The three-dimensional solution structure of NaD1, a new floral defensin from Nicotiana alata and its application to a homology model of the crop defense protein alfAFP

Journal of Molecular Biology

Volumn 325, Issue 1, 2003, Pages 175-188

  Lay, Fung T ^a   Schirra, Horst Joachim ^b   Scanlon, Martin J ^c   Anderson, Marilyn A ^a   Craik, David J ^b  

^a LA TROBE UNIVERSITY   (Australia)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c MONASH UNIVERSITY   (Australia)

Author keywords

Antifungal; CS motif; Nuclear magnetic resonance spectroscopy; Plant defensin; Protein structure

Indexed keywords

CYSTEINE; DEFENSIN; PROTEIN; PROTEIN ALFAFP; PROTEIN NAD1; SCORPION VENOM; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID SEQUENCE; ANTIFUNGAL ACTIVITY; ARTICLE; BETA SHEET; CALCULATION; CROP PROTECTION; DISULFIDE BOND; FLOWER; INSECTICIDAL ACTIVITY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN ISOLATION; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION; SWEETNESS;

INSECTA; MEDICAGO SATIVA; NICOTIANA ALATA; RAPHANUS SATIVUS; SCORPIONES; SOLANUM TUBEROSUM;

EID: 0037260694     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)01103-8     Document Type: Article

References (59)

1. Bowles, D. J. (1990). Defense-related proteins in higher plants. Annu. Rev. Biochem. 59, 873-907.
2. Broekaert, W. F., Cammue, B. P. A., Debolle, M. F. C., Thevissen, K., Desamblanx, G. W. & Osborn, R. W. (1997). Antimicrobial peptides from plants. Crit. Rev. Plant Sci. 16, 297-323.
3. Terras, F. R. G., Eggermont, K., Kovaleva, V., Raikhel, N. V., Osborn, R. W., Kester, A. et al. (1995). Small cysteine-rich antifungal proteins from radish: Their role in host defense. Plant Cell, 7, 573-588.
4. Osborn, R. W. & Broekaert, W. F. (1999). Antifungal proteins. In Seed Proteins (Shewry, P. R. & Casey, R., eds), pp. 727-751, Kluwer Academic, Dordrecht.
5. Broekaert, W. F., Terras, F. R. G., Cammue, B. P. A. & Osborn, R. W. (1995). Plant defensins: Novel antimicrobial peptides as components of the host defense system. Plant Physiol. 108, 1353-1358.
6. Terras, F. R. G., Schoofs, H. M. E., De Bolle, M. F. C., Van Leuven, F., Rees, S. B., Vanderleyden, J. et al. (1992). Analysis of two novel classes of plant antifungal proteins from radish (Raphanus sativus L.) seeds. J. Biol. Chem. 267, 15301-15309.
7. Segura, A., Monero, M., Molina, A. & Garcia-Olmedo, F. (1998). Novel defensin subfamily from spinach (Spinacia oleracea). FEBS Letters, 435, 159-162.
8. Wijaya, R., Neumann, G. M., Condron, R., Hughes, A. B. & Polya, G. M. (2000). Defense proteins from seed of Cassia fistula include a lipid transfer protein homologue and a protease inhibitory plant defensin. Plant Sci. 159, 243-255.
9. Bloch, C., Jr & Richardson, M. (1991). A new family of small (5 kDa) protein inhibitors of insect alpha-amylases from seeds of sorghum (Sorghum bicolor (L) Moench) have sequence homologies with wheat gamma-purothionins. FEBS Letters, 279, 101-104.
10. Thevissen, K., Ghazi, A., Desamblanx, G. W., Brownlee, C., Osborn, R. W. & Broekaert, W. F. (1996). Fungal membrane responses induced by plant defensins and thionins. J. Biol. Chem. 271, 15018-15025.
11. Thevissen, K., Osborn, R. W., Acland, D. P. & Broekaert, W. F. (1997). Specific, high affinity binding sites for an antifungal plant defensin on Neurospora crassa hyphae and microsomal membranes. J. Biol. Chem. 272, 32176-32181.
12. Thevissen, K., Osborn, R. W., Acland, D. P. & Broekaert, W. F. (2000). Specific binding sites for an antifungal plant defensin from dahlia (Dahlia merckii) on fungal cells are required for antifungal activity. Mol. Plant-Micr. Interact. 13, 54-61.
13. Bohlmann, H. (1994). The role of thionins in plant protection. Crit. Rev. Plant Sci. 13, 1-16.
14. Lowenberger, C. A., Smartt, C. T., Bulet, P., Ferdig, M. T., Severson, D. W., Hoffman, J. A. & Christensen, B. M. (1999). Insect immunity: Molecular cloning, expression and characterization of cDNAs and genomic DNA encoding three isoforms of insect defensin in Aedes aegypti. Insect Mol. Biol. 8, 107-118.
15. Gao, A. G., Hakimi, S. M., Mittanck, C. A., Wu, Y., Woerner, B. M., Stark, D. M. et al. (2000). Fungal pathogen protection in potato by expression of a plant defensin peptide. Nature Biotechnol. 18, 1307-1310.
16. Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids, Wiley, New York.
17. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W. et al. (1998). Crystallography and NMR system (CNS): A new software system for macromolecular structure determination. Acta Crystallog. Sect. D, 54, 905-921.
18. Cornet, B., Bonmatin, J. M., Hetru, C., Hoffmann, J. A., Ptak, M. & Vovelle, F. (1995). Refined three-dimensional solution structure of insect defensin A. Structure, 3, 435-448.
19. Bontems, F., Roumestand, C., Gilquin, B., Menez, A. & Toma, F. (1991). Refined structure of charybdotoxin - Common motifs in scorpion toxins and insect defensins. Science, 254, 1521-1523.
20. 1H NMR. J. Mol. Biol. 279, 257-270.
21. Kobayashi, Y., Takashima, H., Tamaoki, H., Kyogoku, Y., Lambert, P., Kuroda, H. et al. (1991). The cysteine stabilised α-helix: A common structural motif of ion channel blocking neurotoxic peptides. Biopolymers, 31, 1213-1220.
22. Caldwell, J. E., Abildgaard, F., Dzakula, Z., Ming, D., Hellekant, G. & Markley, J. L. (1998). Solution structure of the thermostable sweet-tasting protein brazzein. Nature Struct. Biol. 5, 427-431.
23. Fehlbaum, P., Bulet, P., Michaut, L., Lagueux, M., Broekaert, W. F., Hetru, C. & Hoffmann, J. A. (1994). Insect immunity. Septic injury of Drosophila induces the synthesis of a potent antifungal peptide with sequence homology to plant antifungal peptides. J. Biol. Chem. 269, 33159-33163.
24. Landon, C., Sodano, P., Hetru, C., Hoffmann, J. A. & Ptak, M. (1997). Solution structure of drosomycin, the first inducible antifungal protein from insects. Protein Sci. 6, 1878-1884.
25. Colilla, F. J., Rocher, A. & Mendez, E. (1990). Gamma-Purothionins: Amino acid sequence of two polypeptides of a new family of thionins from wheat endosperm. FEBS Letters, 270, 191-194.
26. Mendez, E., Moreno, A., Colilla, F., Pelaez, F., Limas, G. G., Mendez, R. et al. (1990). Primary structure and inhibition of protein synthesis in eukaryotic cell-free system of a novel thionin, gamma-hordothionin, from barley endosperm. Eur. J. Biochem. 194, 533-539.
27. Osborn, R. W., De Samblanx, G. W., Thevissen, K., Goderis, I., Torrekens, S., Van Leuven, F. et al. (1995). Isolation and characterisation of plant defensins from seeds of Asteraceae, Fabaceae, Hippocastanaceae and Saxifragaceae. FEBS Letters, 368, 257-262.
28. Kushmerick, C., Castro, M. D., Cruz, J. S., Bloch, C. & Beirao, P. S. L. (1998). Functional and structural features of gamma-zeathionins, a new class of sodium channel blockers. FEBS Letters, 440, 302-306.
29. Dauplais, M., Gilquin, B., Possani, L. D., Gurrola-Briones, G., Roumestand, C. & Menez, A. (1995). Determination of the three-dimensional solution structure of noxiustoxin: Analysis of structural differences with related short-chain scorpion toxins. Biochemistry, 34, 16563-16573.
30. Landon, C., Cornet, B., Bonmatin, J. M., Kopeyan, C., Rochat, H., Vovelle, F. & Ptak, M. (1997). H-1-NMR-derived secondary structure and the overall fold of the potent anti-mammal and anti-insect toxin III from the scorpion Leiurus quinquestriatus quinquestriatus. Eur. J. Biochem. 236, 395-404.
31. Fant, F., Vranken, W. F., Martins, J. C. & Borremans, F. A. M. (1997). Solution conformation of Raphanus sativus antifungal protein 1 (Rs-AFP1) by 1H nuclear magnetic resonance. Resonance assignments, secondary structure and global fold. Bull. Soc. Chim. Belg. 106, 51-57.
32. De Samblanx, G. W., Goderis, I. J., Thevissen, K., Raemaekers, R., Fant, F., Borremans, F. et al. (1997). Mutational analysis of a plant defensin from radish (Raphanus sativus L.) reveals two adjacent sites important for antifungal activity. J. Biol. Chem. 272, 1171-1179.
33. Fant, F., Vranken, W. F. & Borremans, F. A. M. (1999). The three-dimensional solution structure of Aesculus hippocastanum antimicrobial protein 1 determined by 1H nuclear magnetic resonance. Proteins: Struct. Funct. Genet. 37, 388-403.
34. Landon, C., Pajon, A., Vovelle, F. & Sodano, P. (2000). The active site of drosomycin, a small insect antifungal protein, delineated by comparison with the modeled structure of Rs-AFP2, a plant antifungal protein. J. Pept. Res. 56, 231-238.
35. Schaaper, W. M. M., Posthuma, G. A., Plasman, H. H., Sijtsma, L., Fant, F., Borremans, F. A. M. et al. (2001). Synthetic peptides derived from the β2-β3 loop of Raphanus sativus antifungal protein 2 that mimic the active site. J. Pept. Res. 57, 409-418.
36. Vita, C., Roumestand, C., Toma, F. & Menez, A. (1995). Scorpion toxins as natural scaffolds for protein engineering. Proc. Natl. Acad. Sci. USA, 92, 6404-6408.
37. 1H spin-spin coupling constants in proteins. Biochem. Biophys. Res. Commun. 113, 967-974.
38. Sklenar, V., Piotto, M., Leppik, R. & Saudek, V. (1993). Gradient-tailored water suppression for H-1-N-15 HSQC experiments optimized to retain full sensitivity. J. Magn. Reson. Ser. A, 102, 241-245.
39. Bax, A. & Davies, D. G. (1985). MLEV-17 based two-dimensional homonuclear magnetisation transfer spectroscopy. J. Magn. Reson. 65, 355-360.
40. 1H NMR spectra of proteins via double quantum filtering. Biochem. Biophys. Res. Commun. 117, 479-485.
41. Braunschweiler, L. & Ernst, R. R. (1983). Coherence transfer by isotropic mixing: Application to protein correlation spectroscopy. J. Magn. Reson. 65, 521-528.
42. Kumar, A., Ernst, R. R. & Wüthrich, K. (1980). A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem. Biophys. Res. Commun. 95, 1-6.
43. Griesinger, C., Sørensen, O. W. & Ernst, R. R. (1985). Two-dimensional correlation of connected MR transitions. J. Am. Chem. Soc. 107, 6394-6396.
44. Bartels, C. H., Xia, T.-H., Billeter, M., Güntert, P. & Wüthrich, K. (1995). The program XEASY for computer supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR, 5, 1-10.
45. Scanlon, M. J., Naranjo, D., Thomas, L., Alewood, P. F., Lewis, R. J. & Craik, D. J. (1997). Solution structure and proposed binding mechanism of a novel potassium channel toxin kappa-conotoxin PVIIA. Structure, 5, 1585-1597.
46. Güntert, P., Mumenthaler, C. & Wüthrich, K. (1997). Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283-298.
47. Linge, J. P., O'Donoghue, S. I. & Nilges, M. (2001). Automated assignment of ambiguous nuclear Overhauser effects with ARIA. Methods Enzymol. 339, 71-90.
48. Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein-structure refinement. Acta Crystallog. Sect. A, 47, 392-400.
49. Nilges, M., Gronenborn, A. M., Brünger, A. T. & Clore, G. M. (1988). Determination of three-dimensional structures of proteins by simulated annealing with interproton distance constraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng. 2, 27-38.
50. Garrett, D. S., Kuszewski, J., Hancock, T. J., Lodi, P. J., Vuister, G. W., Gronenborn, A. M. & Clore, G. M. (1994). The impact of direct refinement against three-bond HN-CαH coupling constants on protein structure determination by NMR. J. Magn. Reson. Ser. B, 104, 99-103.
51. Linge, J. P. & Nilges, M. (1999). Influence of non-bonded parameters on the quality of NMR structures: A new force-field for NMR structure determination. J. Biomol. NMR, 13, 51-59.
52. Koradi, R., Billeter, M. & Wüthrich, K. (1996). MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55.
53. Hutchinson, E. G. & Thornton, J. M. (1996). PROMOTIF - A program to identify and analyse structural motifs in proteins. Protein Sci. 5, 212-220.
54. Laskowski, R. A., Rullman, J. A., MacArthur, M. W., Kaptein, R. & Thornton, J. M. (1996). AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR, 8, 477-486.
55. Bruix, M., Jimenez, M. A., Santoro, J., Gonzalez, C., Colilla, F. J., Mendez, E. & Rico, M. (1993). Solution structure of γ1-H and γ1-P thionins from barley and wheat endosperm determined by 1H-NMR: A structural motif common to toxic arthropod proteins. Biochemistry, 32, 715-724.
56. Bruix, M., Gonzalez, C., Santoro, J., Soriano, F., Rocher, A. & Mendez, E. (1995). H-1-NMR studies on the structure of a new thionin from barley endosperm. Biopolymers, 36, 751-763.
57. 1H NMR structure of an antifungal gamma-thionin protein SIα1: Similarity to scorpion toxins. Proteins: Struct. Funct. Genet. 32, 334-349.
58. Wishart, D. S., Sykes, B. D. & Richards, F. M. (1992). The chemical shift index - A fast and simple method for the assignment of protein secondary structure through NMR-spectroscopy. Biochemistry, 31, 1647-1651.
59. Nicholls, A., Sharp, K. A. & Honig, B. (1991). Protein folding and association - Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11, 281-296.