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Local interactions and protein folding : A model study on the square and triangular lattices

Irbäck, Anders LU and Sandelin, Erik LU (1998) In Journal of Chemical Physics 108(5). p.2245-2250
Abstract

We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength κ of the local interactions; κ=0 corresponds to the well-known HP model [K. F. Lau and K. A. Dill, Macromolecules 22, 3986 (1989)]. By exhaustive enumerations for short chains, we obtain all structures which act as a unique and pronounced energy minimum for at least one sequence. We find that the number of such designable structures depends strongly on κ. Also, we find that the number of designable structures can differ widely for the two lattices at a given κ. This is the case, for example, at κ=0, which implies that the HP model... (More)

We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength κ of the local interactions; κ=0 corresponds to the well-known HP model [K. F. Lau and K. A. Dill, Macromolecules 22, 3986 (1989)]. By exhaustive enumerations for short chains, we obtain all structures which act as a unique and pronounced energy minimum for at least one sequence. We find that the number of such designable structures depends strongly on κ. Also, we find that the number of designable structures can differ widely for the two lattices at a given κ. This is the case, for example, at κ=0, which implies that the HP model exhibits different behavior on the two lattices. Our findings clearly show that sequence-independent local properties of the chains can play an important rote in the formation of unique minimum energy structures.

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author
organization
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type
Contribution to journal
publication status
published
in
Journal of Chemical Physics
volume
108
issue
5
pages
6 pages
publisher
American Institute of Physics
external identifiers
  • scopus:0000553651
ISSN
0021-9606
DOI
10.1063/1.475605
language
English
LU publication?
yes
id
6215b4d7-b348-44d2-b4a8-5144bc953db2
date added to LUP
2016-08-17 17:53:37
date last changed
2018-01-07 11:23:26
@article{6215b4d7-b348-44d2-b4a8-5144bc953db2,
  abstract     = {<p>We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength κ of the local interactions; κ=0 corresponds to the well-known HP model [K. F. Lau and K. A. Dill, Macromolecules 22, 3986 (1989)]. By exhaustive enumerations for short chains, we obtain all structures which act as a unique and pronounced energy minimum for at least one sequence. We find that the number of such designable structures depends strongly on κ. Also, we find that the number of designable structures can differ widely for the two lattices at a given κ. This is the case, for example, at κ=0, which implies that the HP model exhibits different behavior on the two lattices. Our findings clearly show that sequence-independent local properties of the chains can play an important rote in the formation of unique minimum energy structures.</p>},
  author       = {Irbäck, Anders and Sandelin, Erik},
  issn         = {0021-9606},
  language     = {eng},
  month        = {02},
  number       = {5},
  pages        = {2245--2250},
  publisher    = {American Institute of Physics},
  series       = {Journal of Chemical Physics},
  title        = {Local interactions and protein folding : A model study on the square and triangular lattices},
  url          = {http://dx.doi.org/10.1063/1.475605},
  volume       = {108},
  year         = {1998},
}