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Analysis of institutional authors

Serrano Pubul, LuisAuthorVerschueren, EAuthorVanhee, PAuthorSerrano, LAuthor

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March 25, 2020
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The multiple-specificity landscape of modular peptide recognition domains

Publicated to: Molecular Systems Biology. 7 484- - 2011-05-06 7(), DOI: 10.1038/msb.2011.18

Authors:

Gfeller, D; Butty, F; Wierzbicka, M; Verschueren, E; Vanhee, P; Huang, HM; Ernst, A; Dar, N; Stagljar, I; Serrano, L; Sidhu, SS; Bader, GD; Kim, PM
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Affiliations

Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. - Author
CRG, EMBL CRG Syst Biol Unit, Barcelona, Spain - Author
Mt Sinai Hosp, Samuel Lunenfeld Res Inst, Toronto, ON M5G 1X5, Canada - Author
Univ Toronto, Dept Biochem, Toronto, ON M5S 3E1, Canada - Author
Univ Toronto, Dept Comp Sci, Toronto, ON M5S 3E1, Canada - Author
Univ Toronto, Dept Mol Genet, Toronto, ON M5S 3E1, Canada - Author
Univ Toronto, Donnelly Ctr, Banting & Best Dept Med Res, Toronto, ON M5S 3E1, Canada - Author
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Abstract

Modular protein interaction domains form the building blocks of eukaryotic signaling pathways. Many of them, known as peptide recognition domains, mediate protein interactions by recognizing short, linear amino acid stretches on the surface of their cognate partners with high specificity. Residues in these stretches are usually assumed to contribute independently to binding, which has led to a simplified understanding of protein interactions. Conversely, we observe in large binding peptide data sets that different residue positions display highly significant correlations for many domains in three distinct families (PDZ, SH3 and WW). These correlation patterns reveal a widespread occurrence of multiple binding specificities and give novel structural insights into protein interactions. For example, we predict a new binding mode of PDZ domains and structurally rationalize it for DLG1 PDZ1. We show that multiple specificity more accurately predicts protein interactions and experimentally validate some of the predictions for the human proteins DLG1 and SCRIB. Overall, our results reveal a rich specificity landscape in peptide recognition domains, suggesting new ways of encoding specificity in protein interaction networks.
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Keywords

Binding specificityComplexityCrystal-structuresHelpInteraction databaseMechanismPdzPdz domainsPeptide recognition domainsPhage displayPredictionProteinsResidue correlationsSequence

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Molecular Systems Biology due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2011, it was in position 24/290, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biochemistry & Molecular Biology.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2026-03-20:

  • WoS: 68
  • Scopus: 63
  • Europe PMC: 52
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-03-20:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 171.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 171 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 3.

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Canada.

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Awards linked to the item

DG acknowledges the financial support of the Swiss National Science Foundation (SNSF) and the European Molecular Biology Organization (EMBO). This work was supported by the Canadian Institutes of Health Research (Grant MOP-84324). The Stagljar lab is supported by grants from the Canada Foundation for Innovation (CFI), the Canadian Institutes of Health Research (CIHR), the Canadian Cancer Society Research Institute (CCSRI), the Heart and Stroke Foundation, the Cystic Fibrosis Foundation, the Ontario Genomics Institute and Novartis. The Kim lab is funded by grants from the Natural Sciences and Engineering Research Council (NSERC), the Canada Foundation for Innovation (CFI) and the Ontario Research Fund (ORF).
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