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Correlation between binding and dynamics at SH2 domain interfaces

Abstract

Protein recognition is a key determinant in regulating biological processes. Structures of complexes of interacting proteins provide significant insights into the mechanism of specific recognition. However, studies performed by modifying residues within a protein interface demonstrate that binding is not fully explained by these static pictures. Thus, structural data alone was not predictive of affinities in binding studies of phospholipase Cγ1 and Syp phosphatase SH2 domains with phosphopeptides. NMR relaxation experiments probing dynamics of methyl groups of these complexes indicate a correlation between binding energy and restriction of motion at the interfacial region responsible for specific binding.

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References

  1. Schreiber, S.L. Signalling an interest. Nature Struct. Biol. 1, 417–420 (1994).

    Article  Google Scholar 

  2. Waksman, G., Shoelson, S.E., Pant, N., Cowburn, D. & Kuriyan, J. 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).

    Article  CAS  Google Scholar 

  3. Eck, M.J., Shoelson, S.E. & Harrison, S.C. Recognition of a high-affinity phosphotyrosyl peptide by the src homology-2 domain of p56lck. Nature 362, 87–91 (1993).

    Article  CAS  Google Scholar 

  4. Pascal, S.M. et al. NMR Structure of an SH2 Domain of phospholipase C-g1 complexed with a high-affinity binding peptide. Cell 77, 461–472 (1994).

    Article  CAS  Google Scholar 

  5. Lee, C.-H. et al. Crystal structures of peptide complexes of the amino-terminal SH2 domain of the Syp tyrosine phosphatase. Structure 2, 423–438 (1994).

    Article  CAS  Google Scholar 

  6. Kabsch, W. & Sander, C. Biopolymers 22, 2577–2637 (1983).

    Article  CAS  Google Scholar 

  7. Clackson, T. & Wells, J.A. A hot spot of binding energy in a hormone-receptor interface. Science 267, 383–386 (1995).

    Article  CAS  Google Scholar 

  8. Kay, L.E., Torchia, D.A. & Bax, A. Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry 28, 8972–8979 (1989).

    Article  CAS  Google Scholar 

  9. Akke, M., Skelton, N.J., Kordel, J., Palmer, A.G.d. & Chazin, W.J. Effects of ion binding on the backbone dynamics of calbindin D9k determined by 15N NMR relaxation. Biochemistry 32, 9832– (1993).

    Article  CAS  Google Scholar 

  10. Cheng, J.W., Lepre, C.A. & Moore, J.M. 15N NMR relaxation studies of the FK506 binding protein: dynamic effects of ligand binding and implications for calcineurin recognition. Biochemistry 33, 4093–100 (1994).

    Article  CAS  Google Scholar 

  11. Rischel, C., Madsen, J.C., Andersen, K.V. & Poulsen, P.M. Comparison of backbone dynamics of apo- and holo-acyl-coenzyme A binding protein using 15N relaxation measurements. Biochemistry 33, 13997–14002 (1994).

    Article  CAS  Google Scholar 

  12. Kaptein, R., Slijper, M. & Boelens, R. Structure and dynamics of the lac represser-operator complex as determined by NMR. Toxicol. Lett. 82, 591–599 (1995).

    Article  Google Scholar 

  13. Pintar, A. et al. Solution studies of the SH2 domain from the fyn tyrosine kinase: secondary structure, backbone dynamics and protein association. Eur Biophys. J. 24, 371–380 (1996).

    Article  CAS  Google Scholar 

  14. Olejniczak, E.T., Zhou, M.M. & Fesik, S.W. Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide. Biochemistry 36, 4118–4124 (1997).

    Article  CAS  Google Scholar 

  15. Hodsdon, M.E. & Cistola, D.P. Ligand binding alters the backbone mobility of intestinal fatty acid- binding protein as monitored by 15N NMR relaxation and 1H exchange. Biochemistry 36, 2278–2290 (1997).

    Article  CAS  Google Scholar 

  16. Farrow, N.A. etal. Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry 33, 5984–6003 (1994).

    Article  CAS  Google Scholar 

  17. Yu, L., Zhu, C.X., Tse-Dinh, Y.C. & Fesik, S.W. Backbone dynamics of the C-terminal domain of Escherichia coli topoisomerase I in the absence and presence of single-stranded DNA. Biochemistry 35, 9661–9666 (1996).

    Article  CAS  Google Scholar 

  18. Henry, G.D., Weiner, J.H. & Sykes, B.D. Backbone dynamics of a model membrane protein: 13C NMR spectroscopy of alanine methyl groups in detergent-solubilized M13 coat protein. Biochemistry 25, 590–598 (1996).

    Article  Google Scholar 

  19. Nicholson, L.K. et aL. Dynamics of methyl groups in proteins as studied by proton-detected 13C NMR spectroscopy.Application to the leucine residues of staphylococcal nuclease. spectroscopy 31, 5253–5263 (1992).

    CAS  Google Scholar 

  20. Wand, A.J., Urbauer, J.L, McEvoy, R.P. & Bieber, R.J. Internal dynamics of human ubiquitin revealed by 13C-relaxation studies of randomly fractionally labeled protein. Biochemistry 35, 6116–6125 (19931993).

    Article  Google Scholar 

  21. LeMaster, D.M. & Kushlan, D.M. Dynamical mapping of E coil thioredoxin via 13C NMR relaxation analysis. J. Am. Chem. Soc. 118, 9255–9264 (1996).

    Article  Google Scholar 

  22. Muhandiram, D., Yamazaki, T., Sykes, B. & Kay, L. Measurements of deuterium T, and Tlrho relaxation times in uniformly 13C labeled and fractionally deuterium labeled proteins in solution. . Am. Chem. Soc. 117, 11536–11544 (1995).

    Article  CAS  Google Scholar 

  23. Kay, L., Muhandiram, D., Farrow, N., Aubin, Y. & Forman-Kay, J. Correlation between dynamics and high affinity binding in an SH2 domain interaction. Biochemistry 35, 361–368 (1996).

    Article  CAS  Google Scholar 

  24. Tamura, A. et al. Dynamics of the three methionyl side chains of Streptomyces subtilisin inhibitor.Deuterium NMR studies in solution and in the solid state. Prot.Sci. 5, 127–39 (1996).

    Article  CAS  Google Scholar 

  25. Mandel, A.M., Akke, M. & Palmer, A.G. Backbone dynamics of Escherichia coli ribonuclease H1: correlations with structure and function in an active enzyme. J.Mol. Biol. 246, 144–63 (1995).

    Article  CAS  Google Scholar 

  26. Nicholson, L.K. et al. Flexibility and function in HIV-1 protease. Nature Struct. Biol. 274–280 (1995).

    Article  CAS  Google Scholar 

  27. Williams, J.C. & McDermott, A.E. Dynamics of the flexible loop of triosephosphate isomerase: the loop motion is not ligand gated. Biochemistry 34, 8309–8319 (1995).

    Article  CAS  Google Scholar 

  28. Stivers, J.T., Abeygunawardana, C. & Mildvan, A.S. 15N NMR relaxation studies of free and inhibitor-bound 4-oxalocrotonate tautomerase: backbone dynamics and entropy changes of an enzyme upon inhibitor binding. Biochemistry 35, 16036–16047 (1996).

    Article  CAS  Google Scholar 

  29. Zhao, Q., Abeygunawardana, C. & Mildvan, A.S. 13C NMR relaxation studies of backbone and side chain motion of the catalytic tyrosine residue in free and steroid-bound delta 5-3- ketosteroid isomerase. Biochemistry 35, 1525–1532 (1996).

    Article  CAS  Google Scholar 

  30. Lipari, G. & Szabo, A. Model-free approach to the interpretation of nuclear magnetic relaxation in macromolecules: 1. Theory and range of validity. J. Am. Chem. Soc. 104, 4546–4559 (1982).

    Article  CAS  Google Scholar 

  31. Lipari, G. & Szabo, A. Model-free approach to the interpretation of nuclear magnetic relaxation in macromolecules: 2.Analysis of experimental results. J. Am. Chem. Soc. 104, 4559–4570 (1982).

    Article  CAS  Google Scholar 

  32. Bax, A. et al. Measurement of homo- and heteronuclear J couplings from quantitative J correlation. Meth. Enz. 239, 79–105 (1994).

    CAS  Google Scholar 

  33. Nicholls, A., Sharp, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Prot. Struct, funct. Genet. 11, 281–296 (1991).

    Article  CAS  Google Scholar 

  34. Felder, S. et al. SH2 domains exhibit high-affinity binding to tyrosine-phosphorylated peptides yet also exhibit rapid dissociation and exchange. Mol. Cell. Biol. 13, 1449–1455 (1993).

    Article  CAS  Google Scholar 

  35. Songyang, Z. et al. SH2 domains recognize specific phosphopeptide sequences. Cell 72, 767–778 (1993).

    Article  CAS  Google Scholar 

  36. Larose, L., Gish, G. & Pawson, T. Construction of an SH2 domain-binding site with mixed specificity. J.Biol. Chem. 270, 3858–3862 (1995).

    Article  CAS  Google Scholar 

  37. Huyer, G., Li, Z.M., Adam, M., Huckle, W.R. & Ramachandran, C. Direct determination of the sequence recognition requirements of the SH2 domains of SH-PTP2. Biochemistry 34, 1040–1049 (1995).

    Article  CAS  Google Scholar 

  38. Case, R. et aL. SH-PTP2/Syp SH2 domain binding specificity is defined by direct interactions with platelet-derived growth factor beta-receptor, epidermal growth factor receptor, and insulin receptor substrate-1-derived phosphopeptides. J.Biol. Chem. 269, 10467–10474 (1994).

    CAS  PubMed  Google Scholar 

  39. Spolar, R.S. & Record, M.T.J. Coupling of local folding to site-specific binding of proteins to DNA. Science 263, 777–784 (1994).

    Article  CAS  Google Scholar 

  40. Kriwacki, R., Hengst, L., Tennant, L., Reed, S. & Wright, P. Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity. Proc. Natl. Acad. Sci. USA 93, 11504–11509 (1996).

    Article  CAS  Google Scholar 

  41. Yang, D. & Kay, L. Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. J Mol. Biol. 263, 369–382 (1996).

    Article  CAS  Google Scholar 

  42. Akke, M., Bruschweiler, R. & Palmer, A.G. NMR order parameters and free energy: an analytic approach and application to cooperative calcium binding by calbindin D9k. LAm. Chem. Soc. 115, 9832–9833 (1993).

  43. Neri, D., Szyperski, T., Otting, G., Senn, H. & Wuthrich, K. Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 represser by biosynthetically directed fractional 13C labeling. Biochemistry 28, 7510–7516 (1989).

    Article  CAS  Google Scholar 

  44. Bax, A. Multidimensional nuclear resonance methods for protein studies. Curr. Opin. Struct. Biol. 4, 738–744 (1994).

    Article  CAS  Google Scholar 

  45. Delaglio, F. et al. NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995).

    Article  CAS  Google Scholar 

  46. Garrett, D.S., Powers, R., Gronenborn, A.M. & Clore, G.M. A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams. J. Magn. Reson. 95, 214–220 (1991).

    CAS  Google Scholar 

  47. Johnson, B. & Blevins, R. NMRView: a computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603–614 (1994).

    Article  CAS  Google Scholar 

  48. Koradi, R., Billeter, M. & Wuthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graphics 14, 51–55 (1996).

    Article  CAS  Google Scholar 

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kay, L., Muhandiram, D., Wolf, G. et al. Correlation between binding and dynamics at SH2 domain interfaces. Nat Struct Mol Biol 5, 156–163 (1998). https://doi.org/10.1038/nsb0298-156

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