Quantum wavepacket ab initio dynamical studies of hydrogen transfer catalysis in enzymes Srinivasan S. Iyengar Indiana University Abstract This proposal deals with the fundamental molecular level description of hydrogen transfer processes in enzymes. Two enzymes are considered: (a) Soybean Lipoxygenase-1 (SLO-1) is a non-heme metalloenzyme that catalyzes oxidation of fatty acids. In mammals, lipoxygenase catalyzes the production of leukotrienes and lipoxins and plays an important role in inflammatory response. Inhibition of this enzyme inhibits tumor-genesis. Thus lipoxygenase has been proposed as a promising cancer chemopreventive agent. (b) Thermophilic alcohol dehydrogenase (ADH), facilitates conversion of alcohols to aldehydes and prevents accumulation of toxic alcohols in mammalian livers. These enzymes present an active challenge to computer simulation protocols since they exhibit unexpected hydrogen/deuterium/tritium kinetic isotope effects. The fundamental reason behind these isotope effects is believed to be based on quantum mechanical tunneling. The computational treatment proposed here utilizes a new time-dependent, first principles method, developed in the P.I.'s group. It allows efficient quantum dynamics of large systems through simultaneous dynamics of electrons and nuclei via a synergy between quantum wavepacket dynamics and ab initio molecular dynamics. In SLO-1, we will study the abnormal primary kinetic isotope effect seen in recent experiments, through simultaneous quantum mechanical dynamics of the tunneling hydrogen nucleus with classical dynamics of active site and surrounding amino acids, and concurrent determination of electronic structure using AIMD with QM/MM approximations. The detailed description undertaken here, through computational mutagenesis studies, will elucidate contributions from amino acid groups and the metal centers. For ADH, we will attempt to describe the fascinating secondary kinetic isotope effects in recent experiments which indicate coupling between primary (transferring) hydrogen atoms and secondary nuclei. The quantum dynamics approach will be generalized to treat multiple particles (primary hydrogens and secondary particles) in parallel with simultaneous classical dynamics of active site, and concurrent determination of electronic structure. This goal will be achieved through a series of proposed methodological advances. The studies will determine, at an unprecedented quantum dynamical level, the coupling between different nuclei in the enzyme active site. The effect of amino acid substitutions and metal center replacements will also be probed. Secondary isotope effects are a direct probe of the reaction coordinate. Hence, our approach will have impact on all hydrogen transfer reactions in biological and synthetic enzymes.
This proposal pertains to the development of new computational methods that will be utilized to conduct a fundamental molecular level study of hydrogen transfer processes in two biological enzymes: Soybean Lipoxygenase-1 (SLO-1) and high temperature thermophilic alcohol dehydrogenase (ADH). The computational methods are based on quantum mechanics and are especially designed to understand the implications of hydrogen tunneling on the function of these enzymes.
|Phatak, Prasad; Venderley, Jordan; Debrota, John et al. (2015) 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. J Phys Chem B 119:9532-46|
|Phatak, Prasad; Sumner, Isaiah; Iyengar, Srinivasan S (2012) Gauging the flexibility of the active site in soybean lipoxygenase-1 (SLO-1) through an atom-centered density matrix propagation (ADMP) treatment that facilitates the sampling of rare events. J Phys Chem B 116:10145-64|
|Sumner, Isaiah; Iyengar, Srinivasan S (2010) Analysis of Hydrogen Tunneling in an Enzyme Active Site using von Neumann Measurements. J Chem Theory Comput 6:6-10|