Abstract
PEPscan is an old approach that has recently gained renewed interest for the identification of interfering peptides (IPs), i.e., peptides able to interfere with protein–protein interactions (PPIs). Its principle is to slice a protein sequence as a series of short overlapping peptides that are synthesized on a peptide array and tested for their ability to bind a partner, with positive spots corresponding to candidate IPs. PEPscan has been applied with a rather large success in various contexts, but the structural determinants underlying this success remain obscure. Here, we analyze the results of 14 PEPscan experiments, and confront the in vitro results with the available structural information. PEPscan identifies candidate IPs in limited numbers that in all cases correspond to solvent-accessible regions of the structures, their location at the protein–protein interface remaining to be further demonstrated. A strong point of PEPscan seems to be its ability to identify specific IPs. IPs identified from the same protein differ depending on the target PPI, and correspond to patches not frequently involved in the interactions seen in the 3D structures available. Overall, PEPscan seems to provide a cheap and rapid manner to identify candidate IPs, that also comes with room for improvement.
Highlights
IntroductionPublisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations
It is important to note that the relationship between the signal intensity and the affinity of the peptide/ligand interaction is not straightforward
Several factors may influence the correlation between signal intensity and binding affinity; the synthesis can lead to different amounts of peptide in the spot and the type of detection assay used can have an influence
Summary
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Peptide arrays are a technology with a wide range of applications in basic and applied research, which is nearly 40 years old and has been commercially available for about ten years. An array comprises hundreds to thousands of different peptides sequences immobilized in a solid support that can be tested simultaneously, offering many possibilities to analyse different signalling pathways between normal and pathological conditions, drug discovery, sequence dependent reactivity etc. One of the most common has been epitope mapping for antibodies [1], including the identification of linear epitopes between the IL-10 and its receptor [2], viral antigen epitopes [3,4], T and
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