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Folding of a small helical protein using hydrogen bonds and hydrophobicity forces.

Favrin, Giorgio LU ; Irbäck, Anders LU and Wallin, Stefan LU (2002) In Proteins 47(2). p.99-105
Abstract
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Go approximation, which ignores non-native interactions. We find that the collapse transition is considerably more abrupt for the protein A sequence than for random sequences with the same composition. The chain collapse is found to be at least as fast as helix formation. Energy minimization restricted to the thermodynamically favored topology gives a structure that has a root-mean-square deviation of 1.8 A from the native structure. The sequence-dependent part of our potential is pairwise additive.... (More)
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Go approximation, which ignores non-native interactions. We find that the collapse transition is considerably more abrupt for the protein A sequence than for random sequences with the same composition. The chain collapse is found to be at least as fast as helix formation. Energy minimization restricted to the thermodynamically favored topology gives a structure that has a root-mean-square deviation of 1.8 A from the native structure. The sequence-dependent part of our potential is pairwise additive. Our calculations suggest that fine-tuning this potential by parameter optimization is of limited use. (Less)
Please use this url to cite or link to this publication:
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organization
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type
Contribution to journal
publication status
published
subject
keywords
Hydrophobicity, Models, Molecular, Molecular Sequence Data, Monte Carlo Method, Peptide Fragments : chemistry, Protein Folding, Protein Structure, Proteins : chemistry, Staphylococcal Protein A : chemistry, Secondary, Kinetics, Support, Non-U.S. Gov't, Hydrogen Bonding, Amino Acid Sequence, Comparative Study
in
Proteins
volume
47
issue
2
pages
99 - 105
publisher
John Wiley & Sons
external identifiers
  • pmid:11933057
  • wos:000174713400001
  • scopus:0036568327
ISSN
0887-3585
DOI
10.1002/prot.10072
language
English
LU publication?
yes
id
df99cd2a-0c34-4d37-a630-b8a5f7e9be1b (old id 107391)
alternative location
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11933057&dopt=Abstract
date added to LUP
2007-07-20 11:55:13
date last changed
2017-08-20 04:31:39
@article{df99cd2a-0c34-4d37-a630-b8a5f7e9be1b,
  abstract     = {A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Go approximation, which ignores non-native interactions. We find that the collapse transition is considerably more abrupt for the protein A sequence than for random sequences with the same composition. The chain collapse is found to be at least as fast as helix formation. Energy minimization restricted to the thermodynamically favored topology gives a structure that has a root-mean-square deviation of 1.8 A from the native structure. The sequence-dependent part of our potential is pairwise additive. Our calculations suggest that fine-tuning this potential by parameter optimization is of limited use.},
  author       = {Favrin, Giorgio and Irbäck, Anders and Wallin, Stefan},
  issn         = {0887-3585},
  keyword      = {Hydrophobicity,Models,Molecular,Molecular Sequence Data,Monte Carlo Method,Peptide Fragments : chemistry,Protein Folding,Protein Structure,Proteins : chemistry,Staphylococcal Protein A : chemistry,Secondary,Kinetics,Support,Non-U.S. Gov't,Hydrogen Bonding,Amino Acid Sequence,Comparative Study},
  language     = {eng},
  number       = {2},
  pages        = {99--105},
  publisher    = {John Wiley & Sons},
  series       = {Proteins},
  title        = {Folding of a small helical protein using hydrogen bonds and hydrophobicity forces.},
  url          = {http://dx.doi.org/10.1002/prot.10072},
  volume       = {47},
  year         = {2002},
}