title: Active Site Dynamical Effects in the Hydrogen Transfer Rate-limiting Step in the Catalysis of Linoleic Acid by Soybean Lipoxygenase-1 (SLO-1): Primary and Secondary Isotope Contributions.
abstract: Using ab initio molecular dynamics (AIMD) simulations that facilitate the treatment of rare events, we probe the active site participation in the rate-determining hydrogen transfer step in the catalytic oxidation of linoleic acid by soybean lipoxygenase-1 (SLO-1). The role of two different active site components is probed. (a) On the hydrogen atom acceptor side of the active site, the hydrogen bonding propensity between the acceptor side hydroxyl group, which is bound to the iron cofactor, and the backbone carboxyl group of isoleucine (residue number 839) is studied toward its role in promoting the hydrogen transfer event. Primary and secondary (H/D) isotope effects are also probed and a definite correlation with subtle secondary H/D isotope effects is found. With increasing average nuclear kinetic energy, the increase in transfer probability is enhanced due to the presence of the hydrogen bond between the backbone carbonyl of I839 and the acceptor oxygen. Further increase in average nuclear kinetic energy reduces the strength of this secondary hydrogen bond which leads to a deterioration in hydrogen transfer rates and finally embrances an Arrhenius-like behavior. (b) On the hydrogen atom donor side, the coupling between vibrational modes predominantly localized on the donor-side linoleic acid group and the reactive mode is probed. There appears to be a qualitative difference in the coupling between modes that belong to linoleic acid and the hydrogen transfer mode, for hydrogen and deuterium transfer. For example, the donor side secondary hydrogen atom is much more labile (by nearly a factor of 5) during deuterium transfer as compared to the case for hydrogen transfer. This appears to indicate a greater coupling between the modes belonging to the linoleic acid scaffold and the deuterium transfer mode and also provides a new rationalization for the abnormal (nonclassical) secondary isotope effect results obtained by Knapp, Rickert, and Klinman in J. Am. Chem. Soc. , 2002 , 124 , 3865 . To substantiate our findings noted in point a above, we have suggested an I839 → A839 or I839 → V839 mutation. This will modify the bulkiness of hydrogen the bonding residue, allowing greater flexibility in the secondary hydrogen bond formation highlighted above and adversely affecting the reaction rate.
authors.affiliation: Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.
authors.forename: Prasad
authors.initials: P
authors.lastname: Phatak
authors.affiliation: Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.
authors.forename: Jordan
authors.initials: J
authors.lastname: Venderley
authors.affiliation: Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.
authors.forename: John
authors.initials: J
authors.lastname: Debrota
authors.affiliation: Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.
authors.forename: Junjie
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.
authors.forename: Srinivasan S
authors.initials: SS
authors.lastname: Iyengar
mesh_terms: D055162:Biocatalysis; D003903:Deuterium / Q000737:chemistry*; D006859:Hydrogen / Q000737:chemistry*; D006860:Hydrogen Bonding; D007700:Kinetics; D019787:Linoleic Acid / Q000378:metabolism*; D008084:Lipoxygenase / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D010084:Oxidation-Reduction; D011487:Protein Conformation; D011789:Quantum Theory; D013025:Glycine max / Q000201:enzymology*; D013816:Thermodynamics; D014732:Vibration
chemical_list: D006859:Hydrogen; D019787:Linoleic Acid; D003903:Deuterium; C101084:lipoxygenase L-1; D008084:Lipoxygenase