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PLoS One. 2013 Nov 21;8(11):e80635. doi: 10.1371/journal.pone.0080635. eCollection 2013.

Maximum allowed solvent accessibilites of residues in proteins.

Author information

1
Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, Illinois, United States of America.

Abstract

The relative solvent accessibility (RSA) of a residue in a protein measures the extent of burial or exposure of that residue in the 3D structure. RSA is frequently used to describe a protein's biophysical or evolutionary properties. To calculate RSA, a residue's solvent accessibility (ASA) needs to be normalized by a suitable reference value for the given amino acid; several normalization scales have previously been proposed. However, these scales do not provide tight upper bounds on ASA values frequently observed in empirical crystal structures. Instead, they underestimate the largest allowed ASA values, by up to 20%. As a result, many empirical crystal structures contain residues that seem to have RSA values in excess of one. Here, we derive a new normalization scale that does provide a tight upper bound on observed ASA values. We pursue two complementary strategies, one based on extensive analysis of empirical structures and one based on systematic enumeration of biophysically allowed tripeptides. Both approaches yield congruent results that consistently exceed published values. We conclude that previously published ASA normalization values were too small, primarily because the conformations that maximize ASA had not been correctly identified. As an application of our results, we show that empirically derived hydrophobicity scales are sensitive to accurate RSA calculation, and we derive new hydrophobicity scales that show increased correlation with experimentally measured scales.

PMID:
24278298
PMCID:
PMC3836772
DOI:
10.1371/journal.pone.0080635
[Indexed for MEDLINE]
Free PMC Article

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