Physical Modeling of Protein Folding

Research output: ThesisDoctoral Thesis (compilation)

Abstract

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.

Details

Authors
  • Stefan Wallin
Organisations
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • 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
Original languageEnglish
QualificationDoctor
Awarding Institution
Supervisors/Assistant supervisor
  • [unknown], [unknown], Supervisor, External person
Award date2003 Jun 4
Publisher
  • Department of Theoretical Physics, Lund University
Print ISBNs91-628-5671-5
Publication statusPublished - 2003
Publication categoryResearch

Bibliographic note

Defence details Date: 2003-06-04 Time: 10:15 Place: Lecture Hall F, Dept. of Theoretical Physics External reviewer(s) Name: Clementi, Cecilia Title: [unknown] Affiliation: Rice University, USA ---

Related research output

Giorgio Favrin, Anders Irbäck & Stefan Wallin, 2004, In : Proteins. 54, 1, p. 8-12

Research output: Contribution to journalArticle

Stefan Wallin, J Farwer & U Bastolla, 2003, In : Proteins. 50, 1, p. 144-157

Research output: Contribution to journalArticle

Anders Irbäck, Björn Samuelsson, Fredrik Sjunnesson & Stefan Wallin, 2003, In : Biophysical Journal. 85, 3, p. 1466-1473

Research output: Contribution to journalArticle

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