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Carol K. Hall's Statistical Thermodynamics Group

Hung D. Nguyen

Currently, Research Associate
 in the group of Prof. Charles L. Brooks III
at the Scripps Research Institute

Ph.D., defended on January 9th, 2004
M.S. in 2000
Chemical Engineering
North Carolina State University

B.S. in 1998
Chemical Engineering
University of Florida

Email: hdnguyen@scripps.edu

Thesis Title: Protein Folding and Aggregation with Solute Interaction

Advisor: Prof. Carol K. Hall

Systems of Interest:

Methods:
  • Recombinant proteins
  • Amyloid-forming peptides
  • Dynamic Monte Carlo
  • Discontinuous Molecular Dynamics

Abstract: We are conducting a program of theoretical research aimed at studying the competition between protein folding and aggregation in the presence of solutes using two main models:

Low-Resolution Model: Using simple exact protein models (Lau and Dill, 1989) in conjunction with dynamic Monte Carlo, we investigate how refolding and aggregation kinetics are affected by the rate of changing solvent conditions (denaturant concentration, temperature, and protein concentration) by simulating various renaturation methods. In addition, we also account for the presence of solutes in order to examine the effects that model solute type, size, length, and concentration have on the refolding yield and aggregation.

Intermediate-Resolution Model: Using a model developed in our group (A.V. Smith and C.K. Hall, Proteins 44, 344, 2001, ibid. 376, 2001), we study the formation of fibrils that are associated with protein deposition diseases. The model is simple enough to allow the simulation of multi-protein systems over relatively long time scales yet contains enough genuine protein-like character to mimic real protein dynamics when used in conjunction with constant-temperature discontinuous molecular dynamics, a fast alternative to conventional molecular dynamics. Simulations have been performed on systems containing 12 to 96 Ac-KA14K-NH2 molecules to investigate the effect of temperature, peptide concentration and chain length on the kinetics and thermodynamics of fibril formation.

Publications:

  • H.D. Nguyen and C.K. Hall, "Effect of rate of chemical or thermal renaturation on refolding and aggregation of a single lattice protein," Biotechnology & Bioengineering, 80(7): 823-834 (2002). Link
  • H.D. Nguyenm, A.J. Marchut and C.K. Hall, "Solvent Effects on the Conformational Transition of a Model Polyalanine Peptide," Protein Science, 13(11): 2909-24 (2004). Link
  • H.D. Nguyen and C.K. Hall, "Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides," the Proceedings of the National Academy of Sciences USA, accepted.
  • H.D. Nguyen and C.K. Hall, "Spontaneous Fibril Formation by Polyalanines; Discontinuous Molecular Dynamics Simulations," J. Mol. Biol., submitted.
  • H.D. Nguyen and C.K. Hall, "Kinetics of Fibril Formation by Polyalanine Peptides," J. Biol. Chem., submitted.
  • H.D. Nguyen and C.K. Hall, "Phase diagrams describing fibrillization by polyalanine peptides," Biophys. J., in press. Link
  • C.K. Hall, H.D. Nguyen, A.J. Marchut, and V. Wagoner, "Protein aggregation simulations: a review" in Misbehaving Proteins: Protein (Mis)Folding, Aggregation, and Stability, Kluwer Academic Press, submitted.

Presentations:

  • H.D. Nguyen and C.K. Hall, "Fibril formation by polyalanine peptides," oral presentation given at the American Institute of Chemical Engineers Annual Meeting, San Francisco, CA, November, 2003
  • H.D. Nguyen and C.K. Hall, "Solvent effects on the conformational transition of a model polyalanine peptide," poster presentation given at the American Institute of Chemical Engineers Annual Meeting, San Francisco, CA, November, 2003
  • H.D. Nguyen and C.K. Hall, "Thermodynamics and Kinetics of Polyalanine Fibril Formation," poster presented at the Biophysical Society Annual Meeting, San Antonio, TX, March, 2003.
  • H.D. Nguyen and C.K. Hall, "Molecular dynamics simulations of Polyalanine Fibril Formation," oral presentation given at the Biophysical Society Annual Meeting, San Antonio, TX, March, 2003.
  • H.D. Nguyen, A.J. Marchut and C.K. Hall, "Molecular dynamics simulations of protein aggregation including fibril formation," poster presented at the Fourth Biannual Triangle Biophysics Symposium, Chapel Hill, NC, November, 2002.
  • H.D. Nguyen and C.K. Hall, "Molecular dynamics simulations of fibril formation from polyalanines," oral presentation given at the American Institute of Chemical Engineers Annual Meeting, Indianapolis, IN, November, 2002.
  • H.D. Nguyen and C.K. Hall, "Computer simulations of protein folding and aggregation in the presence of solutes," poster presented at the American Institute of Chemical Engineers Annual Meeting, Indianapolis, IN, November, 2002.
  • H.D. Nguyen and C.K. Hall, "Computer simulations of protein aggregation," poster presented at the Mid-Atlantic Meeting on Thermodynamics, College Park, MD, April, 2002.
  • H.D. Nguyen and C.K. Hall, "Computer simulations of protein aggregation," poster presented at the Biophysical Society Annual Meeting, San Francisco, CA, February, 2002.
  • H.D. Nguyen and C.K. Hall, "Computer simulations of protein folding and aggregation using lattice models," oral presentation given at the American Institute of Chemical Engineers Annual Meeting, Reno, NV, November, 2001.

Curriculum Vitae





hdnguyen@scripps.edu