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Anders Irbäck. Photo.

Anders Irbäck

Professor

Anders Irbäck. Photo.

Evidence for nonrandom hydrophobicity structures in protein chains

Author

  • A Irbäck
  • C Peterson
  • F Potthast

Summary, in English

The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along the protein chains. Theoretical expectations of these variables from random distributions of hydrophobicities are compared with those obtained from functional proteins. The results, which are based upon proteins in the SWISS-PROT data base, convincingly show that the amino acid sequences in proteins differ from what is expected from random sequences in a statistically significant way. By performing Fourier transforms on the random walks, one obtains additional evidence for nonrandomness of the distributions. We have also analyzed results from a synthetic model containing only two amino acid types, hydrophobic and hydrophilic. With reasonable criteria on good folding properties in terms of thermodynamical and kinetic behavior, sequences that fold well are isolated. Performing the same statistical analysis on the sequences that fold well indicates similar deviations from randomness as for the functional proteins. The deviations from randomness can be interpreted as originating from anticorrelations in terms of an Ising spin model for the hydrophobicities. Our results, which differ from some previous investigations using other methods, might have impact on how permissive with respect to sequence specificity protein folding process is-only sequences with nonrandom hydrophobicity distributions fold well. Other distributions give rise to energy landscapes with poor folding properties and hence did not survive the evolution.

Department/s

  • Computational Biology and Biological Physics

Publishing year

1996-09-03

Language

English

Pages

8-9533

Publication/Series

Proceedings of the National Academy of Sciences

Volume

93

Issue

18

Document type

Journal article

Publisher

National Acad Sciences

Keywords

  • Databases, Factual
  • Fourier Analysis
  • Protein Conformation
  • Proteins
  • Water

Status

Published

ISBN/ISSN/Other

  • ISSN: 0027-8424