Multi‐template approach to modeling engineered disulfide bonds
- 28 June 2006
- journal article
- research article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 65 (1), 192-202
- https://doi.org/10.1002/prot.21059
Abstract
The key issue for disulfide bond engineering is to select the most appropriate location in the protein. By surveying the structure of experimentally engineered disulfide bonds, we found about half of them that have geometry incompatible with any native disulfide bond geometry. To improve the current prediction methods that tend to apply either ideal geometrical or energetical criteria to single three-dimensional structures, we have combined a novel computational protocol with the usage of multiple protein structures to take into account protein backbone flexibility. The multiple structures can be selected from either independently determined crystal structures for identical proteins, models of nuclear magnetic resonance experiments, or crystal structures of homology-related proteins. We have validated our approach by comparing the predictions with known disulfide bonds. The accuracy of prediction for native disulfide bonds reaches 99.6%. In a more stringent test on the reported engineered disulfide bonds, we have obtained a success rate of 93%. Our protocol also determines the oxido-reduction state of a predicted disulfide bond and the corresponding mutational cost. From the energy ranking, the user can easily choose top predicted sites for mutagenesis experiments. Our method provides information about local stability of the engineered disulfide bond surroundings. Proteins 2006.Keywords
This publication has 75 references indexed in Scilit:
- Stabilization of a Tetrameric Malate Dehydrogenase by Introduction of a Disulfide Bridge at the Dimer–Dimer InterfaceJournal of Molecular Biology, 2003
- Engineering a Disulfide Bond in Recombinant Manganese Peroxidase Results in Increased ThermostabilityBiotechnology Progress, 2000
- The Protein Data BankNucleic Acids Research, 2000
- Disulfide engineering at the dimer interface of lactobacillus casei thymidylate synthase: Crystal structure of the T155C/E188C/C244T mutantProtein Science, 1999
- A bivalent disulfide-stabilized fv with improved antigen binding to erbb2Journal of Molecular Biology, 1998
- All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of ProteinsThe Journal of Physical Chemistry B, 1998
- Antibody scFv fragments without disulfide bonds, made by molecular evolutionJournal of Molecular Biology, 1998
- Disulfide Mutants of Barnase I: Changes in Stability and Structure Assessed by Biophysical Methods and X-ray CrystallographyJournal of Molecular Biology, 1995
- Protein engineering of a disulfide bond in a .beta./.alpha.-barrel proteinBiochemistry, 1992
- Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesisProtein Engineering, Design and Selection, 1989