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Evidence for nonrandom hydrophobicity structures in protein chains

Irbäck, A LU ; Peterson, C LU and Potthast, F LU (1996) In Proceedings of the National Academy of Sciences 93(18). p.8-9533
Abstract

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... (More)

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.

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author
organization
publishing date
type
Contribution to journal
publication status
published
keywords
Databases, Factual, Fourier Analysis, Protein Conformation, Proteins, Water
in
Proceedings of the National Academy of Sciences
volume
93
issue
18
pages
6 pages
publisher
National Academy of Sciences
external identifiers
  • Scopus:0029793096
ISSN
0027-8424
language
English
LU publication?
yes
id
787eb347-fd38-43a2-a9be-e43d0b7b4fbe
alternative location
http://www.jstor.org/stable/39745
date added to LUP
2016-08-17 16:30:29
date last changed
2016-10-30 04:49:17
@misc{787eb347-fd38-43a2-a9be-e43d0b7b4fbe,
  abstract     = {<p>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.</p>},
  author       = {Irbäck, A and Peterson, C and Potthast, F},
  issn         = {0027-8424},
  keyword      = {Databases, Factual,Fourier Analysis,Protein Conformation,Proteins,Water},
  language     = {eng},
  month        = {09},
  number       = {18},
  pages        = {8--9533},
  publisher    = {ARRAY(0x857a860)},
  series       = {Proceedings of the National Academy of Sciences},
  title        = {Evidence for nonrandom hydrophobicity structures in protein chains},
  volume       = {93},
  year         = {1996},
}