title: New Insights on the Reaction Pathway Leading to Lactyl-ThDP: A Theoretical Approach.
abstract: In all ThDP-dependent enzymes, the catalytic cycle is initiated with the attack of the C2 atom of the ylide intermediate on the Cα atom of a pyruvate molecule to form the lactyl-ThDP (L-ThDP) intermediate. In this study, the reaction between the ylide intermediate and pyruvate leading to the formation of L-ThDP is addressed from a theoretical point of view. The study includes molecular dynamics, exploration of the potential energy surface by means of QM/MM calculations, and reactivity analysis on key centers. The results show that the reaction occurs via a concerted mechanism in which the carboligation and the proton transfers occur synchronically. It is also observed that during the reaction the protonation state of the N1' atom changes: the reaction starts with the ylide having the N1' atom deprotonated and reaches a transition state showing the N1' atom protonated. This conversion leads to the reaction path of minimum energy, with an activation energy of about 20 kcal mol(-1). On the other hand, it is also observed that the approaching distance between the pyruvate and the ylide, i.e., the Cα-C2 distance, plays a fundamental role in the reaction mechanism since it determines the nucleophilic character of key atoms of the ylide, which in turn trigger the elemental reactions of the mechanism.
authors.affiliation: Computational Chemistry Group, Faculty of Chemical Sciences, Universidad de Concepción , Concepción, Chile.
authors.forename: Ignacio
authors.initials: I
authors.lastname: Lizana
authors.affiliation: Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Sede Concepción, Universidad Andrés Bello , Concepción, Chile.
authors.forename: Gonzalo A
authors.initials: GA
authors.lastname: Jaña
authors.affiliation: Computational Chemistry Group, Faculty of Chemical Sciences, Universidad de Concepción , Concepción, Chile.
authors.forename: Eduardo J
authors.initials: EJ
authors.lastname: Delgado
mesh_terms: D000095:Acetolactate Synthase / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D019289:Pyruvic Acid / Q000737:chemistry / Q000378:metabolism*; D011789:Quantum Theory; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism; D013816:Thermodynamics; D013835:Thiamine Pyrophosphate / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism
chemical_list: C497352:C2-alpha-lactylthiamin diphosphate; D019289:Pyruvic Acid; D000095:Acetolactate Synthase; D013835:Thiamine Pyrophosphate