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Local interactions and protein folding : A three-dimensional off-lattice approach

Irbäck, Anders LU ; Peterson, Carsten LU ; Potthast, Fránk LU and Sommelius, Ola LU (1997) In Journal of Chemical Physics 107(1). p.273-282
Abstract

The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobia and hydrophilic. In absence of local interactions, native structure formation does not occur for the temperatures considered. By including sequence independent local interactions, which qualitatively reproduce local properties of functional proteins, the dominance of a native state for many sequences is observed. As in lattice model approaches, folding takes place by gradual compactification, followed by a sequence dependent folding transition. Our results differ from lattice approaches in that bimodal energy distributions are not observed and that high folding temperatures are... (More)

The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobia and hydrophilic. In absence of local interactions, native structure formation does not occur for the temperatures considered. By including sequence independent local interactions, which qualitatively reproduce local properties of functional proteins, the dominance of a native state for many sequences is observed. As in lattice model approaches, folding takes place by gradual compactification, followed by a sequence dependent folding transition. Our results differ from lattice approaches in that bimodal energy distributions are not observed and that high folding temperatures are accompanied by relatively low temperatures for the peak of the specific heat. Also, in contrast to earlier studies using lattice models, our results convincingly demonstrate that one does not need more than two types of residues to generate sequences with good thermodynamic folding properties in three dimensions. © 1997 American Institute of Physics.

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author
publishing date
type
Contribution to journal
publication status
published
in
Journal of Chemical Physics
volume
107
issue
1
pages
10 pages
publisher
American Institute of Physics
external identifiers
  • Scopus:0000699921
ISSN
0021-9606
DOI
10.1063/1.474357
language
English
LU publication?
no
id
04d710ee-53b4-44a1-ae6d-3781ccac7441
date added to LUP
2016-08-17 17:58:58
date last changed
2016-10-13 05:12:31
@misc{04d710ee-53b4-44a1-ae6d-3781ccac7441,
  abstract     = {<p>The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobia and hydrophilic. In absence of local interactions, native structure formation does not occur for the temperatures considered. By including sequence independent local interactions, which qualitatively reproduce local properties of functional proteins, the dominance of a native state for many sequences is observed. As in lattice model approaches, folding takes place by gradual compactification, followed by a sequence dependent folding transition. Our results differ from lattice approaches in that bimodal energy distributions are not observed and that high folding temperatures are accompanied by relatively low temperatures for the peak of the specific heat. Also, in contrast to earlier studies using lattice models, our results convincingly demonstrate that one does not need more than two types of residues to generate sequences with good thermodynamic folding properties in three dimensions. © 1997 American Institute of Physics.</p>},
  author       = {Irbäck, Anders and Peterson, Carsten and Potthast, Fránk and Sommelius, Ola},
  issn         = {0021-9606},
  language     = {eng},
  month        = {07},
  number       = {1},
  pages        = {273--282},
  publisher    = {ARRAY(0xbe761e8)},
  series       = {Journal of Chemical Physics},
  title        = {Local interactions and protein folding : A three-dimensional off-lattice approach},
  url          = {http://dx.doi.org/10.1063/1.474357},
  volume       = {107},
  year         = {1997},
}