Research Article

Untangling influences of hydrophobicity on protein sequences and structures

  1. Mehdi Yahyanejad1,*,
  2. Christopher B. Burge2,
  3. Mehran Kardar3

Article first published online: 22 DEC 2005

DOI: 10.1002/prot.20775

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Volume 62, Issue 4, pages 1101–1106, 1 March 2006

Additional Information

How to Cite

Yahyanejad, M., Burge, C. B. and Kardar, M. (2006), Untangling influences of hydrophobicity on protein sequences and structures. Proteins: Structure, Function, and Bioinformatics, 62: 1101–1106. doi: 10.1002/prot.20775

Author Information

  1. 1

    Department of Pathology, Stanford University, Stanford, California

  2. 2

    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts

  3. 3

    Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts

*Department of Pathology, Stanford University, Stanford, CA 94305

Publication History

  1. Issue published online: 8 FEB 2006
  2. Article first published online: 22 DEC 2005
  3. Manuscript Accepted: 24 AUG 2005
  4. Manuscript Received: 13 JUN 2005

Funded by

  • Functional Genomics Innovation Award
  • National Science Foundation. Grant Number: DMR-0426677

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Keywords:

  • hydrophobicity;
  • solvent accessibility;
  • protein sequences;
  • correlations;
  • Boltzmann weight;
  • Fourier transform

Abstract

We perform a statistical analysis of solvent accessibility and hydrophobicity profiles of a representative set of proteins. The joint probability distribution is well fitted to a multivariable Gaussian, which takes a relatively simple form when expressed in terms of the Fourier transforms of the profiles. This allows us to quantify the asymmetric manner by which these profiles influence each other. For example, the α-helix periodicity in sequence hydrophobicity is dictated by the solvent accessibility of structures, and not vice versa, possibly indicating the faster evolution of sequences compared to structures. The decorrelated hydrophobicity and solvent accessibility profiles show distinct behaviors at long periods, where sequence hydrophobicity fluctuates less, while solvent accessibility fluctuates more than average. The correlations between the two profiles can be interpreted as the Boltzmann weight of the solvation energy at room temperature, consistent with earlier observations. Proteins 2006. © 2005 Wiley-Liss, Inc.

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