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Residual dipolar couplings: Synergy between NMR and structural genomics

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Abstract

Structural genomics is on a quest for the structure and function of a significant fraction of gene products. Current efforts are focusing on structure determination of single-domain proteins, which can readily be targeted by X-ray crystallography, NMR spectroscopy and computational homology modeling. However, comprehensive association of gene products with functions also requires systematic determination of more complex protein structures and other biomolecules participating in cellular processes such as nucleic acids, and characterization of biomolecular interactions and dynamics relevant to function. Such NMR investigations are becoming more feasible, not only due to recent advances in NMR methodology, but also because structural genomics is providing valuable structural information and new experimental and computational tools. The measurement of residual dipolar couplings in partially oriented systems and other new NMR methods will play an important role in this synergistic relationship between NMR and structural genomics. Both an expansion in the domain of NMR application, and important contributions to future structural genomics efforts can be anticipated.

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References

  • Al-Hashimi, H.M., Gorin, A., Majumdar, A. and Patel, D.J. (2001a), submitted.

  • Al-Hashimi, H.M., Majumdar, A., Gorin, A., Kettani, A., Skripkin, E. and Patel, D. J. (2001b) J. Am. Chem. Soc., 123, 633–640.

    Google Scholar 

  • Al-Hashimi, H.M., Gosser, Y., Gorin, A., Hu, W., Majumdar, A. and Patel, D.J. (2002) J. Mol Biol., 315,95–102.

    Google Scholar 

  • Al-Hashimi, H.M., Valafar, H., Terrell, M., Zartler, E.R., Eidsness, M.K. and Prestegard, J.H. (2000) J. Magn. Reson., 143,402–406.

    Google Scholar 

  • Baker, D. and Sali, A. (2001) Science, 294,93–96.

    Google Scholar 

  • Bax, A., Kontaxis, G. and Tjandra, N. (2001) Meth. Enzymol., 339,127–174.

    Google Scholar 

  • Bewley, C.A. and Clore, G.M. (2000) J. Am. Chem. Soc., 122,6009–6016.

    Google Scholar 

  • Bothner-By, A.A. (1995) In Encyclopedia of Nuclear Magnetic Resonance. Grant, D.M. and Harris, R.K. (Eds.), Wiley, Chichester, pp. 2932–2938.

    Google Scholar 

  • Case, D.A. (1999) J. Biomol. NMR, 15, 95–102.

    Google Scholar 

  • Chou, J.J., Li, S.P. and Bax, A. (2000a) J. Biomol. NMR,18, 217–227.

    Google Scholar 

  • Chou, S.H., Tseng, Y.Y. and Chu, B.Y. (2000b) J. Biomol. NMR, 17,1–16.

    Google Scholar 

  • Dingley, A.J. and Grzesiek, S. (1998) J. Am. Chem. Soc., 120, 8293–8297.

    Google Scholar 

  • Doudna, J.A. (2000) Nat Struct Biol., 7 (Suppl), 954-956.

    Google Scholar 

  • Drohat, A.C., Tjandra, N., Baldisseri, D.M. and Weber, D.J. (1999) Protein Sci., 8, 800–809.

    Google Scholar 

  • Dyson, H.J. and Wright, P.E. (1998) Nat. Struct. Biol., 5,499–503.

    Google Scholar 

  • Ellis, R.J. (2001) Trends Biochem Sci., 26,597–604.

    Google Scholar 

  • Ferentz, A.E. and Wagner, G. (2000) Q. Rev. Biophys.,33,29–65.

    Google Scholar 

  • Fischer, M.W.F., Losonczi, J.A., Weaver, J.L. and Prestegard, J.H. (1999) Biochemistry, 38, 9013–9022.

    Google Scholar 

  • Gardner, K.H. and Kay, L.E. 1999. In Biological Magnetic Resonance, Vol. 17, Krishna, N.R. and Berliner, L.J. (Eds.), Plenum, New York, NY, pp. 27–69.

    Google Scholar 

  • Gohlke, H., Hendlich, M. and Klebe, G. (2000) J. Mol. Biol., 295, 337–356.

    Google Scholar 

  • Hermann, T. and Patel, D.J. (1999) J Mol. Biol.,294,829–849.

    Google Scholar 

  • Ishima, R. and Torchia, D.A. (2000) Nat. Struct. Biol., 7,740–743.

    Google Scholar 

  • Kay, L.E. (1998) Nat. Struct. Biol., 5,513–517.

    Google Scholar 

  • Kay, L.E. (2001) Meth. Enzymol., 339, 174–203.

    Google Scholar 

  • Koehl, P. and Levitt, M. (1999) Nat Struct Biol., 6, 108–111.

    Google Scholar 

  • Koppensteiner, W.A., Lackner, P., Wiederstein, M. and Sippl, M.J. (2000) J. Mol. Biol.,296,1139–1152.

    Google Scholar 

  • Majumdar, A. and Patel, D.J. (2001) Accounts Chem. Res. (in press). 8

  • Marti-Renom, M.A., Stuart, A.C., Fiser, A., Sanchez, R., Melo, F. and Sali, A. (2000) Annu. Rev. Biophys. Biomol. Struct.,29, 291–325.

    Google Scholar 

  • Meiler, J., Prompers, J.J., Peti, W., Griesinger, C. and Bruschweiler, R. (2001) J. Am. Chem. Soc., 123,6098–6107.

    Google Scholar 

  • Mollova, E.T. and Pardi, A. (2000) Curr. Opin. Struct. Biol., 10, 298–302.

    Google Scholar 

  • Mollova, E.T., Hansen, M.R. and Pardi, A. (2000) J. Am. Chem. Soc., 122, 11561–11562.

    Google Scholar 

  • Montelione, G.T., Zheng, D., Huang, Y.J., Gunsalus, K.C. and Szyperski, T. (2000) Nat. Struct. Biol., 7 (Suppl.),982–985.

    Google Scholar 

  • Mumenthaler, C., Guntert, P., Braun, W. and Wuthrich, K. (1997) J. Biomol. NMR, 10, 351–362.

    Google Scholar 

  • Norin, M. and Sundstrom, M. (2001) Curr. Opin. Drug. Discov. Devel., 4, 284–290.

    Google Scholar 

  • Orengo, C.A., Pearl, F.M.G., Bray, J.E., Todd, A.E., Martin, A.C., Lo Conte, L. and Thornton, J.M. (1999) Nucl. Acids Res., 27, 275–279.

    Google Scholar 

  • Palmer, A.G., 3rd, Kroenke, C.D. and Loria, J.P. (2001) Meth. Enzymol., 339,204–238.

    Google Scholar 

  • Permi, P. and Annila, A. (2000) J. Biomol. NMR, 16, 221–227.

    Google Scholar 

  • Pervushin, K., Ono, A., Fernandez, C., Szyperski, T., Kainosho, M. and Wuthrich, K. (1998) Proc. Natl. Acad. Sci. USA, 95,14147–14151.

    Google Scholar 

  • Pervushin, K., Riek, R., Wider, G. and Wuthrich, K. (1997) Proc. Natl. Acad. Sci. USA, 94, 12366–12371.

    Google Scholar 

  • Phan, A.T. (2000) J. Biomol. NMR, 16, 175–178.

    Google Scholar 

  • Prestegard, J.H. (1998) Nat. Struct. Biol., 5,517–522.

    Google Scholar 

  • Prestegard, J.H. and Kishore, A.I. (2001) Curr. Opin. Chem. Biol., 5,584–590.

    Google Scholar 

  • Prestegard, J.H., Al-Hashimi, H.M. and Tolman, J.R. (2000) Q. Rev. Biophys., 33,371–424.

    Google Scholar 

  • Prestegard, J.H., Tolman, J.R., Al-Hashimi, H.M. and Andrec, M. (1999) In Biological Magnetic Resonance, Vol. 17, Krishna, N.R. and Berliner, L.J. (Eds.), Plenum, New York, NY, pp. 311–355.

    Google Scholar 

  • Prestegard, J.H., Valafar, H., Glushka, J. and Tian, F. (2001) Biochemistry,40,8677–8685.

    Google Scholar 

  • Ram, P. and Prestegard, J.H. (1988) Biochim. Biophys. Acta, 940, 289–294.

    Google Scholar 

  • Ramirez, B.E. and Bax, A. (1998) J. Am. Chem. Soc., 120, 9106–9107.

    Google Scholar 

  • Robert, C.H. and Janin, J. (1998) J. Mol. Biol., 283, 1037–1047.

    Google Scholar 

  • Sali, A. (1998) Nat. Struct. Biol., 5,1029–1032.

    Google Scholar 

  • Sanchez, R. and Sali, A. (1998) Proc. Natl. Acad. Sci. USA,95, 13597–13602.

    Google Scholar 

  • Sanders, C.R. and Prosser, R.S. (1998) Struct. Fold. Des.,6,1227–1234.

    Google Scholar 

  • Saupe, A. (1968) Angew. Chem., Int. Ed. Engl., 7,97–112.

    Google Scholar 

  • Shortle, D. and Ackerman, M. S. (2001) Science, 293,487–489.

    Google Scholar 

  • Tian, F., Valafar, H. and Prestegard, J.H. (2001) J. Am. Chem. Soc., in press.

  • Tjandra, N. and Bax, A. (1997) Science,278,1111–1114.

    Google Scholar 

  • Tolman, J.R. (2001) Curr. Opin. Struct. Biol.,11, 532–539.

    Google Scholar 

  • Tolman, J.R., Al-Hashimi, H.M., Kay, L.E. and Prestegard, J.H. (2001) J. Am. Chem. Soc.,23,1416–1424.

    Google Scholar 

  • Tolman, J.R., Flanagan, J.M., Kennedy, M.A. and Prestegard, J.H. (1997) Nat. Struct. Biol.,4,292–297.

    Google Scholar 

  • Veglia, G. and Opella, S.J. (2000) J. Am. Chem. Soc.,122, 11733–11734.

    Google Scholar 

  • Venters, R.A., Huang, C.C., Farmer, B.T., 2nd, Trolard, R., Spicer, L.D. and Fierke, C.A. (1995) J. Biomol. NMR,5, 339–344.

    Google Scholar 

  • Vold, R.R. and Prosser, R.S. (1996) J. Magn. Reson. Ser.,B113, 267–271.

    Google Scholar 

  • Wang, L.C., Pang, Y.X., Holder, T., Brender, J.R., Kurochkin, A.V. and Zuiderweg, E.R.P. (2001) Proc. Natl. Acad. Sci. USA 98, 7684–7689.

    Google Scholar 

  • Williamson, J.R. (2000) Nat. Struct. Biol.,7,834–837.

    Google Scholar 

  • Xu, R., Ayers, B., Cowburn, D. and Muir, T.W. (1999) Proc. Natl. Acad. Sci. USA,96,388–393.

    Google Scholar 

  • Yamazaki, T., Otomo, T., Oda, N., Kyogoku, Y., Uegaki, K., Ito, N., Ishino, Y. and Nakamura, H. (1998) J. Am. Chem. Soc.,120, 5591–5592.

    Google Scholar 

  • Yang, D.W., Venters, R.A., Mueller, G.A., Choy, W.Y. and Kay, L.E. (1999) J. Biomol. NMR,14,333–343.

    Google Scholar 

  • Zhou, H., Vermeulen, A., Jucker, F.M. and Pardi, A. (1999) Biopolymers, 52,168–180.

    Google Scholar 

  • Zidek, L., Stefl, R. and Sklenar, V. (2001) Curr. Opin. Struct. Biol., 11,275–281.

    Google Scholar 

  • Zweckstetter, M. and Bax, A. (2001) J Am Chem Soc.,123, 9490–9491.

    Google Scholar 

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Authors and Affiliations

  1. Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10021, U.S.A.

    Hashim M. Al-Hashimi & Dinshaw J. Patel

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  1. Hashim M. Al-Hashimi
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Correspondence to Hashim M. Al-Hashimi.

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Al-Hashimi, H.M., Patel, D.J. Residual dipolar couplings: Synergy between NMR and structural genomics. J Biomol NMR 22, 1–8 (2002). https://doi.org/10.1023/A:1013801714041

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