Protocol abstract
Nature Protocols 2, - 1070 - 1083 (2007)
Published online: 26 April 2007 | doi:10.1038/nprot.2007.119
Subject Categories: Chemical modification | Computational and theoretical biology | Biochemistry and protein analysis
Identification and insertion of 3-carbon bridges in protein disulfide bonds: a computational approach
Mire Zloh1, Sunil Shaunak2, Sibu Balan3 & Steve Brocchini3
Abstract
More than 42,000 3D structures of proteins are available on the Internet. We have shown that the chemical insertion of a 3-carbon bridge across the native disulfide bond of a protein or peptide can enable the site-specific conjugation of PEG to the protein without a loss of its structure or function. For success, it is necessary to select an appropriate and accessible disulfide bond in the protein for this chemical modification. We describe how to use public protein databases and molecular modeling programs to select a protein rationally and to identify the optimum disulfide bond for experimental studies. Our computational approach can substantially reduce the time required for the laboratory-based chemical modification. Identification of solvent-accessible disulfides using published structural information takes approximately 2 h. Predicting the structural effects of the disulfide-based modification can take 3 weeks.
- Department of Pharmaceutical and Biological Chemistry, University of London, 29/39 Brunswick Square, London WC1N 1AX, UK.
- Faculty of Medicine, Imperial College London, Hammersmith Hospital, Ducane Road, London W12 0NN, UK.
- Department of Pharmaceutics, The School of Pharmacy, University of London, 29/39 Brunswick Square, London WC1N 1AX, UK.
Correspondence to: Mire Zloh1 e-mail: mire.zloh@pharmacy.ac.uk