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On Hydrophobicity and Conformational Specificity in Proteins

Stockholm Bioinformatics Center, AlbaNova, Stockholms Universitet, Stockholm, Sweden

Correspondence: Address reprint requests to Erik Sandelin, Stockholm Bioinformatics Center, AlbaNova, Stockholms Universitet, Stockholm 106 91, Sweden. E-mail: erik{at}sbc.su.se.

In this study we examine the distribution of hydrophobic residues in a nonredundant set of monomeric globular single-domain proteins. We find that the total fraction of hydrophobic residues is roughly constant and has no discernible dependence on protein size. This results in a decrease of the hydrophobicity of the core as the size of proteins increases. Using a normalized measure, and by comparing with sets of randomly reshuffled sequences, we show that this change in the composition of the core is statistically significant and robust with respect to which amino acids are considered hydrophobic and to how buried residues are defined. Comparison with model sequences optimized for stability, while still required to retain their native state as a unique minimum energy conformation, suggests that the size-independence of the total fraction of hydrophobic residues could be a result of requiring proteins to be conformationally specific.

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