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Identifying Loop-Mediated Protein–Protein Interactions Using LoopFinder

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Modeling Peptide-Protein Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1561))

Abstract

Peptides are an increasingly useful class of molecules, finding unique applications as chemical probes and potential drugs. They are particularly adept at inhibiting protein–protein interactions, which are often difficult to target using small molecules. The identification and rational design of protein-binding epitopes remains a bottleneck in the development of bioactive peptides. One fruitful strategy has been using structured scaffolds to present essential hot spot residues involved in protein–protein recognition, and this process has been greatly advanced by computational tools that can identify hot spot residues. Here we discuss LoopFinder, a program that uses structures from the Protein Data Bank to comprehensively search for protein–protein interactions that are mediated by nonhelical, nonsheet loop structures. We developed LoopFinder to identify these “hot loops” and to assist in the design of cyclic peptides that mimic these important structures. In this article, we provide all key files, outline step-by-step methods for users to conduct independent LoopFinder searches, and provide guidance on additional potential applications for the LoopFinder program.

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Authors and Affiliations

  1. Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA

    Timothy R. Siegert, Michael Bird & Joshua A. Kritzer

Authors
  1. Timothy R. Siegert
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  2. Michael Bird
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  3. Joshua A. Kritzer
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Corresponding author

Correspondence to Joshua A. Kritzer .

Editor information

Editors and Affiliations

  1. Microbiology and Molecular Genetics, Hebrew University Hadassah Medical School, Jerusalem, Israel

    Ora Schueler-Furman

  2. Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel

    Nir London

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Siegert, T.R., Bird, M., Kritzer, J.A. (2017). Identifying Loop-Mediated Protein–Protein Interactions Using LoopFinder. In: Schueler-Furman, O., London, N. (eds) Modeling Peptide-Protein Interactions. Methods in Molecular Biology, vol 1561. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6798-8_15

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  • DOI: https://doi.org/10.1007/978-1-4939-6798-8_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6796-4

  • Online ISBN: 978-1-4939-6798-8

  • eBook Packages: Springer Protocols

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