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Solution structure of cyanovirin-N, a potent HIV-inactivating protein

Nature Structural Biology volume 5, pages 571–578 (1998)Cite this article

Abstract

The solution structure of cyanovirin-N, a potent 11,000 Mr HIV-inactivating protein that binds with high affinity and specificity to the HIV surface envelope protein gp120, has been solved by nuclear magnetic resonance spectroscopy, including extensive use of dipolar couplings which provide a priori long range structural information. Cyanovirin-N is an elongated, largely β-sheet protein that displays internal two-fold pseudosymmetry. The two sequence repeats (residues 1–50 and 51–101) share 32% sequence identity and superimpose with a backbone atomic root-mean-square difference of 1.3 Å. The two repeats, however, do not form separate domains since the overall fold is dependent on numerous contacts between them. Rather, two symmetrically related domains are formed by strand exchange between the two repeats. Analysis of surface hydrophobic clusters suggests the location of potential binding sites for protein–protein interactions.

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Figure 1: Secondary structure elements and structure alignment of cyanovirin-N.
Figure 2: Overall structure of cyanovirin-N.
Figure 3: Internal two-fold symmetry of cyanovirin-N.
Figure 4: Side chain contacts forming the core of cyanovirin-N.
Figure 5
Figure 6: a,b Two views mapping the electrostatic potential (left-hand panels) and the two highest ranking surface hydrophobic clusters (center panels) on the molecular surface of cyanovirin-N.

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References

  1. Freed, E.O. & Martin, M.A. The role of human immunodeficiency virus type I envelope glycoproteins in virus infection. J. Biol. Chem. 270, 23883–23886 ( 1995).

    Article  CAS  Google Scholar 

  2. Wilkinson, D. HIV-1: cofactors provide the entry keys. Curr. Biol. 6, 1051 –1053 (1996).

    Article  CAS  Google Scholar 

  3. D'Souza, M.P. & Harden, V.A. Chemokines and HIV-1 second receptors - confluence of two fields generates optimism in AIDS research. Nature Med. 2, 1293–1300 (1996).

    Article  CAS  Google Scholar 

  4. Boyd, M.R. et al. Discovery of cyanovirin-N, a novel human immunodeficiency virus-inactivating protein that binds viral surface envelope glycoprotein gp120: potential applications to microbicide development. Antimicrob. Agents Chemother. 41, 1521–1530 (1997).

    Article  CAS  Google Scholar 

  5. Mori, T. et al. Analysis of sequence requirements for biological activity of cyanovirin-N, a potent HIV-inactivating protein. Biochem. Biophys. Res. Comm . 238, 218–222 ( 1997).

    Article  CAS  Google Scholar 

  6. Boyd, M.R. In AIDS, etiology, diagnosis, treatment and prevention. (DeVita, V. R., Hellman, S. & Rosenberg, S. A., eds) 305–319 (Alan Liss, New York; 1988).

    Google Scholar 

  7. Gustafson, K.R. et al. Isolation, primary sequence determination, and disulfide bond structure of cyanovirin-N, an anti-HIV protein from the cyanobacterium Nostoc ellipsosporum. Biochem. Biophys. Res. Comm. 238, 223 –228 (1997).

    Article  CAS  Google Scholar 

  8. Mori, T. et al. Recombinant production of cyanovirin-N, a potent human immunodeficiency virus-inactivating protein derived from a cultured cyanobacterium. Protein Exp. Purific. 12, 151–158 ( 1998).

    Article  CAS  Google Scholar 

  9. Clore, G.M. & Gronenborn, A.M. Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy. Science 252, 1390–1399 ( 1991).

    Article  CAS  Google Scholar 

  10. Clore, G.M. & Gronenborn, A.M. Determining the structures of larger proteins and protein complexes by NMR. Trends Biotech. 16, 22–34 ( 1998).

    Article  CAS  Google Scholar 

  11. Bax, A. & Grzesiek, S. Methdological advances in protein NMR Acc. Chem. Res. 26, 131–138 (1993).

    Article  CAS  Google Scholar 

  12. Nilges, M., Gronenborn, A.M., Brünger, A.T. & Clore G.M. Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Prot. Engng. 2, 27–38 (1988 ).

    Article  CAS  Google Scholar 

  13. Tjandra, N., Omichinski, J.G., Gronenborn, A.M., Clore, G.M. & Bax, A. Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nature Struct. Biol. 4, 732–738 ( 1997).

    Article  CAS  Google Scholar 

  14. Hutchinson, E.G. & Thornton, J.M. PROMOTIF - a program to identify and analyze structural motifs in proteins. Protein Sci. 5, 212–220 (1996).

    Article  CAS  Google Scholar 

  15. Altschul, S.F. et al. Basic local alignment search tool. J. Mol. Biol. 215 , 403–410 (1990).

    Article  CAS  Google Scholar 

  16. Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123–138 (1993).

    Article  CAS  Google Scholar 

  17. Kuriyan, J. & Cowburn, D. Structures of SH2 and SH3 domains . Curr. Opin. Struct. Biol. 3, 828– 837 (1993).

    Article  CAS  Google Scholar 

  18. Edmondson, S.P., Qiu, L., Schriver, J.W. Solution structure of the DNA-binding domain of Sac7d from the hyperthermophile Sulfolobus acidocaldarius. Biochemistry 34, 13289–13304 (1995).

    Article  CAS  Google Scholar 

  19. Jones, S. & Thornton, J.M. Principles of protein-protein interactions. Proc. Natl. Acad. Sci. U. S. A. 93, 13–20 (1996).

    Article  CAS  Google Scholar 

  20. Young, L., Jernigan, R.L. & Covell, D.G. A role for surface hydrophobicity in protein- protein recognition. Prot. Sci. 3, 717– 729 (1994).

    Article  CAS  Google Scholar 

  21. Covell, D.G., Smythers, G.W., Gronenborn, A.M. & Clore, G.M. Analysis of hydrophobicity in the α and β chemokine families and its relevance to dimerization . Prot. Sci. 3, 2064–2072 (1994).

    Article  CAS  Google Scholar 

  22. Villoutreix, B.O., Härdig, Y., Wallqvist, A., Covell, D.G., de Frutos, G. & Dählback, B. Structural investigation of C4p-binding protein by molecular modeling: localization of putative binding sites. Prot. Sci. in the press (1998).

  23. 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 

  24. 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 

  25. Bax, A. et al. Measurement of homo- and hetero-nuclear J couplings from quantitative J correlation . Meth. Enz. 239, 79–106 (1994).

    Article  CAS  Google Scholar 

  26. Ottiger, M. & Bax, A. An empirical correlation between amide deuterium isotope effects on 13Cα chemical shifts and protein backbone conformation. J. Am. Chem. Soc. 119 , 8070–8075 (1997).

    Article  CAS  Google Scholar 

  27. Grzesiek, S. & Bax, A. Measurement of amide proton exchange rates and NOE with water in 13C/15N enriched calcineurin B. J. Biomol. NMR 3, 627– 638 (1993).

    CAS  PubMed  Google Scholar 

  28. Tjandra, N. & Bax, A. Direct measurement of distances and angles in biomolecules by NMR in dilute liquid crystalline medium. Science 278, 1111–1114 ( 1997).

    Article  CAS  Google Scholar 

  29. Ottiger, M., Delaglio, F. & Bax, A. Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. J. Magn. Reson. 131, 373– 378 (1998).

    Article  CAS  Google Scholar 

  30. Delaglio, F., Torchia, D.A. & Bax, A. Measurement of 15N-13C J couplings in staphylococcal nuclease. J. Biomol. NMR 1, 439–446 (1991).

    Article  CAS  Google Scholar 

  31. Clore, G.M., Gronenborn, A.M. & Bax, A. A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information . J. Magn. Reson. 133, 216– 221 (1998).

    Article  CAS  Google Scholar 

  32. Grzesiek, S. & Bax, A. The importance of not saturating H 2O in protein NMR: application to sensitivity enhancement and NOE measurements . J. Am. Chem. Soc. 115, 12593– 12594 (1993).

    Article  CAS  Google Scholar 

  33. Nilges, M. A calculational strategy for the structure determination of symmetric dimers by 1H-NMR . Proteins Struct. Funct. Genet. 17, 297 –309 (1993).

    Article  CAS  Google Scholar 

  34. Clore, G.M. & Gronenborn, A.M. New methods of structure refinement for macromolecular structure determination by NMR. Proc. Natl. Acad. Sci. U.S.A. 95, 5891–5898 (1998).

    Article  CAS  Google Scholar 

  35. Brünger, A.T. et al. Crystallography and NMR system (CNS): a new software suite for macromolecular structure determination. Acta Crystallogr. D ( 1998) In the press.

  36. Garrett, D.S. et al. The impact of direct refinement against three-bond HN-CαH coupling constants on protein structure determination by NMR. J. Magn. Reson. B 104, 99–103 (1994).

    Article  CAS  Google Scholar 

  37. Kuszewski, J., Qin, J., Gronenborn, A.M. & Clore, G.M. The impact of direct refinement against 13Cα and 13Cβ chemical shifts on protein structure determination by NMR. J. Magn. Reson. B 106, 92–96 ( 1995).

    Article  CAS  Google Scholar 

  38. Kuszewski, J., Gronenborn, A.M. & Clore, G.M. The impact of direct refinement against proton chemical shifts on protein structure determination by NMR. J. Magn. Reson. B 107 , 293–297 (1995).

    Article  CAS  Google Scholar 

  39. Kuszewski, J., Gronenborn, A.M. & Clore, G.M. A potential involving multiple proton chemical-shift restraints for non-stereospecifically assigned methyl and methylene protons. J. Magn. Reson. B 112, 79–81 (1996).

    Article  CAS  Google Scholar 

  40. Clore, G.M., Gronenborn, A.M. & Tjandra, N. Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude. J. Magn. Reson. 131, 159–162 (1998).

    Article  CAS  Google Scholar 

  41. Kuszewski, J., Gronenborn, A.M. & Clore, G.M. Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases. Prot. Sci. 5, 1067–1080 (1996).

    Article  CAS  Google Scholar 

  42. Kuszewski, J., Gronenborn, A.M. & Clore, G.M. Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids. J. Magn. Reson. 125, 171–177 (1997).

    Article  CAS  Google Scholar 

  43. Koradi, R., Billeter, M. & Wuthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14 51-5, 29– 32 (1996).

    Google Scholar 

  44. Nichols, A., Sharp, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281–296 (1991).

    Article  Google Scholar 

  45. Carson, M. RIBBONS 4.0. J. Appl. Crystallogr. 24, 958– 961 (1991).

    Article  Google Scholar 

  46. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: A program to check the stereochemical quality of protein structures . J. Appl. Crystallogr. 26, 283– 291 (1993).

    Article  CAS  Google Scholar 

  47. Musacchio, A., Noble, M., Pauptit, R., Wierenga, R. & Saraste, M. Crystal structure of a Src-homology 3 (SH3) domain. Nature 359, 851–855 ( 1992).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank D. Garrett and F. Delaglio for software support; R. Tschudin and L. Cartner for technical support; L. Pannell for mass spectrometry; M. Caffrey, M. Cai, B. O'Keefe and N. Tjandra for numerous useful discussions. C.A.B. is a recipient of a Cancer Research Institute postdoctoral fellowship. This work was supported by the AIDS Targeted Antiviral Program of the Office of the Director of the National Institutes of Health to G.M.C., A.M.G and A.B.

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Authors and Affiliations

  1. Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892-0520, Maryland, USA

    Carole A. Bewley, Ad Bax, G. Marius Clore & Angela M. Gronenborn

  2. Laboratory of Drug Discovery Research and Development, National Cancer Institute, Frederick, 21702-1201, Maryland, USA

    Kirk R. Gustafson & Michael R. Boyd

  3. Frederick Cancer Research and Development Center, National Cancer Institute, Frederick, 21702-1201, Maryland, USA

    David G. Covell

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  1. Carole A. Bewley
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Correspondence to G. Marius Clore or Angela M. Gronenborn.

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Bewley, C., Gustafson, K., Boyd, M. et al. Solution structure of cyanovirin-N, a potent HIV-inactivating protein . Nat Struct Mol Biol 5, 571–578 (1998). https://doi.org/10.1038/828

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