Residue Scale Characterization of Protein Structure Fluctuations

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Real time measurements of energy and angular fluctuations in peptides and proteins using ultrafast optical, stimulated IR echoes, 2D IR and single molecule spectroscopy are proposed to examine interactions and correlations between vibrational modes and their surroundings for isotopic selections of peptides and proteins. Time correlation functions for amide-I, amide-II, CH3 and amide-A groups selected by carbon, oxygen and deuterium isotopic replacement will be measured and modeled. The influence of electrostatics, solvent interactions and structural heterogeniety on delocalization of vibrational energy in peptides will be examined. IR photon echoes and dynamic 2D IR will allow characterization of the solvent related energy fluctuations of selected pieces of alpha helices, and evaluation of effects of charged residues and polar solvents from the vibrational dynamics, and fast hydrogen bond dissociation dynamics of water molecules (HDO) from ions nearby to proteins. The dynamics of cytochrome c at equilibrium and following CO photolysis will be examined by 2D IR of 18O, 13C and deuterium labeled residues to determine the fluctuations in the Met (80) residue and Phe (82). Infrared transitions of optically excited aggregates will be examined and theoretical models for amide IR spectra in secondary structures will be developed. Single molecule experiments based on spectra, lifetime and photon arrival time distributions will address equilibrium fluctuations of the glass and hydrogel encapsulated calcium calmodulin peptide complex via Nile Red fluorecence quenching, LH2 complexes, trehalose protein interactions and the distributions of rates of energy transfer in donor and acceptor labeled peptides immobilized in glasses and gels near the glass transitions.