Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase.
Nuclear quantum mechanical effects have been examined for the proton transfer reaction catalyzed by triosephosphate isomerase, with the normal mode centroid path integral molecular dynamics based on the potential energy surface from the recently developed reaction path potential method. In the simulation, the primary and secondary hydrogens and the C and O atoms involving bond forming and bond breaking were treated quantum mechanically, while all other atoms were dealt classical mechanically. The quantum mechanical activation free energy and the primary kinetic isotope effects were examined. Because of the quantum mechanical effects in the proton transfer, the activation free energy was reduced by 2.3 kcal/mol in comparison with the classical one, which accelerates the rate of proton transfer by a factor of 47.5. The primary kinetic isotope effects of kH/kD and kH/kT were estimated to be 4.65 and 9.97, respectively, which are in agreement with the experimental value of 4+/-0.3 and 9. The corresponding Swain-Schadd exponent was predicted to be 3.01, less than the semiclassical limit value of 3.34, indicating that the quantum mechanical effects mainly arise from quantum vibrational motion rather than tunneling. The reaction path potential, in conjunction with the normal mode centroid molecular dynamics, is shown to be an efficient computational tool for investigating the quantum effects on enzymatic reactions involving proton transfer.
Wang
Mingliang
M
Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
Lu
Zhenyu
Z
Yang
Weitao
W
D002244:Carbon / Q000737:chemistry; D002384:Catalysis; D002627:Chemistry, Physical / Q000379:methods*; D003903:Deuterium / Q000737:chemistry; D004798:Enzymes / Q000737:chemistry*; D008962:Models, Theoretical; D008968:Molecular Conformation; D010100:Oxygen / Q000737:chemistry; D011522:Protons; D011789:Quantum Theory; D012984:Software; D013816:Thermodynamics; D013997:Time Factors; D014305:Triose-Phosphate Isomerase / Q000737:chemistry*; D014316:Tritium / Q000737:chemistry
D004798:Enzymes; D011522:Protons; D014316:Tritium; D002244:Carbon; D003903:Deuterium; D014305:Triose-Phosphate Isomerase; D010100:Oxygen