title: Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods.
abstract: A two-step procedure for the determination of reaction paths in enzyme systems is presented. This procedure combines two chain-of-states methods: a quantum mechanical/molecular mechanical (QM/MM) implementation of the nudged elastic band (NEB) method and a second order parallel path optimizer method both recently developed in our laboratory. In the first step, a reaction path determination is performed with the NEB method, along with a restrained minimization procedure for the MM environment to obtain a first approximation to the reaction path. In the second step, the calculated path is refined with the parallel path optimizer method. By combining these two methods the reaction paths are determined accurately, and in addition, the number of path optimization iterations are significantly reduced. This procedure is tested by calculating both steps of the isomerization of 2-oxo-4-hexenedioate by 4-oxalocrotonate tautomerase, which have been previously determined by our group. The calculated paths agree with the previously reported results and we obtain a reduction of 45%-55% in the number of path optimization cycles.
authors.affiliation: Department of Chemistry, Duke University, Durham, North Carolina 27708-0346, USA.
authors.forename: G Andrés
authors.initials: GA
authors.lastname: Cisneros
authors.forename: Haiyan
authors.initials: H
authors.lastname: Liu
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Lu
authors.forename: Weitao
authors.initials: W
authors.lastname: Yang
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004798:Enzymes / Q000737:chemistry*; D007700:Kinetics; D019563:Mechanics; D008956:Models, Chemical; D008958:Models, Molecular; D009097:Multienzyme Complexes / Q000737:chemistry*; D011485:Protein Binding; D011789:Quantum Theory
chemical_list: D004798:Enzymes; D009097:Multienzyme Complexes