Identification of protein oligomerization states by analysis of interface conservation
- *Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109; and ‡Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093-0365
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Edited by Gregory A. Petsko, Brandeis University, Waltham, MA, and approved January 17, 2001 (received for review August 28, 2000)
Abstract
The discrimination of true oligomeric protein–protein contacts from nonspecific crystal contacts remains problematic. Criteria that have been used previously base the assignment of oligomeric state on consideration of the area of the interface and/or the results of scoring functions based on statistical potentials. Both techniques have a high success rate but fail in more than 10% of cases. More importantly, the oligomeric states of several proteins are incorrectly assigned by both methods. Here we test the hypothesis that true oligomeric contacts should be identifiable on the basis of an increased degree of conservation of the residues involved in the interface. By quantifying the degree of conservation of the interface and comparing it with that of the remainder of the protein surface, we develop a new criterion that provides a highly effective complement to existing methods.
Footnotes
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↵ † To whom reprint requests should be addressed. E-mail: adrian-elcock{at}uiowa.edu.
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This paper was submitted directly (Track II) to the PNAS office.
- Abbreviations:
- SASA,
- solvent accessible surface area;
- PQS,
- Protein Quaternary Structure
- Copyright © 2001, The National Academy of Sciences
