PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions?
In a previous study, we have shown that PEPscan can provide a cheap and rapid means to identify candidate interfering peptides (IPs), i.e., peptides able to disrupt a target protein-protein interaction. PEPscan was shown to be effective in identifying a limited number of candidate IPs specific to th...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-01-01
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| Series: | Biomolecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2218-273X/12/2/178 |
| _version_ | 1797482295318282240 |
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| author | Angelita Rebollo Louise Fliedel Pierre Tuffery |
| author_facet | Angelita Rebollo Louise Fliedel Pierre Tuffery |
| author_sort | Angelita Rebollo |
| collection | DOAJ |
| description | In a previous study, we have shown that PEPscan can provide a cheap and rapid means to identify candidate interfering peptides (IPs), i.e., peptides able to disrupt a target protein-protein interaction. PEPscan was shown to be effective in identifying a limited number of candidate IPs specific to the target interaction. Here, we investigate the results of 14 new PEPscan experiments for protein complexes of known 3D structures. We show that for almost all complexes, PEPscan is able to identify candidate IPs that are located at the protein-protein interface. The information it provides about the binding site seems, however, too ambiguous to be exploited in a simple manner to assist the modeling of protein complexes. Moreover, these candidates are associated with false positives. For these, we suggest they could correspond to non-specific binders, which leaves room for further optimization of the PEPscan protocol. Another unexpected advance comes from the observation of the applicability of PEPscan for polysaccharides and labeled peptides, suggesting that PEPscan could become a large spectrum approach to investigate protein-binder interactions, the binder not necessarily being a protein. |
| first_indexed | 2024-03-09T22:31:14Z |
| format | Article |
| id | doaj.art-c25d91da474d4177b92f523dfcb0b5c0 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-09T22:31:14Z |
| publishDate | 2022-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-c25d91da474d4177b92f523dfcb0b5c02023-11-23T18:57:44ZengMDPI AGBiomolecules2218-273X2022-01-0112217810.3390/biom12020178PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions?Angelita Rebollo0Louise Fliedel1Pierre Tuffery2Université de Paris, INSERM U 1267, CNRS U 8258, UTCBS, F-75006 Paris, FranceUniversité de Paris, INSERM U 1267, CNRS U 8258, UTCBS, F-75006 Paris, FranceUnité de Biologie Fonctionnelle et Adaptative, Université de Paris, CNRS U 8251, INSERM U 1133, F-75013 Paris, FranceIn a previous study, we have shown that PEPscan can provide a cheap and rapid means to identify candidate interfering peptides (IPs), i.e., peptides able to disrupt a target protein-protein interaction. PEPscan was shown to be effective in identifying a limited number of candidate IPs specific to the target interaction. Here, we investigate the results of 14 new PEPscan experiments for protein complexes of known 3D structures. We show that for almost all complexes, PEPscan is able to identify candidate IPs that are located at the protein-protein interface. The information it provides about the binding site seems, however, too ambiguous to be exploited in a simple manner to assist the modeling of protein complexes. Moreover, these candidates are associated with false positives. For these, we suggest they could correspond to non-specific binders, which leaves room for further optimization of the PEPscan protocol. Another unexpected advance comes from the observation of the applicability of PEPscan for polysaccharides and labeled peptides, suggesting that PEPscan could become a large spectrum approach to investigate protein-binder interactions, the binder not necessarily being a protein.https://www.mdpi.com/2218-273X/12/2/178PEPscanprotein-protein interactionprotein-peptide interactionsprotein-polysaccharide interactions |
| spellingShingle | Angelita Rebollo Louise Fliedel Pierre Tuffery PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions? Biomolecules PEPscan protein-protein interaction protein-peptide interactions protein-polysaccharide interactions |
| title | PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions? |
| title_full | PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions? |
| title_fullStr | PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions? |
| title_full_unstemmed | PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions? |
| title_short | PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions? |
| title_sort | pepscan a broad spectrum approach for the characterization of protein binder interactions |
| topic | PEPscan protein-protein interaction protein-peptide interactions protein-polysaccharide interactions |
| url | https://www.mdpi.com/2218-273X/12/2/178 |
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