Primary and 3-D modelled structures of two cyclotides from Viola odorata

Phytochemistry

Volumn 64, Issue 1, 2003, Pages 135-142

  Svangård, Erika ^a   Göransson, Ulf ^a   Smith, Derek ^b   Verma, Chandra ^b   Backlund, Anders ^a   Bohlin, Lars ^a   Claeson, Per ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF YORK   (United Kingdom)

Author keywords

Cyclotide; Homology modelling; Isolation; Macrocyclic polypeptide; Primary structure; Sweet violet; Viola odorata L.; Violaceae; Vodo M; Vodo N

Indexed keywords

AMINO ACID; CYCLOSERYLTRYPTOPHYLPROLYLVALYLCYSTEINYLTYROSYLARGINYLASPARAGINYLGLYCYLALAN YLPROLYLISOLEUCYLCYSTEINYLGLYCYLGLUTAMYLSERYLCYSTEINYLPHENYLALANYLTHREONYLGLYCYL LYSYLCYSTEINYLTYROSYLTHREONYLVALYLGLUTAMINYLCYSTEINYLSERYLCYSTEINE; CYCLOSERYLTRYPTOPHYLPROLYLVALYLCYSTEINYLTYROSYLARGINYLASPARAGINYLGLYCYLLEUC YLPROLYLVALYLCYSTEINYLGLYCYLGLUTAMYLTHREONYLCYSTEINYLTHREONYLLEUCYLGLYCYLLYSYLCY STEINYLTYROSYLTHREONYLALANYLGLYCYLCYSTEINYLSERYLCYSTEINE; POLYPEPTIDE; UNCLASSIFIED DRUG;

AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; ARTICLE; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; DISULFIDE BOND; DRUG ISOLATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ION EXCHANGE CHROMATOGRAPHY; MASS SPECTROMETRY; THREE DIMENSIONAL IMAGING; VIOLA ODORATA; VIOLACEAE;

VIOLA (ANGIOSPERM); VIOLA ODORATA; VIOLACEAE;

EID: 0041320830     PISSN: 00319422     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0031-9422(03)00218-8     Document Type: Article

References (27)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J., 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
2. Bokesch, H.R., Pannell, L.K., Cochran, P.K., Sowder, R.C., McKee, T.C., Boyd, M.R., 2001. A novel anti-HIV macrocyclic peptide from Palicourea condensate. J. Nat. Prod. 64, 249-250.
3. Bower, M.J., Cohen, F.E., Dunbrack Jr, R.L., 1997. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J. Mol. Biol. 267, 1268-1282.
4. Broussalis, A.M., Göransson, U., Coussio, J.D., Ferraro, G., Martino, V., Claeson, P., 2001. First cyclotide from Hybanthus (Violaceae). Phytochemistry 58, 47-51.
5. Cheetham, G.M.T., Jeruzalmi, D., Steitz, T.A., 1999. Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature 399, 80-83.
6. Claeson, P., Göransson, U., Johansson, S., Luijendijk, T., Bohlin, L., 1998. Fractionation protocol for the isolation of polypeptides from plant biomass. J. Nat. Prod. 61, 77-81.
7. Craik, D.J., 2001. Plant cyclotides: circular, knotted peptide toxins. Toxicon. 39, 1809-1813.
8. Craik, D.J., Daly, N.L., Bond, T., Waine, C., 1999. Plant cyclotides: A unique family of cyclic and knotted proteins that defines the cyclic cystine knot structural motif. J. Mol. Biol. 294, 1327-1336.
9. Craik, D.J., Simonsen, S., Daly, N.L., 2002. The cyclotides: novel macrocyclic peptides as scaffolds in drug design. Curr. Opin. Drug Discovery Dev. 5, 251-260.
10. Gran, L., 1973. Isolation of oxytocic peptides from Oldenlandia affininis by solvent extraction of tetraphenylborate complexes and chromatography on Sephadex LH-20. Lloydia 36, 207-208.
11. Gustafson, K.R., Sowder II, R.C., Henderson, L.E., Parsons, I.C., Kashman, Y., Cardellina II, J.H., McMahon, J.B., Buckheit Jr, R.W., Pannell, L.K., Boyd, M.R., 1994. Circulins A and B: novel HIV-inhibitory macrocyclic peptides from the tropical tree Chassalia parvifolia. J. Am. Chem. Soc. 116, 9337-9338.
12. Göransson, U., Luijendijk, T., Johansson, S., Bohlin, L., Claeson, P., 1999. Seven novel macrocyclic polypeptides from Viola arvensis. J. Nat. Prod. 62, 283-286.
13. Hallock, Y.F., Sowder, R.C., Pannell, L.K., Hughes, C.B., Johnson, D.G., Gulakowski, R., Cardellina, J.H., Boyd, M.R., 2000. Cycloviolins A-D, anti-HIV macrocyclic peptides from Leonia cymosa. J. Org. Chem. 65, 124-128.
14. Jennings, C., West, J., Waine, C., Craik, D.J., Anderson, M., 2001. Biosynthesis and insecticidal properties of plant cyclotides: the cyclic knotted proteins from Oldenlandia affinis. Proc. Natl. Acad. Sci. USA 98, 10614-10619.
15. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L., 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
16. Kelley, L.A., Sutcliffe, M.J., 1997. OLDERADO: on-line database of ensemble representatives and domains. Protein Sci. 6, 2628-2630.
17. Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M., 1993. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.
18. Lindholm, P., Göransson, U., Johansson, S., Claeson, P., Gullbo, J., Larsson, R., Bohlin, L., Backlund, A., 2002. Cyclotides-a novel type of cytotoxic agents. Mol. Cancer Therap. 1, 365-369.
19. MacKerell, A.D., Bashford, D., Bellott, M., Dunbrack, R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, W.E., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., Karplus, M., 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586-3616.
20. Oldfield, T.J., 1992. SQUID: a program for the analysis and display of data from crystallography and molecular dynamics. J. Mol. Graphics 10, 247-252.
21. Saether, O., Craik, D.J., Campbell, I.D., Sletten, K., Juul, J., Norman, D.G., 1995. Elucidation of the primary and three-dimensional structure of the uterotonic polypeptide kalata B1. Biochemistry 34, 4147-4158.
22. Sali, A., Blundell, T.L., 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815.
23. Schöpke, T., Hasan Agha, M.I., Kraft, R., Otto, A., Hiller, K., 1993. Hämolytisch aktive Komponenten aus Viola tricolor L. und Viola arvensis. Murray. Sci. Pharm 61, 145-153.
24. Sippl, M.J., 1993. Recognition of errors in three-dimensional structures of proteins. Proteins 17, 355-362.
25. Tam, J.P., Lu, Y.A., Yang, J.L., Chiu, K.W., 1999. An unusual structural motif of antimicrobial peptides containing end-to-end macrocycle and cystine-knot disulfides. Proc. Natl. Acad. Sci. USA 96, 8913-8918.
26. Trabi, M., Craik, D.J., 2002. Circular proteins-no end in sight. Trends Biochem. Sci. 27, 132-138.
27. Tung, C.S., Joseph, S., Sanbonmatsu, K.Y., 2002. All-atom homology model of the Eschericia coli 30S ribosomal subunit. Nat. Struct. Biol. 9, 750-755.