title: Modeling of transition state by molecular dynamics. Prediction of catalytic efficiency of the mutants of mandelate racemase.
abstract: Modeling of transition state by molecular dynamic method often requires modification of the force field parameters to describe energy profile accurately. In this work, we avoided the modification by modeling a series of mutants at binding-related site. In predicting the catalytic efficiency (k(cat)/K(m)) of the mutants of mandelate racemase (MR), the prediction performance of three energy subsets was investigated. It was indicated that the interaction-energy subset exhibited better prediction performance than whole-system subset and binding-site subset in both quantity and trend. When prediction error (PE) criterion was equal to 5%, 10 out of 12 samples were predicted correctly within interaction-energy subset, which demonstrated a great application potential of this method in prediction of enzyme catalytic efficiency and enzyme rational design.
authors.affiliation: Institute of Bioengineering, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, PR China, 310027. yuhongwei@zju.edu.cn
authors.forename: Mei
authors.initials: M
authors.lastname: Zhuohang
authors.forename: Liu
authors.initials: L
authors.lastname: Ji
authors.forename: Yu
authors.initials: Y
authors.lastname: Hongwei
mesh_terms: D001665:Binding Sites; D055162:Biocatalysis; D020134:Catalytic Domain; D004734:Energy Metabolism; D008333:Mandelic Acids / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D019998:Racemases and Epimerases / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D008333:Mandelic Acids; D050505:Mutant Proteins; D019998:Racemases and Epimerases; C021540:mandelate racemase; C037938:mandelic acid