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Protein Science (2006), 15:795-807. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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New approaches to high-throughput structure characterization of SH3 complexes: The example of Myosin-3 and Myosin-5 SH3 domains from S. cerevisiae

Valeria Musi1, Berry Birdsall1, Gregorio Fernandez-Ballester2, Remo Guerrini3, Severo Salvatori3, Luis Serrano2 and Annalisa Pastore1

1 National Institute for Medical Research, London NW71AA, United Kingdom
2 The European Molecular Biology Laboratory (EMBL), D69117 Heidelberg, Germany
3 Dipartimento di Scienze Farmaceutiche, Universita` di Ferrara, Ferrara, Italy

(RECEIVED August 16, 2005; FINAL REVISION January 11, 2005; ACCEPTED January 15, 2005)

SH3 domains are small protein modules that are involved in protein–protein interactions in several essential metabolic pathways. The availability of the complete genome and the limited number of clearly identifiable SH3 domains make the yeast Saccharomyces cerevisae an ideal proteomic-based model system to investigate the structural rules dictating the SH3-mediated protein interactions and to develop new tools to assist these studies. In the present work, we have determined the solution structure of the SH3 domain from Myo3 and modeled by homology that of the highly homologous Myo5, two myosins implicated in actin polymerization. We have then implemented an integrated approach that makes use of experimental and computational methods to characterize their binding properties. While accommodating their targets in the classical groove, the two domains have selectivity in both orientation and sequence specificity of the target peptides. From our study, we propose a consensus sequence that may provide a useful guideline to identify new natural partners and suggest a strategy of more general applicability that may be of use in other structural proteomic studies.

Keywords: myosin; NMR; protein design; S.cerevisiae; structure; Wilskott-Aldrich syndrome


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