3gbq Citations

Solution structure of the Grb2 N-terminal SH3 domain complexed with a ten-residue peptide derived from SOS: direct refinement against NOEs, J-couplings and 1H and 13C chemical shifts.

J. Mol. Biol. 267 933-52 (1997)
Related entries: 4gbq, 2gbq, 1gbq

Cited: 38 times
EuropePMC logo PMID: 9135122

Abstract

Refined ensembles of solution structures have been calculated for the N-terminal SH3 domain of Grb2 (N-SH3) complexed with the ac-VPPPVPPRRR-nh2 peptide derived from residues 1135 to 1144 of the mouse SOS-1 sequence. NMR spectra obtained from different combinations of both 13C-15N-labeled and unlabeled N-SH3 and SOS peptide fragment were used to obtain stereo-assignments for pro-chiral groups of the peptide, angle restraints via heteronuclear coupling constants, and complete 1H, 13C, and 15N resonance assignments for both molecules. One ensemble of structures was calculated using conventional methods while a second ensemble was generated by including additional direct refinements against both 1H and 13C(alpha)/13C(beta) chemical shifts. In both ensembles, the protein:peptide interface is highly resolved, reflecting the inclusion of 110 inter-molecular nuclear Overhauser enhancement (NOE) distance restraints. The first and second peptide-binding sub-sites of N-SH3 interact with structurally well-defined portions of the peptide. These interactions include hydrogen bonds and extensive hydrophobic contacts. In the third highly acidic sub-site, the conformation of the peptide Arg8 side-chain is partially ordered by a set of NOE restraints to the Trp36 ring protons. Overall, several lines of evidence point to dynamical averaging of peptide and N-SH3 side-chain conformations in the third subsite. These conformations are characterized by transient charge stabilized hydrogen bond interactions between the peptide arginine side-chain hydrogen bond donors and either single, or possibly multiple, acceptor(s) in the third peptide-binding sub-site.

Articles - 3gbq mentioned but not cited (1)



Reviews citing this publication (6)

  1. SH3 domains and drug design: ligands, structure, and biological function. Dalgarno DC, Botfield MC, Rickles RJ. Biopolymers 43 383-400 (1997)
  2. Recognition of proline-rich motifs by protein-protein-interaction domains. Ball LJ, Kühne R, Schneider-Mergener J, Oschkinat H. Angew. Chem. Int. Ed. Engl. 44 2852-2869 (2005)
  3. Quantitative account of the enhanced affinity of two linked scFvs specific for different epitopes on the same antigen. Zhou HX. J. Mol. Biol. 329 1-8 (2003)
  4. Recognition of proline-rich motifs by protein-protein-interaction domains. Ball LJ, Kühne R, Schneider-Mergener J, Oschkinat H. Angew. Chem. Int. Ed. Engl. 44 2852-2869 (2005)
  5. Quantitative account of the enhanced affinity of two linked scFvs specific for different epitopes on the same antigen. Zhou HX. J. Mol. Biol. 329 1-8 (2003)
  6. SH3 domains and drug design: ligands, structure, and biological function. Dalgarno DC, Botfield MC, Rickles RJ. Biopolymers 43 383-400 (1997)

Articles citing this publication (31)

  1. Stimulation of phosphatidylinositol 3-kinase by fibroblast growth factor receptors is mediated by coordinated recruitment of multiple docking proteins. Ong SH, Hadari YR, Gotoh N, Guy GR, Schlessinger J, Lax I. Proc. Natl. Acad. Sci. U.S.A. 98 6074-6079 (2001)
  2. FAK-mediated src phosphorylation of endophilin A2 inhibits endocytosis of MT1-MMP and promotes ECM degradation. Wu X, Gan B, Yoo Y, Guan JL. Dev. Cell 9 185-196 (2005)
  3. SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination. Trempe JF, Chen CX, Grenier K, Camacho EM, Kozlov G, McPherson PS, Gehring K, Fon EA. Mol. Cell 36 1034-1047 (2009)
  4. Characterization of domain-peptide interaction interface: prediction of SH3 domain-mediated protein-protein interaction network in yeast by generic structure-based models. Hou T, Li N, Li Y, Wang W. J. Proteome Res. 11 2982-2995 (2012)
  5. Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains. Hou T, Xu Z, Zhang W, McLaughlin WA, Case DA, Xu Y, Wang W. Mol. Cell Proteomics 8 639-649 (2009)
  6. The HIV-TSG101 interface: recent advances in a budding field. Freed EO. Trends Microbiol. 11 56-59 (2003)
  7. The role of backbone motions in ligand binding to the c-Src SH3 domain. Wang C, Pawley NH, Nicholson LK. J. Mol. Biol. 313 873-887 (2001)
  8. Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. Hou T, Chen K, McLaughlin WA, Lu B, Wang W. PLoS Comput. Biol. 2 e1 (2006)
  9. The effect of the polyproline II (PPII) conformation on the denatured state entropy. Ferreon JC, Hilser VJ. Protein Sci. 12 447-457 (2003)
  10. Interaction of nebulin SH3 domain with titin PEVK and myopalladin: implications for the signaling and assembly role of titin and nebulin. Ma K, Wang K. FEBS Lett. 532 273-278 (2002)
  11. Molecular and cellular analysis of Grb2 SH3 domain mutants: interaction with Sos and dynamin. Vidal M, Goudreau N, Cornille F, Cussac D, Gincel E, Garbay C. J. Mol. Biol. 290 717-730 (1999)
  12. SH3 domains of Grb2 adaptor bind to PXpsiPXR motifs within the Sos1 nucleotide exchange factor in a discriminate manner. McDonald CB, Seldeen KL, Deegan BJ, Farooq A. Biochemistry 48 4074-4085 (2009)
  13. Evolving specificity from variability for protein interaction domains. Kaneko T, Sidhu SS, Li SS. Trends Biochem. Sci. 36 183-190 (2011)
  14. Structural basis for ubiquitin recognition by SH3 domains. He Y, Hicke L, Radhakrishnan I. J. Mol. Biol. 373 190-196 (2007)
  15. Crystallographic structure of the SH3 domain of the human c-Yes tyrosine kinase: loop flexibility and amyloid aggregation. Martín-García JM, Luque I, Mateo PL, Ruiz-Sanz J, Cámara-Artigas A. FEBS Lett. 581 1701-1706 (2007)
  16. Toward quantitative characterization of the binding profile between the human amphiphysin-1 SH3 domain and its peptide ligands. He P, Wu W, Wang HD, Yang K, Liao KL, Zhang W. Amino Acids 38 1209-1218 (2010)
  17. Structural basis of the differential binding of the SH3 domains of Grb2 adaptor to the guanine nucleotide exchange factor Sos1. McDonald CB, Seldeen KL, Deegan BJ, Farooq A. Arch. Biochem. Biophys. 479 52-62 (2008)
  18. Solution structure of the human Hck SH3 domain and identification of its ligand binding site. Horita DA, Baldisseri DM, Zhang W, Altieri AS, Smithgall TE, Gmeiner WH, Byrd RA. J. Mol. Biol. 278 253-265 (1998)
  19. Assembly of the Sos1-Grb2-Gab1 ternary signaling complex is under allosteric control. McDonald CB, Seldeen KL, Deegan BJ, Bhat V, Farooq A. Arch. Biochem. Biophys. 494 216-225 (2010)
  20. Estrogen receptor alpha--identification by a modeling approach of a potential polyproline II recognizing domain within the AF-2 region of the receptor that would play a role of prime importance in its mechanism of action. Jacquot Y, Gallo D, Leclercq G. J. Steroid Biochem. Mol. Biol. 104 1-10 (2007)
  21. Recognition of lysine-rich peptide ligands by murine cortactin SH3 domain: CD, ITC, and NMR studies. Rubini C, Ruzza P, Spaller MR, Siligardi G, Hussain R, Udugamasooriya DG, Bellanda M, Mammi S, Borgogno A, Calderan A, Cesaro L, Brunati AM, Donella-Deana A. Biopolymers 94 298-306 (2010)
  22. Coevolution of the domains of cytoplasmic tyrosine kinases. Nars M, Vihinen M. Mol. Biol. Evol. 18 312-321 (2001)
  23. Multivalent binding and facilitated diffusion account for the formation of the Grb2-Sos1 signaling complex in a cooperative manner. McDonald CB, Balke JE, Bhat V, Mikles DC, Deegan BJ, Seldeen KL, Farooq A. Biochemistry 51 2122-2135 (2012)
  24. Sampling small-scale and large-scale conformational changes in proteins and molecular complexes. Yun MR, Mousseau N, Derreumaux P. J Chem Phys 126 105101 (2007)
  25. High-resolution crystal structure of spectrin SH3 domain fused with a proline-rich peptide. Gushchina LV, Gabdulkhakov AG, Nikonov SV, Filimonov VV. J. Biomol. Struct. Dyn. 29 485-495 (2011)
  26. Application of ring-closing metathesis to Grb2 SH3 domain-binding peptides. Liu F, Giubellino A, Simister PC, Qian W, Giano MC, Feller SM, Bottaro DP, Burke TR. Biopolymers 96 780-788 (2011)
  27. Allostery mediates ligand binding to Grb2 adaptor in a mutually exclusive manner. McDonald CB, El Hokayem J, Zafar N, Balke JE, Bhat V, Mikles DC, Deegan BJ, Seldeen KL, Farooq A. J. Mol. Recognit. 26 92-103 (2013)
  28. Structure determination of [Arg8]vasopressin methylenedithioether in dimethylsulfoxide using NMR. Iwadate M, Nagao E, Williamson MP, Ueki M, Asakura T. Eur. J. Biochem. 267 4504-4510 (2000)
  29. Targeting Molecular Recognition: Exploring the Dual Role of Functional Pseudoprolines in the Design of SH3 Ligands This work was supported by the Swiss National Science Foundation. Tuchscherer G, Grell D, Tatsu Y, Durieux P, Fernandez-Carneado J, Hengst B, Kardinal C, Feller S. Angew. Chem. Int. Ed. Engl. 40 2844-2848 (2001)
  30. Identification of polyproline II regions derived from the proline-rich nuclear receptor coactivators PNRC and PNRC2: new insights for ERα coactivator interactions. Byrne C, Miclet E, Broutin I, Gallo D, Pelekanou V, Kampa M, Castanas E, Leclercq G, Jacquot Y. Chirality 25 628-642 (2013)
  31. Conformational change of Sos-derived proline-rich peptide upon binding Grb2 N-terminal SH3 domain probed by NMR. Ogura K, Okamura H. Sci Rep 3 2913 (2013)


Related citations provided by authors (3)

  1. Orientation of Peptide Fragments from SOS Proteins Bound to the N-Terminal SH3 Domain of Grb2 Determined by NMR Spectroscopy. Wittekind M, Mapelli C, Farmer II BT, Suen KL, Goldfarb V, Tsao J, Lavoie T, Barbacid M, Meyers CA, Mueller L Biochemistry 33 13531- (1994)
  2. Molecular Cloning of the Mouse Grb2 Gene: Differential Interaction of the Grb2 Adaptor Protein with Epidermal Growth Factor and Nerve Growth Factor Receptors. Suen KL, Bustelo XR, Pawson T, Barbacid M Mol. Cell. Biol. 13 5500- (1993)
  3. Identification of Murine Homologues of the Drosophila Son of Sevenless Gene: Potential Activators of Ras. Bowtell D, Fu P, Simon M, Senior P Proc. Natl. Acad. Sci. U.S.A. 89 6511- (1992)