Thermodynamics of Protein Folding and Design

Summary, in English

The protein folding and protein design problems are addressed, using coarse-grained models with only two types of amino acids, hydrophobic and hydrophilic. In addition to hydrophobicity forces, the models contain sequence-independent local interactions which are found to strongly influence the thermodynamics of these models. The models are studied using the dynamical-parameter Monte Carlo method. A Monte Carlo approach to protein design based on this method is developed, and the usefulness of the method for another difficult problem in computational biology, sequence assembly, is explored. Finally, the statistical distribution of hydrophobicity in real and model protein sequences is studied.

• Author: Erik Sandelin
• Department/s: Computational Biology and Biological Physics - Undergoing reorganization
• Publishing year: 2000
• Language: English
• Document type: Dissertation
• Publisher: Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
• Topic: Biophysics
• Keywords: protein folding; hydrophobicity; Monte Carlo; sequence analysis; sequence assembly; shotgun sequencing; Mathematical and general theoretical physics; classical mechanics; quantum mechanics; relativity; gravitation; statistical physics; Matematisk och allmän teoretisk fysik; thermodynamics; termodynamik; Fysicumarkivet A:2000:Sandelin; statistisk fysik; relativitet; protein design; klassisk mekanik; kvantmekanik
• Status: Published
• Supervisor: [unknown] [unknown]
• ISBN/ISSN/Other: ISBN: 91-628-4305-2
• Defence date: 20 October 2000
• Defence time: 10:15
• Defence place: Sal F, Theoretical Physics
• Opponent: Hue Sun Chan