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Statistical Physics of Protein Folding and Aggregation

Favrin, Giorgio LU (2004)
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... (More)
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. (Less)
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author
opponent
  • Associate Professor Hansmann, Ulrich H E, Department of Physics Michigan Technological University
organization
publishing date
type
Thesis
publication status
published
subject
keywords
Two State, Physics, Fysik, Statistics, operations research, programming, aktuariematematik, programmering, operationsanalys, actuarial mathematics, Statistik, Simulations, Aggregation, Protein Folding, Fysicumarkivet A:2004:Favrin
pages
124 pages
publisher
Lund University
defense location
N/A
defense date
2004-05-19 10:15
ISBN
91-628-6073-9
language
English
LU publication?
yes
id
d7287604-83f2-4bbe-a994-c598e10c1aa1 (old id 466939)
date added to LUP
2007-08-09 09:04:26
date last changed
2016-09-19 08:45:07
@misc{d7287604-83f2-4bbe-a994-c598e10c1aa1,
  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.},
  author       = {Favrin, Giorgio},
  isbn         = {91-628-6073-9},
  keyword      = {Two State,Physics,Fysik,Statistics,operations research,programming,aktuariematematik,programmering,operationsanalys,actuarial mathematics,Statistik,Simulations,Aggregation,Protein Folding,Fysicumarkivet A:2004:Favrin},
  language     = {eng},
  pages        = {124},
  publisher    = {ARRAY(0x897e9d8)},
  title        = {Statistical Physics of Protein Folding and Aggregation},
  year         = {2004},
}