Advanced

Hydrogen bonds, hydrophobicity forces and the character of the collapse transition

Irbäck, A LU ; Sjunnesson, F LU and Wallin, S LU (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)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
in
Journal of Biological Physics
volume
27
issue
2-3
pages
11 pages
publisher
Kluwer
external identifiers
  • 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
2016-10-13 05:12:28
@misc{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    = {ARRAY(0x9a1cd50)},
  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},
  volume       = {27},
  year         = {2001},
}