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Thermodynamics of Protein Folding and Design

Sandelin, Erik LU (2000)
Abstract (Swedish)
Popular Abstract in Swedish

Proteinvecknings- och proteindesign-problemen studeras med hjälp av modeller med låg upplösning och endast två typer av aminosyror, hydrofoba och hydrofila. Förutom hydrofoba krafter innehåller modellerna sekvensoberoende lokal växelverkan som visar sig ha stor påverkan på termodynamiken hos dessa modeller. Modellerna studeras med hjälp av dynamisk-parameter Monte Carlo-metoden. Vi utvecklar en Monte Carlo-algoritm för proteindesign baserad på denna metod. Vi testar också metodens användbarhet för ett annat svårt problem i beräkningsbiologi, sekvensrekonstruerings- problemet. Till sist studerar vi den statistiska fördelningen av hydrofobicitet, hos verkliga proteiner såväl som modellproteiner.
Abstract
The protein folding and protein design problems are addressed, using coarse-grained models with only two types of amino acids, hydrophobic and hydrophilic. In addition to hydrophobicity forces, the models contain sequence-independent local interactions which are found to strongly influence the thermodynamics of these models. The models are studied using the dynamical-parameter Monte Carlo method. A Monte Carlo approach to protein design based on this method is developed, and the usefulness of the method for another difficult problem in computational biology, sequence assembly, is explored. Finally, the statistical distribution of hydrophobicity in real and model protein sequences is studied.
Please use this url to cite or link to this publication:
author
opponent
  • Chan, Hue Sun
organization
publishing date
type
Thesis
publication status
published
subject
keywords
protein folding, hydrophobicity, Monte Carlo, sequence analysis, sequence assembly, shotgun sequencing, Mathematical and general theoretical physics, classical mechanics, quantum mechanics, relativity, gravitation, statistical physics, Matematisk och allmän teoretisk fysik, thermodynamics, termodynamik, Fysicumarkivet A:2000:Sandelin, statistisk fysik, relativitet, protein design, klassisk mekanik, kvantmekanik
pages
139 pages
publisher
Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
defense location
Sal F, Theoretical Physics
defense date
2000-10-20 10:15
ISBN
91-628-4305-2
language
English
LU publication?
yes
id
f87707c5-9a5d-4998-9283-d60599f75431 (old id 40804)
date added to LUP
2007-08-01 11:50:33
date last changed
2016-09-19 08:45:08
@misc{f87707c5-9a5d-4998-9283-d60599f75431,
  abstract     = {The protein folding and protein design problems are addressed, using coarse-grained models with only two types of amino acids, hydrophobic and hydrophilic. In addition to hydrophobicity forces, the models contain sequence-independent local interactions which are found to strongly influence the thermodynamics of these models. The models are studied using the dynamical-parameter Monte Carlo method. A Monte Carlo approach to protein design based on this method is developed, and the usefulness of the method for another difficult problem in computational biology, sequence assembly, is explored. Finally, the statistical distribution of hydrophobicity in real and model protein sequences is studied.},
  author       = {Sandelin, Erik},
  isbn         = {91-628-4305-2},
  keyword      = {protein folding,hydrophobicity,Monte Carlo,sequence analysis,sequence assembly,shotgun sequencing,Mathematical and general theoretical physics,classical mechanics,quantum mechanics,relativity,gravitation,statistical physics,Matematisk och allmän teoretisk fysik,thermodynamics,termodynamik,Fysicumarkivet A:2000:Sandelin,statistisk fysik,relativitet,protein design,klassisk mekanik,kvantmekanik},
  language     = {eng},
  pages        = {139},
  publisher    = {ARRAY(0xb19c228)},
  title        = {Thermodynamics of Protein Folding and Design},
  year         = {2000},
}