title: From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.
abstract: Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis.
authors.affiliation: Department of Physical Chemistry and Institute of Biotechnology, University of Granada, Campus Fuentenueva s/n, Granada, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Zafra Ruano
authors.affiliation: MLG, Départment d'Informatique, Université Libre de Bruxelles, Brussels, Belgium.|Interuniversity Institute of Bioinformatics in Brussels (IB2), ULB-VUB, La Plaine Campus, Brussels, Belgium.
authors.forename: Elisa
authors.initials: E
authors.lastname: Cilia
authors.affiliation: VIB SWITCH Laboratory, Leuven, Belgium.|Department of Cellular and Molecular Medicine, KU Leuven, Campus Gasthuisberg O&N1, Leuven, Belgium.
authors.forename: José R
authors.initials: JR
authors.lastname: Couceiro
authors.affiliation: Department of Physical Chemistry and Institute of Biotechnology, University of Granada, Campus Fuentenueva s/n, Granada, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Ruiz Sanz
authors.affiliation: VIB SWITCH Laboratory, Leuven, Belgium.|Department of Cellular and Molecular Medicine, KU Leuven, Campus Gasthuisberg O&N1, Leuven, Belgium.
authors.forename: Joost
authors.initials: J
authors.lastname: Schymkowitz
authors.affiliation: VIB SWITCH Laboratory, Leuven, Belgium.|Department of Cellular and Molecular Medicine, KU Leuven, Campus Gasthuisberg O&N1, Leuven, Belgium.
authors.forename: Frederic
authors.initials: F
authors.lastname: Rousseau
authors.affiliation: Department of Physical Chemistry and Institute of Biotechnology, University of Granada, Campus Fuentenueva s/n, Granada, Spain.
authors.forename: Irene
authors.identifier: 0000-0003-2757-4779
authors.initials: I
authors.lastname: Luque
authors.affiliation: MLG, Départment d'Informatique, Université Libre de Bruxelles, Brussels, Belgium.|Interuniversity Institute of Bioinformatics in Brussels (IB2), ULB-VUB, La Plaine Campus, Brussels, Belgium.|AI-lab, Vakgroep Computerwetenschappen, Vrije Universiteit Brussel, Brussels, Belgium.
authors.forename: Tom
authors.identifier: 0000-0003-3645-1455
authors.initials: T
authors.lastname: Lenaerts
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D003198:Computer Simulation; D019143:Evolution, Molecular; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D009154:Mutation; D011485:Protein Binding; D016415:Sequence Alignment; D013816:Thermodynamics; D018909:src Homology Domains / Q000235:genetics
chemical_list: D008024:Ligands