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PMID: 11296285 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Prediction of protein deamidation rates from primary and three-dimensional structure.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 98 ·No. 8 ·2001-04-10 ·Pages 4367-72

Robinson NE, Robinson AB

Abstract

A method for the quantitative estimation of instability with respect to deamidation of the asparaginyl (Asn) residues in proteins is described. The procedure involves the observation of several simple aspects of the three-dimensional environment of each Asn residue in the protein and a calculation that includes these observations, the primary amino acid residue sequence, and the previously reported complete set of sequence-dependent rates of deamidation for Asn pentapeptides. This method is demonstrated and evaluated for 23 proteins in which 31 unstable and 167 stable Asn residues have been reported and for 7 unstable and 63 stable Asn residues that have been reported in 61 human hemoglobin variants. The relative importance of primary structure and three-dimensional structure in Asn deamidation is estimated.

MeSH Terms
Amides/chemistry Amino Acid Sequence Kinetics Molecular Sequence Data Protein Conformation Proteins/chemistry
Chemicals
Amides Proteins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Robinson N E
Division of Chemistry, California Institute of Technology, Pasadena, CA 91125, USA.
Robinson A B
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.071066498
Published
2001-04-10
Pages
4367-72
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC31841
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.071066498 PMC Full Text View journal details
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