University of Illinois Urbana-Champaign

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

Kim, Seung Joong

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https://hdl.handle.net/2142/8857

Description

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
Issue Date
2008-08-11
Director of Research (if dissertation) or Advisor (if thesis)
Gruebele, Martin
Doctoral Committee Chair(s)
Ha, Taekjip
Committee Member(s)
  • Ceperley, David M.
  • Aksimentiev, Aleksei
Department of Study
Physics
Discipline
Physics
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
  • Small Angle X-ray Scattering (SAXS)
  • Terahertz (THz)
  • Simulation
  • Kinetic Terahertz Absorption (KITA)
  • Protein-protein interaction
  • Biophysics
  • Protein-water interaction
  • hydration
Language
en
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.
Type of Resource
text
Permalink
http://hdl.handle.net/2142/8857
Copyright and License Information
Copyright 2008 by Seung Joong Kim. All Rights Reserved.

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