title: Comparative computational analysis of different active site conformations and substrates in a chalcone isomerase catalyzed reaction.
abstract: Chalcone isomerase catalyzes the transformation of chalcones to flavanones. We present a computational study of the rate-limiting chemical step, an intramolecular Michael addition of a 2'-oxyanion to the alpha,beta-double bound. By using quantum mechanical/molecular mechanical hybrid methods we traced the free-energy profiles associated with the reaction of two different substrates (chalcone and 6'-deoxychalcone) in two different conformations of the active site that are described in the different crystallographic structures available. We have obtained significant differences (about 4 kcal/mol) in the free-energy barriers calculated for the two active sites. According to our results, the active site conformation with larger catalytic power presents a positively charged lysine residue much closer to the substrate than the other. Complementary electronic and electrostatic analysis shows that the charge is transferred from the 2'-oxyanion to the beta-carbon atom. Interactions of the environment with these two atoms are essential to understand the differences between both active sites and also the origin of catalysis in this enzyme.
authors.affiliation: Departamento de Química Física, Universitat de València, 46100 Burjassot, Spain.
authors.forename: J Javier
authors.initials: JJ
authors.lastname: Ruiz-Pernía
authors.forename: Estanislao
authors.initials: E
authors.lastname: Silla
authors.forename: Iñaki
authors.initials: I
authors.lastname: Tuñón
mesh_terms: D000838:Anions; D001665:Binding Sites; D002244:Carbon / Q000737:chemistry; D002384:Catalysis; D003198:Computer Simulation; D006863:Hydrogen-Ion Concentration; D019753:Intramolecular Lyases / Q000737:chemistry*; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D011487:Protein Conformation; D011789:Quantum Theory; D012984:Software; D013816:Thermodynamics
chemical_list: D000838:Anions; D002244:Carbon; D019753:Intramolecular Lyases; C019865:chalcone isomerase