Our work is centered on studying the structural and dynamical properties of proteins in order to understand the molecular mechanisms of protein function. We have developed new spectroscopic methods to obtain the vibrational spectra of specific protein groups and/or bound ligands, even within large proteins. With these techniques, it is possible to determine bond lengths with an accuracy of better than 0.01 Angstroms. We also have developed techniques to monitor atomic motion in proteins on multiple time scales, as fast as picoseconds and out to minutes.
The primary problem of the lab is to understand the dynamics of enzymatic catalysis at a molecular level. This involves measurement of (1) static structures of enzymes complexes with their ligands and (2) how atomic motion evolves during the catalytic event. Structure is probed with vibrational spectroscopic tools that are capable of determining the Raman and IR spectra of bound substrates and specific protein molecular moieties. Vibrational spectroscopy yields a very high resolution of structure (better than 0.01 Anstroms), and changes on this order are key to understanding enzymatic catalysis. We have developed new, novel, and powerful methods for measuring the motions of atoms in proteins on the nanosecond to minute time scales. See: Time-Resolved Approaches to Characterize the Dynamical Nature of Enzyme Catalysis, Robert Callender and R. Brian Dyer, Chemical Reviews 106, 3031-3042 (2006).
Modern paradigms for enzymatic catalysis all include atomic motion of the catalyst and reactants, either implicitly or explicitly. Binding of a substrate to form the Michaelis complex involves motions: formation of encounter complex(es), movement of the substrate towards the enzyme active site, desolvation of substrate, and often loop or flap closure or domain motion. Once the Michaelis complex is formed, movement of atoms and groups at the binding site occur to bring about the proper catalyzed chemistry and achieve these catalytic states with the incredible rate enhancements approaching 1018 relative to uncatalyzed reactions. We have recently developed kinetic approaches that can measure molecular motions in proteins on fast time scales (down to 10 ps), here-to-fore inaccessible to measurement, based on initiating chemical and structural changes via a laser induced temperature jump. Measurements of the evolving structure is probed using optical and vibrational spectroscopies.
We also wish to understand how proteins arrive at their three dimensional structure (the protein folding problem). A number of studies are underway to understand the thermodynamics of folding. In addition, the crucial kinetic events of protein folding occur faster than the conventional millisecond time scale of stopped-flow mixing techniques. These early kinetic events in the folding process are being studied using our fast advanced initiation techniques.