Protein deamidation

Creators: Robinson, Noah E.

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Abstract

A completely automatic computerized technique for the quantitative estimation of the deamidation rates of any protein for which the three-dimensional structure is known has been developed. Calculations of the specific deamidation rates of 170,014 asparaginyl residues in 13,335 proteins have been carried out. The calculated values have good quantitative reliability when compared with experimental measurements. These rates demonstrate that deamidation may be a biologically relevant phenomenon in a remarkably large percentage of proteins.

Additional Information

© 2002 National Academy of Sciences. Communicated by Bruce Merrifield, The Rockefeller University, New York, NY, February 21, 2002 (received for review January 3, 2002). I thank Drs. H. B. Gray, R. B. Merrifield, and A. B. Robinson for advice and encouragement, the A. Reynolds Morse Foundation for their grant support, and a Caltech Special Institute Fellowship for financial support. Additional information, including computer programs, deamidation coefficients, and deamidation indexes for all proteins in the Brookhaven Protein Data Bank of 3D structures as of April 2001, is available at www.deamidation.org. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.

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