Statistical Physics of Protein Folding and Aggregation

Giorgio Favrin

Research output: ThesisDoctoral Thesis (compilation)

Abstract

The mechanisms of protein folding and aggregation are investigated by computer simulations of all-atom and reduced models with sequence-based potentials. A quasi local Monte Carlo update is developed in order to efficiently sample proteins in the folded phase. A small helical protein, the B-domain of staphylococcal protein A, is studied using a reduced model. In the thermodynamically favoured topology, energy minimisation leads to a conformation whose root mean square deviation form the experimental structure is 1.8Å. We also study the thermodynamics and kinetics of small fast folding proteins without a clear free-energy barrier between the folded and unfolded states. Analytical calculations using a square well-potential enable us to predict the relaxation time within a factor of two. Finally using an all atom model, we study the aggregation properties of a 7-amino acid fragment of Alzheimer's amyloid beta peptide. We find that the system of three and six such fragments form aggregated structures with a high content of antiparallel beta-sheet structure, which is in line with experimental data.
Original languageEnglish
QualificationDoctor
Awarding Institution
  • Computational Biology and Biological Physics
Supervisors/Advisors
  • [unknown], [unknown], Supervisor, External person
Award date2004 May 19
Publisher
ISBN (Print)91-628-6073-9
Publication statusPublished - 2004

Bibliographical note

Defence details

Date: 2004-05-19
Time: 10:15
Place: N/A

External reviewer(s)

Name: Hansmann, Ulrich H E
Title: Associate Professor
Affiliation: Department of Physics Michigan Technological University

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Subject classification (UKÄ)

  • Biophysics

Keywords

  • Two State
  • Physics
  • Fysik
  • Statistics
  • operations research
  • programming
  • aktuariematematik
  • programmering
  • operationsanalys
  • actuarial mathematics
  • Statistik
  • Simulations
  • Aggregation
  • Protein Folding
  • Fysicumarkivet A:2004:Favrin

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