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Published online before print February 6, 2004, 10.1110/ps.03431704
Protein Science (2004), 13:752-762. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins

Susanne Moelbert1,2, Eldon Emberly1,3 and Chao Tang1

1 NEC Laboratories America, Princeton, New Jersey 08540, USA
2 Institut de Physique Théorique, Université de Lausanne, 1015 Lausanne, Switzerland
3 Center for Studies in Physics and Biology, Rockefeller University, New York, New York 10021, USA

(RECEIVED September 10, 2003; FINAL REVISION November 26, 2003; ACCEPTED November 28, 2003)



Abstract

Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tend to occur at the surface of a folded protein. By analyzing the known protein structures, we quantify the degree to which the hydrophobicity sequence of a protein correlates with its pattern of surface exposure. We have assessed the statistical significance of this correlation for several hydrophobicity scales in the literature, and find that the computed correlations are significant but far from optimal. We show that this less than optimal correlation arises primarily from the large degree of mutations that naturally occurring proteins can tolerate. Lesser effects are due in part to forces other than hydrophobicity, and we quantify this by analyzing the surface-exposure distributions of all amino acids. Lastly, we show that our database findings are consistent with those found from an off-lattice hydrophobic–polar model of protein folding.

Keywords: hydrophobicity; protein folding; surface exposure; secondary structure; designability

Reprint requests to: Chao Tang, NEC Laboratories America, Princeton, NJ 08540, USA; e-mail: tang{at}nec-labs.com; fax: (609) 951-2483.

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.03431704.


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