Folding of a small helical protein using hydrogen bonds and hydrophobicity forces.
(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:
https://lup.lub.lu.se/record/107391
- author
- Favrin, Giorgio LU ; Irbäck, Anders LU and Wallin, Stefan LU
- organization
- publishing date
- 2002
- 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 Inc.
- 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
- 2016-04-01 16:56:30
- date last changed
- 2024-04-12 10:31:41
@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}}, 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}}, language = {{eng}}, number = {{2}}, pages = {{99--105}}, publisher = {{John Wiley & Sons Inc.}}, series = {{Proteins}}, title = {{Folding of a small helical protein using hydrogen bonds and hydrophobicity forces.}}, url = {{http://dx.doi.org/10.1002/prot.10072}}, doi = {{10.1002/prot.10072}}, volume = {{47}}, year = {{2002}}, }