Hydrogen bonds, hydrophobicity forces and the character of the collapse transition
(2001) In Journal of Biological Physics 27(2-3). p.79-169- Abstract
We study the thermodynamic behavior of a model protein with 54 amino acidsthat is designed to form a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid, and has the Ramachandran torsion angles as its only degrees of freedom.The force field is based on hydrogen bonds and effective hydrophobicity forces. We study how the character of the collapse transition depends on the strengths of these forces. For a suitable choice of these two parameters, it is found that the collapse transition is first-order-like and coincides with the folding transition. Also shown is that the corresponding one- and two-helix segments make less stable secondary structure than the three-helix... (More)
We study the thermodynamic behavior of a model protein with 54 amino acidsthat is designed to form a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid, and has the Ramachandran torsion angles as its only degrees of freedom.The force field is based on hydrogen bonds and effective hydrophobicity forces. We study how the character of the collapse transition depends on the strengths of these forces. For a suitable choice of these two parameters, it is found that the collapse transition is first-order-like and coincides with the folding transition. Also shown is that the corresponding one- and two-helix segments make less stable secondary structure than the three-helix sequence.
(Less)
- author
- Irbäck, A LU ; Sjunnesson, F LU and Wallin, S LU
- organization
- publishing date
- 2001-06
- type
- Contribution to journal
- publication status
- published
- in
- Journal of Biological Physics
- volume
- 27
- issue
- 2-3
- pages
- 11 pages
- publisher
- Springer
- external identifiers
-
- pmid:23345742
- scopus:0035681698
- ISSN
- 0092-0606
- DOI
- 10.1023/A:1013155018382
- language
- English
- LU publication?
- yes
- id
- 51c9a97b-16be-44b8-a1bf-8adfb0b3af9c
- date added to LUP
- 2016-08-17 16:25:46
- date last changed
- 2024-06-28 13:32:53
@article{51c9a97b-16be-44b8-a1bf-8adfb0b3af9c, abstract = {{<p>We study the thermodynamic behavior of a model protein with 54 amino acidsthat is designed to form a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid, and has the Ramachandran torsion angles as its only degrees of freedom.The force field is based on hydrogen bonds and effective hydrophobicity forces. We study how the character of the collapse transition depends on the strengths of these forces. For a suitable choice of these two parameters, it is found that the collapse transition is first-order-like and coincides with the folding transition. Also shown is that the corresponding one- and two-helix segments make less stable secondary structure than the three-helix sequence.</p>}}, author = {{Irbäck, A and Sjunnesson, F and Wallin, S}}, issn = {{0092-0606}}, language = {{eng}}, number = {{2-3}}, pages = {{79--169}}, publisher = {{Springer}}, series = {{Journal of Biological Physics}}, title = {{Hydrogen bonds, hydrophobicity forces and the character of the collapse transition}}, url = {{http://dx.doi.org/10.1023/A:1013155018382}}, doi = {{10.1023/A:1013155018382}}, volume = {{27}}, year = {{2001}}, }