Direct observation of specific protein vibrations

PHYS 222

Floyd Romesberg, floyd@scripps.edu, Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, CB262R, La Jolla, CA 92037
Proteins have evolved for function. As the products of selection for activity, proteins may be very different from abiological molecules, whose presence in the environment results from stability. Substitution of a C-D bond for a specific C-H bond is a non-perturbative experimental approach to studying specific protein motions that shifts the bond stretching absorption into a transparent region of the protein's IR spectrum, thus allowing for its direct characterization. We have introduced CD bonds at various positions throughout the redox protein cytochrome c, and used the observable stretching absorptions to characterize the protein with small molecule-like detail. Redox-dependent changes in local protein flexibility, and the detailed equilibrium folding pathways induced by guanidinium-hydrochloride, urea, and base will be presented. Initial efforts to use the technique to characterize other proteins will also be presented, as will our efforts to use C-D and time-resolved IR spectroscopy to characterize dynamics and folding in real time.