How Do Side Chains Orient Globally in Protein Structures?

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2005-11-15
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Yan, Aimin
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Jernigan, Robert
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Bioinformatics and Computational Biology
The Bioinformatics and Computational Biology (BCB) Program at Iowa State University is an interdepartmental graduate major offering outstanding opportunities for graduate study toward the Ph.D. degree in Bioinformatics and Computational Biology. The BCB program involves more than 80 nationally and internationally known faculty—biologists, computer scientists, mathematicians, statisticians, and physicists—who participate in a wide range of collaborative projects.
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Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of
Abstract

An angle Ω is defined to serve as a metric for global side-chain orientations, which reflects the orientation of the side chain relative to the radial vector from the center of the protein to an amino acid. The side-chain orientations of buried residues exhibit characteristically different orientations than do exposed residues, in both monomeric and dimeric structures. Overall, buried side chains point mostly inward, whereas surface side chains tend to point outward from the surface. This difference in behavior also correlates well with the residue hydrophobicity; so a global side-chain orientation can be viewed as a direct structural manifestation of hydrophobicity. When various solvent-accessible layers are considered, the behavior is relatively continuous between centrally located and exposed residues. In the case of interfacial residues between subunits, there are statistically significant differences between exposed residues and interface residues for ALA, ARG, ASN, ASP, GLU, HIS, LYS, THR, VAL, MET, PRO, and overall the interface residues have an increased tendency to point inward. Presumably, these substantial differences in orientations of side chains may be a manifestation of hydrophobic forces.

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This is the peer reviewed version of the following article: Yan, Aimin, and Robert L. Jernigan. "How do side chains orient globally in protein structures?." Proteins: Structure, Function, and Bioinformatics 61, no. 3 (2005): 513-522, which has been published in final form at doi: 10.1002/prot.20638. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.

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Sat Jan 01 00:00:00 UTC 2005
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