title: Understanding the mode of action of ThDP in benzoylformate decarboxylase.
abstract: The mechanism of all elementary steps involved in the catalytic cycle of benzoylformate decarboxylase (BFD, E.C. 4.1.1.7) to generate the acyloin linkage is investigated by extensive molecular dynamics simulations. Models involving different charge states of amino acids and/or mutants of critical residues were constructed to understand the involvement of the catalytically active residues and the reactivity differences between different substrates in this reaction. Our calculations confirm that H70, S26, and H281 are catalytically active amino acids. H281 functions as a base to accept H(donor) in the first nucleophilic attack and as an acid in the second, to donate the proton back to O(acceptor). S26 assists H281 in deprotonation of the donor aldehyde and protonation of the acceptor aldehyde. In both the first and second nucleophilic attacks, H70 interacts with O(aldehyde) and aligns it toward the nucleophilic center. H70 has been found to have an electrostatic effect on the approaching aldehyde whose absence would block the initiation of the reaction. The reactivity difference between benzaldehyde (BA) and acetaldehyde (AA) is mainly explained by the steric interactions of the acceptor aldehyde with the surrounding amino acids in the active center of the enzyme.
authors.affiliation: Department of Chemistry, Bogazici University, Istanbul 34342, Turkey.
authors.forename: Kevser Gocmen
authors.initials: KG
authors.lastname: Topal
authors.forename: Canan
authors.initials: C
authors.lastname: Atilgan
authors.forename: Ayhan S
authors.initials: AS
authors.lastname: Demir
authors.forename: Viktorya
authors.initials: V
authors.lastname: Aviyente
mesh_terms: D002262:Carboxy-Lyases / Q000737:chemistry*; D005233:Fatty Alcohols / Q000737:chemistry; D008274:Magnesium / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D013835:Thiamine Pyrophosphate / Q000737:chemistry*
chemical_list: D005233:Fatty Alcohols; C011159:acyloin; D002262:Carboxy-Lyases; C019778:benzoylformate decarboxylase; D008274:Magnesium; D013835:Thiamine Pyrophosphate