Modeling protein-peptide interactions using protein fragments: fitting the pieces?
© Vanhee et al; licensee BioMed Central Ltd. 2010
Published: 07 December 2010
An estimated 15-40% of all interactions in the cell are mediated through protein-peptide interactions [1, 2] meaning that, at the most extreme, nearly every protein is affected either directly or indirectly by peptide-binding events.
We show the usefulness of our method by redesigning the interaction scaffold of nine protein-peptide complexes, for which five of the peptides can be modelled to within 1 Å RMSD of the original peptide position.
These data suggest that the wealth of structural data on monomeric proteins could be harvested to model protein-peptide interactions and, more importantly, that sequence homology is no prerequisite. In addition, we have made our dataset of 505 non-redundant protein-peptide complexes from 1431 entries in the PDB available at http://pepx.switchlab.org and the BriX database at http://brix.crg.es.
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