Local interactions and protein folding : A three-dimensional off-lattice approach
(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.
(Less)
- author
- Irbäck, Anders LU ; Peterson, Carsten LU ; Potthast, Fránk LU and Sommelius, Ola LU
- organization
- publishing date
- 1997-07-01
- type
- Contribution to journal
- publication status
- published
- in
- Journal of Chemical Physics
- volume
- 107
- issue
- 1
- pages
- 10 pages
- publisher
- American Institute of Physics (AIP)
- external identifiers
-
- scopus:0000699921
- ISSN
- 0021-9606
- DOI
- 10.1063/1.474357
- language
- English
- LU publication?
- yes
- id
- 04d710ee-53b4-44a1-ae6d-3781ccac7441
- date added to LUP
- 2016-08-17 17:58:58
- date last changed
- 2024-01-04 10:59:37
@article{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.</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 = {{American Institute of Physics (AIP)}}, 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}}, doi = {{10.1063/1.474357}}, volume = {{107}}, year = {{1997}}, }