Statistical Physics of Protein Folding and Aggregation
(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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/466939
- author
- Favrin, Giorgio LU
- supervisor
- opponent
-
- Associate Professor Hansmann, Ulrich H E, Department of Physics Michigan Technological University
- organization
- publishing date
- 2004
- 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 10:15:00
- ISBN
- 91-628-6073-9
- language
- English
- LU publication?
- yes
- id
- d7287604-83f2-4bbe-a994-c598e10c1aa1 (old id 466939)
- date added to LUP
- 2016-04-04 11:01:57
- date last changed
- 2018-11-21 21:02:14
@phdthesis{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}}, keywords = {{Two State; Physics; Fysik; Statistics; operations research; programming; aktuariematematik; programmering; operationsanalys; actuarial mathematics; Statistik; Simulations; Aggregation; Protein Folding; Fysicumarkivet A:2004:Favrin}}, language = {{eng}}, publisher = {{Lund University}}, school = {{Lund University}}, title = {{Statistical Physics of Protein Folding and Aggregation}}, year = {{2004}}, }