title: Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis.
abstract: Pol η belongs to the important Y family of DNA polymerases that can catalyze translesion synthesis across sites of damaged DNA. This activity involves the reduced fidelity of Pol η for 8-oxo-7,8-dhyedro-2'-deoxoguanosin(8-oxoG). The fundamental interest in Pol η has grown recently with the demonstration of the importance of a 3rd Mg2+ ion. The current work explores both the fidelity of Pol η and the role of the 3rd metal ion, by using empirical valence bond (EVB) simulations. The simulations reproduce the observed trend in fidelity and shed a new light on the role of the 3rd metal ion. It is found that this ion does not lead to a major catalytic effect, but most probably plays an important role in reducing the product release barrier. Furthermore, it is concluded, in contrast to some implications, that the effect of this metal does not violate transition state theory, and the evaluation of the catalytic effect must conserve the molecular composition upon moving from the reactant to the transition state. Proteins 2017; 85:1446-1453. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California, 90089-1062.
authors.forename: Hanwool
authors.identifier: http://orcid.org/0000-0002-7761-4321
authors.initials: H
authors.lastname: Yoon
authors.affiliation: Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California, 90089-1062.
authors.forename: Arieh
authors.initials: A
authors.lastname: Warshel
mesh_terms: D020816:Amino Acid Motifs; D001665:Binding Sites; D055162:Biocatalysis; D020134:Catalytic Domain; D002413:Cations, Divalent; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry*; D006151:Guanosine / Q000031:analogs & derivatives* / Q000737:chemistry; D006801:Humans; D007700:Kinetics; D008274:Magnesium / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D011522:Protons; D013379:Substrate Specificity; D013816:Thermodynamics; D014867:Water / Q000737:chemistry; D000099270:Y-Family DNA Polymerases
chemical_list: D002413:Cations, Divalent; D004259:DNA-Directed DNA Polymerase; D006151:Guanosine; D008274:Magnesium; D011522:Protons; D014867:Water; C046215:8-hydroxyguanosine; C112338:Rad30 protein; D000099270:Y-Family DNA Polymerases
keywords: DNA polymerase η; Translesion synthesis; enzyme catalysis; free energy perturbation; reduced fidelity; third metal; transition state theory