title: Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase.
abstract: The rate enhancement provided by the chorismate mutase (CM) enzyme for the Claisen rearrangement of chorismate to prephenate has been investigated by application of the concept of near attack conformations (NACs). Using a combined QM/MM Monte Carlo/free-energy perturbation (MC/FEP) method, 82% and 100% of chorismate conformers were found to be NAC structures in water and in the CM active site, respectively. Consequently, the conversion of non-NACs to NACs does not contribute to the free energy of activation from preorganization of the substrate into NACs. The FEP calculations yielded differences in free energies of activation that well reproduce the experimental data. Additional calculations indicate that the rate enhancement by CM over the aqueous phase results primarily from conformational compression of NACs by the enzyme and that this process is enthalpically controlled. This suggests that preferential stabilization of the transition state in the enzyme environment relative to water plays a secondary role in the catalysis by CM.
authors.affiliation: Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, USA.
authors.forename: Cristiano Ruch Werneck
authors.initials: CR
authors.lastname: Guimarães
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Repasky
authors.forename: Jayaraman
authors.initials: J
authors.lastname: Chandrasekhar
authors.forename: Julian
authors.initials: J
authors.lastname: Tirado-Rives
authors.forename: William L
authors.initials: WL
authors.lastname: Jorgensen
mesh_terms: D001412:Bacillus subtilis / Q000201:enzymology / Q000378:metabolism; D002826:Chorismate Mutase / Q000737:chemistry* / Q000378:metabolism*; D004795:Enzyme Stability; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009010:Monte Carlo Method; D011487:Protein Conformation; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D002826:Chorismate Mutase