic Acid; D050743:Pyruvate Synthase; D013831:Thiamine