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Anders Irbäck. Photo.

Anders Irbäck

Professor

Anders Irbäck. Photo.

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

Author

  • Giorgio Favrin
  • Anders Irbäck
  • Stefan Wallin

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.

Department/s

  • Computational Biology and Biological Physics

Publishing year

2002

Language

English

Pages

99-105

Publication/Series

Proteins

Volume

47

Issue

2

Document type

Journal article

Publisher

John Wiley and Sons

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