1jyu Citations

Crystal structures of the SH2 domain of Grb2: highlight on the binding of a new high-affinity inhibitor.

J. Mol. Biol. 315 1167-77 (2002)
Related entries: 1jyr, 1jyq

Cited: 37 times
EuropePMC logo PMID: 11827484


The activation of growth factor receptors induces phosphorylation of tyrosine residues in its C-terminal part, creating binding sites for SH2 domain-containing proteins. Grb2 is a protein that recruits Sos, the exchange factor for Ras. Recruitment of Sos allows for Ras activation and subsequent signal transmission. This promotes translocation of MAP kinases into the nucleus and activation of early transcription factors. Grb2, a 25 kDa protein, is composed of one SH2 domain surrounded by two SH3 domains. The SH2 domain of Grb2 binds to class II phosphotyrosyl peptides with the consensus sequence pYXNX. Thus, Grb2 is a good example of a bifunctional adaptor protein that brings proteins into close proximity, allowing signal transduction through proteins located in different compartments. To explore the interactions between Grb2 and phosphorylated ligands, we have solved the crystal structure of complexes between the Grb2-SH2 domain and peptides corresponding to Shc-derived sequences. Two structures are described: the Grb2-SH2 domain in complex with PSpYVNVQN at 1.5 A; and the Grb2-SH2 domain in complex with mAZ*-pY-(alphaMe)pY-N-NH2 pseudo-peptide, at 2 A. Both are compared to an unliganded SH2 structure determined at 2.7 A which, interestingly enough, forms a dimer through two swapping subdomains from two symmetry-related molecules. The nanomolar affinity of the mAZ-pY-(alphaMe)pY-N-NH2 pseudo-peptide for Grb2-SH2 is related to new interactions with non- conserved residues. The design of Grb2-SH2 domain inhibitors that prevent interaction with tyrosine kinase proteins or other adaptors like Shc or IRS1 should provide a means to interrupt the Ras signaling pathway. Newly synthesized pseudo-peptides exhibit nanomolar affinities for the Grb2-SH2 domain. It will then be possible to design new inhibitors with similar affinity and simpler chemical structures.

Reviews citing this publication (4)

  1. Progress towards the development of SH2 domain inhibitors. Kraskouskaya D, Duodu E, Arpin CC, Gunning PT. Chem Soc Rev 42 3337-3370 (2013)
  2. The intertwining of structure and function: proposed helix-swapping of the SH2 domain of Grb7, a regulatory protein implicated in cancer progression and inflammation. Pias S, Peterson TA, Johnson DL, Lyons BA. Crit. Rev. Immunol. 30 299-304 (2010)
  3. Dynamic interactions of proteins in complex networks: a more structured view. Stein A, Pache RA, Bernadó P, Pons M, Aloy P. FEBS J. 276 5390-5405 (2009)
  4. Structural systems biology: modelling protein interactions. Aloy P, Russell RB. Nat. Rev. Mol. Cell Biol. 7 188-197 (2006)

Articles citing this publication (33)

  1. Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid. Hino N, Okazaki Y, Kobayashi T, Hayashi A, Sakamoto K, Yokoyama S. Nat. Methods 2 201-206 (2005)
  2. MMDB: Entrez's 3D-structure database. Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler-Bauer A, Marchler GH, Mazumder R, Nikolskaya AN, Rao BS, Panchenko AR, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. Nucleic Acids Res. 31 474-477 (2003)
  3. Structural basis for the requirement of two phosphotyrosine residues in signaling mediated by Syk tyrosine kinase. Groesch TD, Zhou F, Mattila S, Geahlen RL, Post CB. J. Mol. Biol. 356 1222-1236 (2006)
  4. Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation. Porter CJ, Matthews JM, Mackay JP, Pursglove SE, Schmidberger JW, Leedman PJ, Pero SC, Krag DN, Wilce MC, Wilce JA. BMC Struct. Biol. 7 58 (2007)
  5. Thermodynamic and Structural Effects of Macrocyclization as a Constraining Method in Protein-Ligand Interactions. Delorbe JE, Clements JH, Whiddon BB, Martin SF. ACS Med Chem Lett 1 448-452 (2010)
  6. Structural and energetic aspects of Grb2-SH2 domain-swapping. Benfield AP, Whiddon BB, Clements JH, Martin SF. Arch. Biochem. Biophys. 462 47-53 (2007)
  7. Grb2 adaptor undergoes conformational change upon dimerization. McDonald CB, Seldeen KL, Deegan BJ, Lewis MS, Farooq A. Arch. Biochem. Biophys. 475 25-35 (2008)
  8. Ligand preorganization may be accompanied by entropic penalties in protein-ligand interactions. Benfield AP, Teresk MG, Plake HR, DeLorbe JE, Millspaugh LE, Martin SF. Angew. Chem. Int. Ed. Engl. 45 6830-6835 (2006)
  9. An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe. Saio T, Ogura K, Shimizu K, Yokochi M, Burke TR, Inagaki F. J. Biomol. NMR 51 395-408 (2011)
  10. Binding specificity of SH2 domains: insight from free energy simulations. Gan W, Roux B. Proteins 74 996-1007 (2009)
  11. The PIR domain of Grb14 is an intrinsically unstructured protein: implication in insulin signaling. Moncoq K, Broutin I, Larue V, Perdereau D, Cailliau K, Browaeys-Poly E, Burnol AF, Ducruix A. FEBS Lett. 554 240-246 (2003)
  12. Prediction of binding sites of peptide recognition domains: an application on Grb2 and SAP SH2 domains. McLaughlin WA, Hou T, Wang W. J. Mol. Biol. 357 1322-1334 (2006)
  13. Evaluation of macrocyclic Grb2 SH2 domain-binding peptide mimetics prepared by ring-closing metathesis of C-terminal allylglycines with an N-terminal beta-vinyl-substituted phosphotyrosyl mimetic. Oishi S, Karki RG, Shi ZD, Worthy KM, Bindu L, Chertov O, Esposito D, Frank P, Gillette WK, Maderia M, Hartley J, Nicklaus MC, Barchi JJ, Fisher RJ, Burke TR. Bioorg. Med. Chem. 13 2431-2438 (2005)
  14. Backbone nuclear relaxation characteristics and calorimetric investigation of the human Grb7-SH2/erbB2 peptide complex. Ivancic M, Spuches AM, Guth EC, Daugherty MA, Wilcox DE, Lyons BA. Protein Sci. 14 1556-1569 (2005)
  15. Application of azide-alkyne cycloaddition 'click chemistry' for the synthesis of Grb2 SH2 domain-binding macrocycles. Choi WJ, Shi ZD, Worthy KM, Bindu L, Karki RG, Nicklaus MC, Fisher RJ, Burke TR. Bioorg. Med. Chem. Lett. 16 5265-5269 (2006)
  16. Development of Grb2 SH2 Domain Signaling Antagonists: A Potential New Class of Antiproliferative Agents. Burke TR. Int J Pept Res Ther 12 33-48 (2006)
  17. Structure-based design of thioether-bridged cyclic phosphopeptides binding to Grb2-SH2 domain. Li P, Peach ML, Zhang M, Liu H, Yang D, Nicklaus M, Roller PP. Bioorg. Med. Chem. Lett. 13 895-899 (2003)
  18. Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain. Phan J, Shi ZD, Burke TR, Waugh DS. J. Mol. Biol. 353 104-115 (2005)
  19. Molecular basis for regulation of Src by the docking protein p130Cas. Nasertorabi F, Tars K, Becherer K, Kodandapani R, Liljas L, Vuori K, Ely KR. J. Mol. Recognit. 19 30-38 (2006)
  20. EGF-receptor specificity for phosphotyrosine-primed substrates provides signal integration with Src. Begley MJ, Yun CH, Gewinner CA, Asara JM, Johnson JL, Coyle AJ, Eck MJ, Apostolou I, Cantley LC. Nat. Struct. Mol. Biol. 22 983-990 (2015)
  21. Utilization of a nitrobenzoxadiazole (NBD) fluorophore in the design of a Grb2 SH2 domain-binding peptide mimetic. Shi ZD, Karki RG, Oishi S, Worthy KM, Bindu LK, Dharmawardana PG, Nicklaus MC, Bottaro DP, Fisher RJ, Burke TR. Bioorg. Med. Chem. Lett. 15 1385-1388 (2005)
  22. Discovery of thioether-bridged cyclic pentapeptides binding to Grb2-SH2 domain with high affinity. Jiang S, Liao C, Bindu L, Yin B, Worthy KW, Fisher RJ, Burke TR, Nicklaus MC, Roller PP. Bioorg. Med. Chem. Lett. 19 2693-2698 (2009)
  23. In vitro phosphorylation of the focal adhesion targeting domain of focal adhesion kinase by Src kinase. Cable J, Prutzman K, Gunawardena HP, Schaller MD, Chen X, Campbell SL. Biochemistry 51 2213-2223 (2012)
  24. A bicyclic peptide scaffold promotes phosphotyrosine mimicry and cellular uptake. Quartararo JS, Eshelman MR, Peraro L, Yu H, Baleja JD, Lin YS, Kritzer JA. Bioorg. Med. Chem. 22 6387-6391 (2014)
  25. High resolution crystal structure of the Grb2 SH2 domain with a phosphopeptide derived from CD28. Higo K, Ikura T, Oda M, Morii H, Takahashi J, Abe R, Ito N. PLoS ONE 8 e74482 (2013)
  26. Secondary structure, a missing component of sequence-based minimotif definitions. Sargeant DP, Gryk MR, Maciejewski MW, Thapar V, Kundeti V, Rajasekaran S, Romero P, Dunker K, Li SC, Kaneko T, Schiller MR. PLoS ONE 7 e49957 (2012)
  27. Protein-ligand interactions: probing the energetics of a putative cation-π interaction. Myslinski JM, Clements JH, Martin SF. Bioorg. Med. Chem. Lett. 24 3164-3167 (2014)
  28. Utilization of a common pathway for the synthesis of high affinity macrocyclic Grb2 SH2 domain-binding peptide mimetics that differ in the configuration at one ring junction. Shi ZD, Karki RG, Worthy KM, Bindu LK, Nicklaus MC, Fisher RJ, Burke TR. Chem. Biodivers. 2 447-456 (2005)
  29. The reactivity and conformational control of cyclic tetrapeptides derived from aziridine-containing amino acids. Chung BKW, White CJ, Scully CCG, Yudin AK. Chem Sci 7 6662-6668 (2016)
  30. Dimerization in the Grb7 protein. Peterson TA, Benallie RL, Bradford AM, Pias SC, Yazzie J, Lor SN, Haulsee ZM, Park CK, Johnson DL, Rohrschneider LR, Spuches A, Lyons BA. J. Mol. Recognit. 25 427-434 (2012)
  31. Synthesis of aryl phosphates based on pyrimidine and triazine scaffolds. Courme C, Gresh N, Vidal M, Lenoir C, Garbay C, Florent JC, Bertounesque E. Eur J Med Chem 45 244-255 (2010)
  32. Structural and biophysical investigation of the interaction of a mutant Grb2 SH2 domain (W121G) with its cognate phosphopeptide. Papaioannou D, Geibel S, Kunze MB, Kay CW, Waksman G. Protein Sci. 25 627-637 (2016)
  33. Preliminary crystallographic characterization of the Grb2 SH2 domain in complex with a FAK-derived phosphotyrosyl peptide. Chen HH, Chen CW, Chang YY, Shen TL, Hsu CH. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 195-197 (2010)