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Physical Modeling of Protein Folding

Wallin, Stefan LU (2003)
Abstract (Swedish)
Popular Abstract in Swedish

Sekvensbaserade proteinveckningsmodeller utvecklas och testas på peptider med både betablad- och alfahelix-struktur, samt på små helix-proteiner. Modellernas potentialer är minimalistiska och baseras huvudsakligen på vätebindningar och effektiva hydrofobicitetskrafter. Den geometriska representationen av proteinkedjan är däremot detaljerad. Vi studerar det termodynamiska uppförandet med hjälp av effektiva Monte Carlo-metoder, och lägger tyngdpunkten på att uppnå en realistisk fysikalisk beskrivning av veckningsprocessen. Vi undersöker speciellt dynamiska aspekter av veckningen, som till exempel tvåtillståndsuppförande och bildandet av sekundärstruktur. I avhandlingen ingår dessutom ett arbete om... (More)
Popular Abstract in Swedish

Sekvensbaserade proteinveckningsmodeller utvecklas och testas på peptider med både betablad- och alfahelix-struktur, samt på små helix-proteiner. Modellernas potentialer är minimalistiska och baseras huvudsakligen på vätebindningar och effektiva hydrofobicitetskrafter. Den geometriska representationen av proteinkedjan är däremot detaljerad. Vi studerar det termodynamiska uppförandet med hjälp av effektiva Monte Carlo-metoder, och lägger tyngdpunkten på att uppnå en realistisk fysikalisk beskrivning av veckningsprocessen. Vi undersöker speciellt dynamiska aspekter av veckningen, som till exempel tvåtillståndsuppförande och bildandet av sekundärstruktur. I avhandlingen ingår dessutom ett arbete om likhetsmått för proteinstrukturer. (Less)
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... (More)
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. (Less)
Please use this url to cite or link to this publication:
author
opponent
  • Clementi, Cecilia, Rice University, USA
organization
publishing date
type
Thesis
publication status
published
subject
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
pages
160 pages
publisher
Department of Theoretical Physics, Lund University
defense location
Lecture Hall F, Dept. of Theoretical Physics
defense date
2003-06-04 10:15
ISBN
91-628-5671-5
language
English
LU publication?
yes
id
af199d10-aa3a-4404-ab38-08d1d2d1a237 (old id 465910)
date added to LUP
2007-08-09 12:07:43
date last changed
2016-09-19 08:45:11
@misc{af199d10-aa3a-4404-ab38-08d1d2d1a237,
  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.},
  author       = {Wallin, Stefan},
  isbn         = {91-628-5671-5},
  keyword      = {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},
  language     = {eng},
  pages        = {160},
  publisher    = {ARRAY(0x8816aa0)},
  title        = {Physical Modeling of Protein Folding},
  year         = {2003},
}