Journal of Structural and Functional Genomics

, Volume 5, Issue 4, pp 241–254 | Cite as

Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target

  • H. Valafar
  • K. L. Mayer
  • C. M. Bougault
  • P. D. LeBlond
  • F. E. JenneyJr.
  • P. S. Brereton
  • M. W. W. Adams
  • J. H. Prestegard


Structural genomics (or proteomics) activities are critically dependent on the availability of high-throughput structure determination methodology. Development of such methodology has been a particular challenge for NMR based structure determination because of the demands for isotopic labeling of proteins and the requirements for very long data acquisition times. We present here a methodology that gains efficiency from a focus on determination of backbone structures of proteins as opposed to full structures with all sidechains in place. This focus is appropriate given the presumption that many protein structures in the future will be built using computational methods that start from representative fold family structures and replace as many as 70% of the sidechains in the course of structure determination. The methodology we present is based primarily on residual dipolar couplings (RDCs), readily accessible NMR observables that constrain the orientation of backbone fragments irrespective of separation in space. A new software tool is described for the assembly of backbone fragments under RDC constraints and an application to a structural genomics target is presented. The target is an 8.7 kDa protein from Pyrococcus furiosus, PF1061, that was previously not well annotated, and had a nearest structurally characterized neighbor with only 33% sequence identity. The structure produced shows structural similarity to this sequence homologue, but also shows similarity to other proteins, which suggests a functional role in sulfur transfer. Given the backbone structure and a possible functional link this should be an ideal target for development of modeling methods.


NMR partial alignment Pyrococcus furiosus RDC structure determination 



pentaethylene glycol monododecyl ether


hexadecyltrimethylammonium bromide


2,2-dimethyl-2-silapentane-5-sulfonic acid




residual dipolar coupling


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  1. 1.
    Montelione, G.T., Zheng, D.Y., Huang, Y.P.J., Gunsalus, K.C., Szyperski, T. 2000Nat. Struct. Biol.7982985Google Scholar
  2. 2.
    Tian, F., Valafar, H., Prestegard, J.H. 2001J. Am. Chem. Soc.1231179111796Google Scholar
  3. 3.
    Orengo, C.A., Todd, A.E., Thornton, J.M. 1999Curr. Opin. Struct. Biol.9374382Google Scholar
  4. 4.
    Sali, A., Kuriyan, J. 1999Trends Biochem. Sci.24M20M24Google Scholar
  5. 5.
    Holm, L., Sander, C. 1991J. Mol. Biol.218183194Google Scholar
  6. 6.
    Lee, C., Subbiah, S. 1991J. Mol. Biol.217373388Google Scholar
  7. 7.
    Adams, M.W.W., Dailey, H.A., Delucas, L.J., Luo, M., Prestegard, J.H., Rose, J.P., Wang, B.C. 2003Acc. Chem. Res.36191198Google Scholar
  8. 8.
    Morris, L.C., Valafar, H., Prestegard, J.H. 2004J. Biomol. NMR2919Google Scholar
  9. 9.
    Schwieters, C.D., Kuszewski, J.J., Tjandra, N., Clore, G.M. 2003J. Magn. Reson.1606573Google Scholar
  10. 10.
    Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E. 2000Nucleic Acids Res.28235242CrossRefGoogle Scholar
  11. 11.
    Tolman, J.R., Flanagan, J.M., Kennedy, M.A., Prestegard, J.H. 1995Proc. Natl. Acad. Sci. USA9292799283Google Scholar
  12. 12.
    Tjandra, N., Bax, A. 1997Science27811111114Google Scholar
  13. 13.
    Cornilescu, G., Delaglio, F., Bax, A. 1999J. Biomol. NMR13289302CrossRefGoogle Scholar
  14. 14.
    Fowler, C.A., Tian, F., Al-Hashimi, H.M., Prestegard, J.H. 2000J. Mol. Biol.304447460Google Scholar
  15. 15.
    Andrec, M., Du, P.C., Levy, R.M. 2001J. Biomol. NMR21335347Google Scholar
  16. 16.
    Prestegard, J.H., Al-Hashimi, H.M., Tolman, J.R. 2000Quart. Rev. Biophys.33371424Google Scholar
  17. 17.
    Bax, A., Kontaxis, G., Tjandra, N. 2001Dipolar couplings in macromolecular structure determination, In Nuclear Magnetic Resonance of Biological Macromolecules, Pt BMethods in Enzymology339127174Google Scholar
  18. 18.
    Prestegard, J.H., Kishore, A.I. 2001CurrOpin. Struct. Biol.5584590Google Scholar
  19. 19.
    Sambrook, J., Russell, D. 2000Molecular Cloning A Laboratory Manual3Cold Spring Harbor Laboratory PressCold Spring Harbor, NY999 ppGoogle Scholar
  20. 20.
    Weisemann, R., Ruterjans, H., Schwalbe, H., Schleucher, J., Bermel, W., Griesinger, C. 1994J. Biomol. NMR4231240Google Scholar
  21. 21.
    Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A. 1995J.Biomol. NMR6277293Google Scholar
  22. 22.
    Varner, S.J., Vold, R.L., Hoatson, G.L. 1996J. Magn. Reson. Ser. A1237280Google Scholar
  23. 23.
    Clore, G.M., Gronenborn, A.M., Bax, A. 1998J. Magn. Reson.133216221Google Scholar
  24. 24.
    Valafar, H., Prestegard, J.H. 2004J. Magn. Reson.167228241Google Scholar
  25. 25.
    Huang, C.C., Couch, G.S., Pettersen, E.F., Ferrin, T.E. 1996Pacific Symp Biocomput.1724Google Scholar
  26. 26.
    Koradi, R., Billeter, M., Wüthrich, K. 1996J.Mol. Graphics145155Google Scholar
  27. 27.
    Al-Hashimi, H.M., Valafar, H., Terrell, M., Zartler, E.R., Eidsness, M.K., Prestegard, J.H. 2000J.Magn. Reson.143402406Google Scholar
  28. 28.
    Pearl, F.M.G., Lee, D., Bray, J.E., Sillitoe, I., Todd, A.E., Harrison, A.P., Thornton, J.M., Orengo, C.A. 2000Nucleic Acids Res28277282Google Scholar
  29. 29.
    Jones, D.T. 1999J. Mol. Biol.287797815Google Scholar
  30. 30.
    Xu, Y., Xu, D., Crawford, O.H., Einstein, J.R., Larimer, F., Uberbacher, E., Unseren, M.A., Zhang, G. 1999Protein Eng12899907Google Scholar
  31. 31.
    Sali, A., Blundell, T.L. 1993J.Mol. Biol.234779815Google Scholar
  32. 32.
    Bax, A. 2003Protein Sci12116Google Scholar
  33. 33.
    Liang, S.D., Grishin, N.V. 2002Protein Sci11322331Google Scholar
  34. 34.
    Mendes, J., Baptista, A.M., Carrondo, M.A., Soares, C.M. 1999Proteins. Struct. Funct. Genet.37530543Google Scholar
  35. 35.
    Looger, L.L., Hellinga, H.W. 2001J.Mol. Biol.307429445Google Scholar
  36. 36.
    Holm, L., Sander, C. 1995Trends Biochem Sci.20478480Google Scholar
  37. 37.
    Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J.H., Zhang, Z., Miller, W., Lipman, D.J. 1997Nucleic Acids Res2533893402PubMedGoogle Scholar
  38. 38.
    Servant, F., Bru, C., Carrere, S., Courcelle, E., Gouzy, J., Peyruc, D., Kahn, D. 2002Brief Bioinform3246251Google Scholar

Copyright information

© Springer 2005

Authors and Affiliations

  • H. Valafar
    • 1
  • K. L. Mayer
    • 1
  • C. M. Bougault
    • 2
  • P. D. LeBlond
    • 1
  • F. E. JenneyJr.
    • 3
  • P. S. Brereton
    • 3
  • M. W. W. Adams
    • 3
  • J. H. Prestegard
    • 4
  1. 1.Southeast Collaboratory for Structural GenomicsUniversity of GeorgiaAthensUSA
  2. 2.Institut de Biologie StructuraleGrenoble Cedex 01France
  3. 3.Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensUSA
  4. 4.Complex Carbohydrate Research CenterUniversity of GeorgiaAthensUSA

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