Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1.
A fully microscopical simulation of the rate-limiting hydrogen abstraction catalyzed by soybean lipoxygenase-1 (SLO-1) has been carried out. This enzyme exhibits the largest, and weakly temperature dependent, experimental H/D kinetic isotope effect (KIE) reported for a biological system. The theoretical model used here includes the complete enzyme with a solvation shell of water molecules, the Fe(III)-OH- cofactor, and the linoleic acid substrate. We have used a hybrid QM(PM3/d-SRP)/MM method to describe the potential energy surface of the whole system, and the ensemble-averaged variational transition-state theory with multidimensional tunneling (EA-VTST/MT) to calculate the rate constant and the primary KIE. The computational results show that the compression of the wild-type active site enzyme results in the huge contribution of tunneling (99%) to the rate of the hydrogen abstraction. Importantly, the active site becomes more flexible in the Ile553Ala mutant reactant complex simulation (for which a markedly temperature dependent KIE has been experimentally determined), thus justifying the proposed key role of the gating promoting mode in the reaction catalyzed by SLO-1. Finally, the results indicate that the calculated KIE for the wild-type enzyme has an important dependence on the barrier width.
Tejero
Ismael
I
Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, 08193, Bellaterra (Barcelona), Spain.
Garcia-Viloca
Mireia
M
Gonzalez-Lafont
Angels
A
Lluch
José M
JM
York
Darrin M
DM
D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D006859:Hydrogen / Q000737:chemistry*; D007501:Iron / Q000737:chemistry; D007700:Kinetics; D008024:Ligands; D008084:Lipoxygenase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D009154:Mutation / Q000235:genetics; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D013025:Glycine max / Q000201:enzymology*; D013379:Substrate Specificity; D014867:Water
D008024:Ligands; D014867:Water; D006859:Hydrogen; D007501:Iron; C101084:lipoxygenase L-1; D008084:Lipoxygenase