PEDS Advance Access originally published online on March 23, 2005
Protein Engineering Design and Selection 2005 18(2):59-64; doi:10.1093/protein/gzi009
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Protein sequence entropy is closely related to packing density and hydrophobicity
1Department of Chemistry and 2Department of General Engineering, San Jose State University, San Jose, CA 95192-0101, 3Sage-N Research, Saratoga, CA 95070-6082 and 4L.H.Baker Center for Bioinformatics and Biological Statistics, Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50014, USA
5 To whom correspondence should be addressed. E-mail: blustig{at}science.sjsu.edu
We investigated the correlation between the Shannon information entropy, ‘sequence entropy’, with respect to the local flexibility of native globular proteins as described by inverse packing density. These are determined at each residue position for a total set of 130 query proteins, where sequence entropies are calculated from each set of aligned residues. For the accompanying aggregate set of 130 alignments, a strong linear correlation is observed between the calculated sequence entropy and the corresponding inverse packing density determined at an associated residue position. This region of linearity spans the range of C
packing densities from 12 to 25 amino acids within a sphere of 9 Å radius. Three different hydrophobicity scales all mimic the behavior of the sequence entropies. This confirms the idea that the ability to accommodate mutations is strongly dependent on the available space and on the propensity for each amino acid type to be buried. Future applications of these types of methods may prove useful in identifying both core and flexible residues within a protein.
Received August 5, 2004; revised January 25, 2005; accepted January 28, 2005.
Edited by Harold Scheraga
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