title: The Binding of Syndapin SH3 Domain to Dynamin Proline-rich Domain Involves Short and Long Distance Elements.
abstract: Dynamin is a GTPase that mediates vesicle fission during synaptic vesicle endocytosis. Its long C-terminal proline-rich domain contains 13 PXXP motifs, which orchestrate its interactions with multiple proteins. The SH3 domains of syndapin and endophilin bind the PXXP motifs called Site 2 and 3 (Pro-786-Pro-793) at the N-terminal end of the proline-rich domain, whereas the amphiphysin SH3 binds Site 9 (Pro-833-Pro-836) toward the C-terminal end. In some proteins, SH3/peptide interactions also involve short distance elements, which are 5-15 amino acid extensions flanking the central PXXP motif for high affinity binding. Here we found two previously unrecognized elements in the central and the C-terminal end of the dynamin proline-rich domain that account for a significant increase in syndapin binding affinity compared with a previously reported Site 2 and Site 3 PXXP peptide alone. The first new element (Gly-807-Gly-811) is short distance element on the C-terminal side of Site 2 PXXP, which might contact a groove identified under the RT loop of the SH3 domain. The second element (Arg-838-Pro-844) is located about 50 amino acids downstream of Site 2. These two elements provide additional specificity to the syndapin SH3 domain outside of the well described polyproline-binding groove. Thus, the dynamin/syndapin interaction is mediated via a network of multiple contacts outside the core PXXP motif over a previously unrecognized extended region of the proline-rich domain. To our knowledge this is the first example among known SH3 interactions to involve spatially separated and extended long-range elements that combine to provide a higher affinity interaction.
authors.affiliation: From the Cell Signalling Unit, Children's Medical Research Institute, University of Sydney, New South Wales 2145, Australia, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia, IMB Center for Inflammation and Disease Research, University of Queensland, Brisbane, Queensland 4072, Australia.
authors.forename: Lin
authors.initials: L
authors.lastname: Luo
authors.affiliation: From the Cell Signalling Unit, Children's Medical Research Institute, University of Sydney, New South Wales 2145, Australia.
authors.forename: Jing
authors.initials: J
authors.lastname: Xue
authors.affiliation: School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia.
authors.forename: Ann
authors.initials: A
authors.lastname: Kwan
authors.affiliation: School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia, School of Science and Health, Western Sydney University, New South Wales 2751, Australia.
authors.forename: Roland
authors.initials: R
authors.lastname: Gamsjaeger
authors.affiliation: ACRF Rational Drug Discovery Center, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.
authors.forename: Jerome
authors.initials: J
authors.lastname: Wielens
authors.affiliation: Group of Cellular Biochemistry, Institute of Chemistry and Biochemistry, Freie Universitaet Berlin, Thielallee 63, 14195 Berlin, Germany.
authors.forename: Lisa
authors.initials: L
authors.lastname: von Kleist
authors.affiliation: School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia, School of Science and Health, Western Sydney University, New South Wales 2751, Australia.
authors.forename: Liza
authors.initials: L
authors.lastname: Cubeddu
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Guo
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia, IMB Center for Inflammation and Disease Research, University of Queensland, Brisbane, Queensland 4072, Australia.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Stow
authors.affiliation: ACRF Rational Drug Discovery Center, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Parker
authors.affiliation: School of Molecular Bioscience, University of Sydney, New South Wales 2006, Australia, joel.mackay@sydney.edu.au.
authors.forename: Joel P
authors.initials: JP
authors.lastname: Mackay
authors.affiliation: From the Cell Signalling Unit, Children's Medical Research Institute, University of Sydney, New South Wales 2145, Australia, probinson@cmri.org.au.
authors.forename: Phillip J
authors.initials: PJ
authors.lastname: Robinson
mesh_terms: D048868:Adaptor Proteins, Signal Transducing; D020816:Amino Acid Motifs; D000818:Animals; D002352:Carrier Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D003598:Cytoskeletal Proteins; D034281:Dynamins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins; D051379:Mice; D009479:Neuropeptides / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D010750:Phosphoproteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D051381:Rats; D018909:src Homology Domains
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D002352:Carrier Proteins; D003598:Cytoskeletal Proteins; D047908:Intracellular Signaling Peptides and Proteins; D009479:Neuropeptides; C114726:Pacsin1 protein, mouse; C117738:Pacsin1 protein, rat; D010750:Phosphoproteins; D034281:Dynamins
keywords: Src homology 3 domain (SH3 domain); dynamin; endocytosis; nuclear magnetic resonance (NMR); structural model