Physical Modeling of Protein Folding
Author
Summary, in English
Sequence-based models for protein folding are developed and tested on peptides with both alpha- and beta-structure, and on small three-helix-bundle proteins. The interaction potentials of the models are minimalistic and based mainly on hydrogen bonding and effective hydrophobicity forces. By contrast, the geometric representation of the protein chain is detailed. We explore the thermodynamic behaviors of these models by using efficient Monte Carlo methods, and focus on obtaining a realistic physical description of the folding process. In particular, we investigate dynamical aspects of folding, such as `two-state' behavior and secondary structure formation. In addition, the thesis includes a study on similarity measures for protein structures.
Publishing year
2003
Language
English
Document type
Dissertation
Publisher
Department of Theoretical Physics, Lund University
Topic
- Biophysics
Keywords
- relativity
- quantum mechanics
- classical mechanics
- three-helix bundle
- similarity measure
- Mathematical and general theoretical physics
- protein dynamics
- protein folding
- two-state
- Matematisk och allmän teoretisk fysik
- thermodynamics
- statistical physics
- gravitation
- klassisk mekanik
- kvantmekanik
- relativitet
- statistisk fysik
- termodynamik
- Fysicumarkivet A:2003:Wallin
Status
Published
Supervisor
- [unknown] [unknown]
ISBN/ISSN/Other
- ISBN: 91-628-5671-5
Defence date
4 June 2003
Defence time
10:15
Defence place
Lecture Hall F, Dept. of Theoretical Physics
Opponent
- Cecilia Clementi