Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Absorption and luminescent excitation spectra of F and M centers in Kcl and NaF

Luminescent excitation spectra were measured for the F and M centers in KCl; in particular, for the F band, M band, and the M2 transition. In all 3 cases, the spectra were nearly double-Gaussian in shape, and the efficiency for luminescence was nearly independent of the wavelength of the exciting light. A comparison of the absorption spectrum with the excitation spectrum of the F-band region of crystals with M centers present and oriented provided further evidence for the existence of the M2 transition of van Doorn and Haven and of Okamoto, and against the energy transfer theory of Lambe and Compton. The efficiency for luminescence of the M center upon M-band excitation was equal to the efficiency for F centers in pulse-annealed crystals of low F-center concentrations. The ratio of the efficiencies of the Ml to M2 transitions was 1.2 ± .25. The oscillator strengths of 3 of the M-center transitions in KCl relative to the oscillator strength for the F center were found to be in better agreement with the results reported by Okamoto, than with the results reported by Delbecq. The polarization of luminescence of M centers in KCl was measured at right angles to the exciting light, and was found to agree with the predictions of the van Doorn-Haven model of the M center. In NaF crystals having no absorption bands to the red side of the M band, the absorption and excitation spectra of the M band were accurately double-Gaussian over a wide range of wavelengths; the efficiency of luminescence of the M center was independent of the wavelength of the exciting light in that range; and the polarization of luminescence upon M-band excitation agreed well with the calculations based on the van DoornHaven model of the M center, In crystals in which the F band was bleached sufficiently to make it smaller in absorption height than the M band, several new color centers appeared on the red side of the M band, in contrast to the results reported by Blum; in these crystals, the polarization of luminescence of the M center upon M-band excitation disagreed strongly with theory, even though the absorptions for the new color centers were small compared to the M-band absorption.