Anders Irbäck
Professor
Folding of a small helical protein using hydrogen bonds and hydrophobicity forces.
Author
Summary, in English
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.
Publishing year
2002
Language
English
Pages
99-105
Publication/Series
Proteins
Volume
47
Issue
2
Document type
Article
Publisher
Wiley-Liss Inc.
Topic
- Biophysics
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
Status
Published
ISBN/ISSN/Other
- ISSN: 0887-3585