Our program explores how atomic motion and organized protein structure within proteins contributes to enzymatic catalysis. We wish to understand: (1) how motions on timescales from femtoseconds to milliseconds prepare the Michaelis complex for traversal of the transition state; (2) the validity of the tight binding transition state model of catalysis; and (3) how nature engineers proteins to create specific dynamic modes that are central to the catalytic process. Through an iterative process of experiment and theory we are exploring non-isotropic vibrational energy channeling in enzymatic reactions.
Vibrational structures of enzyme active sites.The interactions that take place between molecular groups when a small molecule binds to a protein affect their vibrational frequencies and are reported by the changes of the frequencies. Structural properties of a molecular group, such as bond orders, bond length/angle, ionization state of ionizable moieties can be determined at very high precision, which make IR and/or Raman spectrsoscopies invaluable tools in understanding enzymatic catalysis.
Loop motion in triosephosphate isomerase.Enzymes often have a 'flap' that close over substrates bound to their active sites. These surface protein flaps or loops are typically key for mechanism. We experimentally characterize the kinetics and thermodynamics of the loop motion involved in the chemistry catalyzed by TIM.
The dynamics of substrate binding in lactate dehydrogenase.In Sebastian McClendon's studies, the pathway of substrate binding to LDH is determined. The kinetic pathway is characterized using florescence emission in T-jump studies. Isotope edited laser induced T-jump studies are employed to determine which specific atoms and molecular groups are moving during the binding process.
The dynamical nature of protein folding: the folding of apomyoglobin.In this body of work carried out principally by Miriam Gulotta and Rudolf Gilmanshin, we have determined the time course of how apomyoglobin folds from unfolded polypeptide to folded protein on time scales from 50 picoseconds to milliseconds.