PROTEIN DYNAMICS AND INTERACTIONS: VIBRATIONAL ECHOES

Stanford University, Stanford CA

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Abstract

Research is proposed to study protein dynamics and intraprotein interactions using an entirely new approach, ultrafast infrared vibrational echo experiments, stimulated vibrational echoes, chemically written stimulated vibrational echoes, and two dimensional vibrational echo spectroscopies. The vibrational echo, which operates on picosecond and femtosecond time scales, is the infrared vibrational equivalent of the NMR spin echo, but it directly examines dynamics and interactions among mechanical degrees of freedom rather than spins. The stimulated vibrational echo experiments extend the time scales that can be investigated, permitting the spectrum of structural fluctuation dynamics to be mapped out over a broad range of time scales. The vibrational echo experiments will initially be applied to the study myoglobin-CO (Mb-CO), hemoglobin-CO (Hb-CO), Mb-NO, lysozyme, Amide I bands and model structures. The time dependent vibrational echo studies of the heme proteins will examine protein dynamics that are felt by a ligand bound at the active site and provide information on how structure, temperature, and viscosity influence protein dynamics. The role played by the protein/solvent boundary in protein dynamics will be studied at room temperature, and the nature of glass like protein dynamics at low temperatures will be investigated. Experiments on intact proteins will be compared to experiments on denatured proteins to examine changes in structural dynamics caused by denaturing. Small molecules will be used as Structural Dynamics Labels that will permit examination of structural fluctuations occurring in different regions of a protein. Vibrational Echo Spectroscopy, a 2D method in which frequency and time are varied, will be used to obtain background suppression and peak enhancement in vibrational spectra of proteins that are not resolvable with conventional IR spectroscopy, e. g., Mb-NO. Two time 2D vibrational echo spectroscopy will be developed and applied to the study of the mechanical coupling between different structural units in proteins. The vibrational echo experiments are the first to use IR coherence experiments on biological systems, moving vibrational spectroscopy along the path that has been so fruitful in the study of biological systems and processes with of magnetic resonance.