Deamidation of Peptides and Proteins

Oregon Institute of Science and Medicine
2251 Dick George Road
Cave Junction, OR 97523
(541) 592-4142

Noah E. Robinson
noah@oism.org
      
Arthur B. Robinson
art@oism.org

    This web site is dedicated to the supply of information about the deamidation of asparaginyl and glutaminyl residues in peptides and proteins. The site began operation in April, 2001.

    Of special interest are the computed deamidation rate CD and ID values for all proteins for which 3-dimensional structures are in the Protein Data Bank. Immediate access to CD values for each of the 237,039 Asn in the 17,935 proteins on file in the Protein Data Bank as of January 2003 and the corresponding Asn S parameters and protein ID values is provided by clicking: CD and ID Database.

    PDB identifiers for individual proteins are available at www.rcsb.org. Additional CD and ID values for any protein of known 3-dimensional structure that is not listed in this database are available by email request from noah@oism.org. The predicted half-life in days of the amide in 37 °C, pH 7.4, 0.15 M Tris buffer is given by (100)(CD). The predicted half-life for the net deamidation of one amide in a protein, with all amides considered, is given by (100)(ID).

    The 443-page book, Molecular Clocks: Deamidation of Asparaginyl and Glutaminyl Residues in Peptides and Proteins by N. E. Robinson and A. B. Robinson provides a complete review of this subject with 1,785 references to the research literature. It can be obtained as listed below.

The book, Molecular Clocks, can also be viewed and read on the Internet at:
http://www.deamidation.org/MolecularClocks.pdf

    
    Experimental and computational research references upon which the computed CD and ID values are based include:

  1. Robinson, N. E. and Robinson, A. B. (2001) Molecular Clocks. Proc. Natl. Acad. Sci. USA 98, 944-949.
  2. Robinson, N. E., Robinson, A. B., and Merrifield, R. B. (2001) Mass Spectrometric Evaluation of Synthetic Peptides as Primary Structure Models for Peptide and Protein Deamidation. J. Peptide Res. 57, 1-12.
  3. Robinson, N. E. and Robinson, A. B. (2001) Prediction of Protein Deamidation Rates from Primary and Three-Dimensional Structure. Proc. Natl. Acad. Sci. USA 98, 4367-4372.
  4. Robinson, N. E. and Robinson, A. B. (2001) Deamidation of Human Proteins. Proc. Natl. Acad. Sci. USA 98, 12409-12413.
  5. Robinson, N. E. (2002) Protein Deamidation. Proc. Natl. Acad. Sci. USA 99, 5283-5288.
  6. Robinson, N. E. and Robinson, A. B. (2004) Amide Molecular Clocks in Drosophila Proteins: Potential Regulators of Aging and Other Processes. Mechanisms of Ageing and Development 125, 259-267.
  7. Robinson, N. E., Robinson, Z. W., Robinson, B. R., Robinson, A. L., Robinson, M. R., and Robinson, A. B. (2004) Structure-Dependent Non-enzymatic Deamidation of Glutaminyl and Asparaginyl Pentapeptides. J. Peptide Res. 63, 426-436.
  8. Robinson, N. E. and Robinson, A. B. (2004) Prediction of Primary Structure Deamidation Rates of Asparaginyl and Glutaminyl Peptides Through Steric and Catalytic Effects. J. Peptide Res. 63, 437-448.
  9. Robinson, N. E. and Robinson, A. B. (2004) Molecular Clocks: Deamidation of Asparaginyl and Glutaminyl Residues in Peptides and Proteins. Althouse Press, Cave Junction, OR.

    Additional research papers on deamidation by these authors as well as other references can be found through Google's Scholar reference search.

    The book, Molecular Clocks: Deamidation of Asparaginyl and Glutaminyl Residues in Peptides and Proteins, can be ordered as follows:


Molecular Clocks:
Deamidation of Asparaginyl and Glutaminyl Residues
in Peptides and Proteins

Noah E. Robinson and Arthur B. Robinson
Oregon Institute of Science and Medicine

Introductory Price: $49.95

This 443 page book reviews all published information on deamidation and includes 1785 references to the research literature, 86 color illustrations, and 16 tables.

The book is organized in a useful way for scientists working in the field of protein chemistry.

Special reference is made to the evidence that deamidation serves as a molecular clock for the regulation of biological processes.

(2004) Hard Cover
ISBN: 1-59087-250-0
All proceeds from the sale of this book will
fund deamidation research at the
Oregon Institute of Science and Medicine

To order: Click Here