Journal
FEBS LETTERS
Volume 586, Issue 17, Pages 2648-2661Publisher
WILEY
DOI: 10.1016/j.febslet.2012.03.056
Keywords
PDZ; Specificity; Sequence context; Extension; beta 2-beta 3 Loop; Linear motifs
Funding
- CNRS, University of Strasbourg and Association de Recherche contre le Cancer (ARC) [3171]
- Region Alsace, ARC
- College Doctoral Europeen de Strasbourg
- Agence Nationale de la Recherche (ANR-MIME) [EPI-HPV-3D]
- National Institute of Health (NIH) [R01CA134737]
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The canonical binding mode of PDZ domains to target motifs involves a small interface, unlikely to fully account for PDZ-target interaction specificities. Here, we review recent work on sequence context, defined as the regions surrounding not only the PDZ domains but also their target motifs. We also address the theoretical problem of defining the core of PDZ domains and the practical issue of designing PDZ constructs. Sequence context is found to introduce structural diversity, to impact the stability and solubility of constructs, and to deeply influence binding affinity and specificity, thereby increasing the difficulty of predicting PDZ-motif interactions. We expect that sequence context will have similar importance for other protein interactions mediated by globular domains binding to short linear motifs. (C) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
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