Modeling of Protein Folding and Genetic Networks

Fredrik Sjunnesson

Modeling of Protein Folding and Genetic Networks

Fredrik Sjunnesson

Research output: Thesis › Doctoral Thesis (compilation)

Abstract

Models for potein folding are developed and applied to peptides and small proteins with both α-helix and β-sheet structure. The energy functions, in which effective hydrophobicity forces and hydrogen bonds are taken to be the two central terms, are sequence-based and deliberately kept simple.
The geometric representations of the protein chains are, by contrast, detailed and have torsion angles as the degrees of freedom. The thermodynamic properties of the models are studied using Monte Carlo methods and quantitative comparisons with experiments are carried out. To improve the sampling of compact states, a semi-local Monte Carlo update in the backbone torsion angles is developed. In addition, the thesis includes a study of a simple model for genetic networks, the Kauffman model.

Original language	English
Qualification	Doctor
Awarding Institution
Supervisors/Advisors	[unknown], [unknown], Supervisor, External person
Award date	2003 Oct 3
Publisher	Department of Theoretical Physics, Lund University
ISBN (Print)	91-628-5783-5
Publication status	Published - 2003

Bibliographical note

Defence details

Date: 2003-10-03
Time: 13:15
Place: Lecture Hall F, Dept. of Theoretical Physics

External reviewer(s)

Name: Bastolla, Ugo
Title: [unknown]
Affiliation: [unknown]

---

Subject classification (UKÄ)

Biophysics

Free keywords

Matematisk och allmän teoretisk fysik
thermodynamics
two-state folding
Protein folding
all-atom model
Mathematical and general theoretical physics
Kauffman model.
local update
Monte Carlo
classical mechanics
quantum mechanics
relativity
statistical physics
gravitation
klassisk mekanik
kvantmekanik
relativitet
statistisk fysik
termodynamik
Fysicumarkivet A:2003:Sjunnesson

3 Article

Folding thermodynamics of three beta-sheet peptides: A model study
Irbäck, A. & Sjunnesson, F., 2004, In: Proteins. 56, 1, p. 110-116
Research output: Contribution to journal › Article › peer-review
Stability of the Kauffman model.
Bilke, S. & Sjunnesson, F., 2002, In: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). 65, 1 Pt 2, p. 016129-1-016129-5
Research output: Contribution to journal › Article › peer-review
Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space
Favrin, G., Irbäck, A. & Sjunnesson, F., 2001, In: Journal of Chemical Physics. 114, 8, p. 8154-8158
Research output: Contribution to journal › Article › peer-review

Cite this

@phdthesis{706759b2aefd49bb90e437cfae45ea5f,

title = "Modeling of Protein Folding and Genetic Networks",

abstract = "Models for potein folding are developed and applied to peptides and small proteins with both α-helix and β-sheet structure. The energy functions, in which effective hydrophobicity forces and hydrogen bonds are taken to be the two central terms, are sequence-based and deliberately kept simple. The geometric representations of the protein chains are, by contrast, detailed and have torsion angles as the degrees of freedom. The thermodynamic properties of the models are studied using Monte Carlo methods and quantitative comparisons with experiments are carried out. To improve the sampling of compact states, a semi-local Monte Carlo update in the backbone torsion angles is developed. In addition, the thesis includes a study of a simple model for genetic networks, the Kauffman model.",

keywords = "Matematisk och allm{\"a}n teoretisk fysik, thermodynamics, two-state folding, Protein folding, all-atom model, Mathematical and general theoretical physics, Kauffman model., local update, Monte Carlo, classical mechanics, quantum mechanics, relativity, statistical physics, gravitation, klassisk mekanik, kvantmekanik, relativitet, statistisk fysik, termodynamik, Fysicumarkivet A:2003:Sjunnesson",

author = "Fredrik Sjunnesson",

note = "Defence details Date: 2003-10-03 Time: 13:15 Place: Lecture Hall F, Dept. of Theoretical Physics External reviewer(s) Name: Bastolla, Ugo Title: [unknown] Affiliation: [unknown] ---",

year = "2003",

language = "English",

isbn = "91-628-5783-5",

publisher = "Department of Theoretical Physics, Lund University",

type = "Doctoral Thesis (compilation)",

}

TY - THES

T1 - Modeling of Protein Folding and Genetic Networks

AU - Sjunnesson, Fredrik

N1 - Defence details Date: 2003-10-03 Time: 13:15 Place: Lecture Hall F, Dept. of Theoretical Physics External reviewer(s) Name: Bastolla, Ugo Title: [unknown] Affiliation: [unknown] ---

PY - 2003

Y1 - 2003

N2 - Models for potein folding are developed and applied to peptides and small proteins with both α-helix and β-sheet structure. The energy functions, in which effective hydrophobicity forces and hydrogen bonds are taken to be the two central terms, are sequence-based and deliberately kept simple. The geometric representations of the protein chains are, by contrast, detailed and have torsion angles as the degrees of freedom. The thermodynamic properties of the models are studied using Monte Carlo methods and quantitative comparisons with experiments are carried out. To improve the sampling of compact states, a semi-local Monte Carlo update in the backbone torsion angles is developed. In addition, the thesis includes a study of a simple model for genetic networks, the Kauffman model.

AB - Models for potein folding are developed and applied to peptides and small proteins with both α-helix and β-sheet structure. The energy functions, in which effective hydrophobicity forces and hydrogen bonds are taken to be the two central terms, are sequence-based and deliberately kept simple. The geometric representations of the protein chains are, by contrast, detailed and have torsion angles as the degrees of freedom. The thermodynamic properties of the models are studied using Monte Carlo methods and quantitative comparisons with experiments are carried out. To improve the sampling of compact states, a semi-local Monte Carlo update in the backbone torsion angles is developed. In addition, the thesis includes a study of a simple model for genetic networks, the Kauffman model.

KW - Matematisk och allmän teoretisk fysik

KW - thermodynamics

KW - two-state folding

KW - Protein folding

KW - all-atom model

KW - Mathematical and general theoretical physics

KW - Kauffman model.

KW - local update

KW - Monte Carlo

KW - classical mechanics

KW - quantum mechanics

KW - relativity

KW - statistical physics

KW - gravitation

KW - klassisk mekanik

KW - kvantmekanik

KW - relativitet

KW - statistisk fysik

KW - termodynamik

KW - Fysicumarkivet A:2003:Sjunnesson

M3 - Doctoral Thesis (compilation)

SN - 91-628-5783-5

PB - Department of Theoretical Physics, Lund University

ER -

Modeling of Protein Folding and Genetic Networks

Abstract

Bibliographical note

Subject classification (UKÄ)

Free keywords

Fingerprint

Research output

Folding thermodynamics of three beta-sheet peptides: A model study

Stability of the Kauffman model.

Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space

Cite this