SH2 domains

SH2 domains are protein domains, the function of which is to recognize and bind specifically phosphorylated tyrosine residues in specific sequence contexts, thereby allowing protein recruitment onto tyrosine-phosphorylated sites of signaling proteins. We have determined the crystal structures of several SH2 domains (Waksman et al., 1992; Waksman et al., 1993; Rety et al., 1996; Futterer et al.; 1998). These studies are part of an extended program on SH2 domains aimed at understanding the molecular events presiding over phosphotyrosine recognition and binding specificity.The techniques used not only include crystallography but also titration calorimetry and fluorescence spectroscopy, and computational biology. We are particularly interested in deciphering the energetics of binding of tyrosine phosphorylated targets to two types of SH2 domains, that of the single SH2 domain of the Src kinase (Bradshaw et al., 1998; Bradshaw and Waksman, 1998 ; Bradshaw and Waksman, 1999 ; Bradshaw et al., 1999 ; Bradshaw et al., 2000 ; Davidson et al., 2002 ; Lubman et al., 2002 ; Lubman and Waksman, 2003 ; Geroult et al., 2006 ; Geroult et al., 2007 ), and that of the tandem SH2 domains of the Syk kinase (Grucza et al., 1999 ; Grucza et al., 2000 ; Kumaran et al., 2003 ).

Explore the following link if you want to learn more about other systems that we have studied in the past and that are also related to signal transduction: Fibroblast growth factor (FGF) and N-myristoyl transferase and posttranslational modification of proteins.




Publications

  • G. Waksman, D. Kominos, S. Robertson, N. Pant, D. Baltimore, R.Birge, D. Cowburn, H. Hanafusa, B. Mayer, M. Overduin, M. Resh, C. Rios, L. Silverman and J. Kuriyan.
    Crystal structure of the phosphotyrosine recognition domain SH2 of v-src complexed with tyrosine-phosphorylated peptides.
    Nature. 358:646-653. (1992)

  • G. Waksman, S. Shoelson, N. Pant, D. Cowburn, and J. Kuriyan.
    Binding of a high affinity phosphotyrosyl peptide to the src SH2 domain: crystal structures of the complexed and peptide-free forms.
    Cell. 72:779-790. (1993)

  • S. Rety, K. Futterer, R. Grucza, C. Munoz, W. Frazier, and G. Waksman.
    pH-dependent self- association of the Src Homology 2 (SH2) domain of the Src Homologous and Collagen-Like (SHC) protein.
    Protein Science. 5:405-413. (1996)

  • J.M. Bradshaw, R.A. Grucza, J.E. Ladbury, G. Waksman.
    Probing the "two pronged-plug two holed-socket" model for the mechanism of binding of the Src SH2 domain to phosphotyrosyl peptides: a thermodynamic study.
    Biochemistry. 37:9083-9090. (1998)

  • K. Futterer, J. Wong, R.A. Grucza, A.C. chan, G. Waksman.
    Structural basis for Syk tyrosine kinase ubiquity in signal transduction pathways revealed by the crystal structure of its regulatory SH2 domains bound to a dually phosphorylated ITAM peptide.
    Journal of Molecular Biology. 281:523-533 (1998)

  • J.M. Bradshaw and G. Waksman.
    Calorimetric investigation of the proton linkage by monitoring both the enthalpy and association constant of binding: application of the interaction of the Src SH2 domain with a high-affinity tyrosyl phosphopeptide
    Biochemistry. 37:15400-15407. (1998)

  • J.M. Bradshaw and G. Waksman.
    Calorimetric investigation of high-affinity Src SH2 domain-tyrosyl phosphopeptide binding: dissection of the phosphopeptide sequence specificity and coupling energetics
    Biochemistry. 38:5147-5154. (1999)

  • J.M. Bradshaw and G. Waksman.
    Investigation of Phosphotyrosine Recognition by the SH2 domain of the Src kinase
    Journal of Molecular Biology. 293:971-985. (1999)

  • R.A. Grucza, K. Futterer, A.C. Chan, and G. Waksman.
    Thermodynamic of study of the binding of the tandem-SH2 domain of the Syk kinase to a dually phosphorylated ITAM peptide: evidence for two conformers
    Biochemistry. 38:5024-5033. (1999)

  • R.A. Grucza, J.M. Bradshaw, K. Futterer, and G. Waksman.
    SH2 domains: from structure to energetics: a dual approach to the study of structure-function relationships
    Medicinal Research Reviews. 19:273-293. (1999)

  • J.M. Bradshaw, V. Mitaxov, and G. Waksman.
    Mutational investigation of the specificity determining region of the Src SH2 domain
    Journal of Molecular Biology. 299:521-535. (2000)

  • R.A. Grucza, J.M. Bradshaw, V. Mitaxov, and G. Waksman.
    Role of electrostatic interactions in SH2 domain recognition: salt dependence of tyrosyl-phosphorylated peptide binding to the tandem SH2 domain of the Syk kinase and the single SH2 domain of the Src kinase
    Biochemistry. 39:10072-10081. (2000)

  • J.M. Bradshaw, R.A. Grucza, and G. Waksman.
    Binding thermodynamics of protein modules involved in tyrosine kinase signaling pathways
    In: The thermodynamics of the drug-receptor interaction. R.B. Raffa Ed. pp451-470. (2000)

  • J.M. Bradshaw and G. Waksman.
    SH2 domains
    In: The Encyclopedia of Molecular Medicine. T.E. Creighton Ed. (2001)

  • J. Davidson, O.Y. Lubman, T. Rose, G. Waksman, and S.F. Martin.
    Calorimetric and structural studies of 1,2,3-trisubstituted cyclopropanes as conformationally constrained peptide inhibitors of Src SH2 domain binding.
    JACS. 124:205-215 (2002)

  • O.Y. Lubman and G. Waksman.
    Dissection of the energetic coupling across the Src SH2 domain- tyrosyl phosphopeptide interface.
    Journal of Molecular Biology. 316:291-304 (2002)

  • J.M. Bradshaw and G. Waksman.
    Molecular Recognition by SH2 domains.
    Advances in Protein Chemistry. 61:161-210 (2002)

  • O.Y. Lubman and G. Waksman.
    Structural and thermodynamic basis for the interaction of the Src SH2 domain with the activated form of the PDGF beta-receptor
    Journal of Molecular Biology. 328:655-668 (2003)

  • S. Kumaran, R.A. Grucza and G. Waksman.
    The tandem Src homology 2 domains of the Syk kinase: a molecular device that adapts to interphosphotyrosine distances.
    Proc. Natl. Acad. Sci. USA. 100:14828-14833 (2003)

  • G. Waksman, S. Kumaran, O.Y. Lubman.
    SH2 domains: role, structure and implications for molecular medicine.
    Expert Rev Mol Med. 6:1-18 (2004)

  • S. Geroult, S. Virdee, and G. Waksman.
    The role of water in computational and experimental derivation of binding thermodynamics of SH2 domains.
    Chemical Biology and Drug Design. 67:38-45 (2006)

  • S. Geroult, M. Hooda, S. Virdee, and G. Waksman.
    Prediction of solvation sites at the interface of Src SH2 domain complexes using molecular dynamics simulations.
    Chemical Biology and Drug Design. 70:87-99 (2007)




    FGF

  • D. Ornitz, A.B. Herr, M. Nillson, J. Westman, C-M. Svahn, and G. Waksman.
    FGF binding and FGF receptor activation by synthetic heparan-derived di- and trisaccharides.
    Science. 268:432-436. (1995)

  • G. Venkataraman, V. Sasisekharan, A.B. Herr, D.M. Ornitz, G. Waksman, C.L. Cooney, R. Langer, and R. Sasisekharan.
    Preferential self-association of FGF is stabilized by heparin during dimerization and activation.
    Proc. Natl. Acad. Sci. USA. 93:845-849. (1996)

  • A.B. Herr, D.M. Ornitz, R. Sasisekharan, G. Venkataraman, and G. Waksman.
    Heparin-induced self-association of FGF-2: evidence for two oligomerization processes.
    Journal of Biological Chemistry. 272:16382-16389. (1997)

  • G. Waksman, and A.B. Herr.
    New insights into heparin-induced FGF oligomerization.
    Nature Struct. Biol. 5:16382-16389. (1998)




    NMT

  • R.S. Bhatnagar,K. Futterer,T.A. Farazi, S. Korolev,C.L. Murray, E. Jackson-Machelski, G.W. Gokel, J.I. Gordon, and G. Waksman .
    Structure of N-myristoyltransferase with bound myristoylCoA and peptide substrate analogs
    Nature Struct. Biol. 5:1091-1097. (1998)

  • R.S. Bhatnagar, K. Futterer, G. Waksman, and J.I. Gordon.
    Structure of myristoylCoA:Protein N-myristoyltransferase
    Biophysica and Biochemica Acta. 23:162-172. (1999)

  • R.S. Bhatnagar, K. Ashrafi, K. Futterer, G. Waksman, and J.I. Gordon.
    The biology and enzymology of protein N-myristoylation.
    The enzymes. F. Tamanoi and D.S. Sigman, Eds. pp241-290. (2000)

  • T.A. Farazi, G. Waksman, and J.I. Gordon.
    The structures of S. cerevisiae myristoylCoA:protein N-myristoyltransferase with bound myristoylCoA and peptide substrates provide insights about substrate recognition and catalysis.
    Biochemistry. 40:6335-6343. (2001)

  • T.A. Farazi, J.K. Manchester, G. Waksman, and J.I. Gordon.
    Pre-steady state kinetic studies of Saccharomyces cerevisiae myristoylCoA: protein N-myristoyltransferase mutants identify residues involved in catalysis
    Biochemistry. 40:9177-9186. (2002)

  • T.A. Farazi, G. Waksman, and J.I. Gordon.
    The biology and enzymology of protein N-myristoylation.
    J. Biol. Chem. 276:39501-2. (2002)