Normalization of nomenclature for peptide motifs as ligands of modular protein domains

Aasland, Rein; Abrams, Charles; Ampe, Christophe; Ball, Linda J.; Bedford, Mark T.; Cesareni, Gianni; Gimona, Mario; Hurley, James H.; Jarchau, Thomas; Lehto, Veli-Pekka; Lemmon, Mark A.; Linding, Rune; Mayer, Bruce J.; Nagai, Makoto; Sudol, Marius; Walter, Ulrich; Winder, Steve J.

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Volume 513, Issue 1 , Pages 141-144, 20 February 2002

Normalization of nomenclature for peptide motifs as ligands of modular protein domains

Edited by Gianni Cesareni and Mario Gimonu

Rein Aasland
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
- Corresponding authors
Charles Abrams
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, PA 19014, USA
Christophe Ampe
- Department of Biochemistry, Ghent University, B-9000 Gent, Belgium
Linda J. Ball
- Department of NMR and Structural Biology, F.M.P. – Research Institute of Molecular Pharmacology, D-13125 Berlin, Germany
- Corresponding authors
Mark T. Bedford
- Department of Carcinogenesis, University of Texas, Smithville, TX 78957, USA
Gianni Cesareni
- Department of Biology, Unviversity of Rome, Tor Vergata, 00133 Rome, Italy
Mario Gimona
- Department of Cell Biology, Austrian Academy of Sciences, 5020 Salzburg, Austria
James H. Hurley
- Laboratory of Molecular Biology, National Institutes of Health, NIDDK, Bethesda, MD 20892, USA
Thomas Jarchau
- Institut für Klinische Biochemie und Pathobiochemie, D-97078 Würzburg, Germany
Veli-Pekka Lehto
- Department of Pathology, University of Oulu, 90410 Oulu, Finland
Mark A. Lemmon
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Rune Linding
- Biocomputing Unit, EMBL, D-69117 Heidelberg, Germany
Bruce J. Mayer
- Department of Genetics and Developmental Biology, University of Connecticut, Farmington, CT 06030, USA
Makoto Nagai
- Department of Medicine, Mt. Sinai Medical Center, New York, NY 10029, USA
Marius Sudol
- Department of Medicine, Mt. Sinai Medical Center, New York, NY 10029, USA
- Corresponding authors
Ulrich Walter
- Institut für Klinische Biochemie und Pathobiochemie, D-97078 Würzburg, Germany
Steve J. Winder
- Division of Biochemistry and Molecular Biology, University of Glasgow, Glasgow G12 8QQ, UK

Received 8 November 2001; received in revised form 20 November 2001; accepted 3 December 2001.

Abstract

We propose a normalization of symbols and terms used to describe, accurately and succinctly, the detailed interactions between amino acid residues of pairs of interacting proteins at protein:protein (or protein:peptide) interfaces. Our aim is to unify several diverse descriptions currently in use in order to facilitate communication in the rapidly progressing field of signaling by protein domains. In order for the nomenclature to be convenient and widely used, we also suggest a parallel set of symbols restricted to the ASCII format allowing accurate parsing of the nomenclature to a computer-readable form. This proposal will be reviewed in the future and will therefore be open for the inclusion of new rules, modifications and changes.

Keywords: Protein–protein interaction, Peptide motif, Protein domain, specificity and recognition, Proteomics, Glossary, Nomenclature, ASCII format