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Ph.D. DissertationPDF


Title:Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation
Author(s):Kim, Seung Joong
Director of Research:Gruebele, Martin
Doctoral Committee Chair(s):Ha, Taekjip
Doctoral Committee Member(s):Ceperley, David M.; Aksimentiev, Aleksei
Department / Program:Physics
Degree Granting Institution:University of Illinois at Urbana-Champaign
Subject(s):Small Angle X-ray Scattering (SAXS)
Terahertz (THz)
Kinetic Terahertz Absorption (KITA)
Protein-protein interaction
Protein-water interaction
Abstract: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.
Issue Date:2008-08-11
Publisher:University of Illinois at Urbana-Champaign
Citation Info:Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Physics in the Graduate College of the University of Illinois at Urbana-Champaign, 2008
Genre:Dissertation / Thesis
Rights Information:Copyright 2008 by Seung Joong Kim. All Rights Reserved.
Date Available in IDEALS:2008-08-11

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