Motions and structural variability within toxins: Implication for their use as scaffolds for protein engineering

Protein Science

Volumn 12, Issue 2, 2003, Pages 266-277

  Gilquin, Bernard ^a   Bourgoin, Marjorie ^a   Ménez, Renée ^a   Le Du, Marie Hélène ^a   Servent, Denis ^a   Zinn Justin, Sophie ^a   Ménez, André ^a  

^a DIF   (France)

Author keywords

Dynamics; Protein engineering; Scaffold; Structure; Toxin

Indexed keywords

TOXIN; TOXIN ALPHA; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; DISULFIDE BOND; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN LOCALIZATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; TOXIN ANALYSIS; X RAY ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; CHARYBDOTOXIN; COBRA NEUROTOXINS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOTION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; STRUCTURE-ACTIVITY RELATIONSHIP; TEMPERATURE;

ANIMALIA; SCORPIONES; SERPENTES;

EID: 0037304388     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0227703     Document Type: Article

References (33)

1. Baker, N.A., Helms, V., and McCammon, J.A. 1999. Dynamical properties of fasciculin-2. Proteins 36: 447-453.
2. Bontems, F., Roumestand, C., Gilquin, B., Ménez, A., and Toma, F. 1991. Refined structure of charybdotoxin: Common motifs in scorpion toxins and insect defensins. Science 254: 1521-1523.
3. Brooks, B.R., Karplus, M., and Pettit, B.M. 1988. Proteins: A theoretical perspective of dynamics, structure and thermodynamics. Adv. Chem. Phys. Vol. LXXI. Wiley, New York.
4. Brünger, A.T. 1992. A system for X-ray crystallography and NMR. Yale University Press, New Haven, CT.
5. Fadel, A.R., Jin, D.Q., Montelione, G.T., and Levy, R.M. 1995. Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-α transforming growth factor. J. Biomol. NMR 6: 221-226.
6. Fryklund, L. and Eaker, D. 1975. The complete covalent structure of a cardiotoxin from the venom of Naja nigricollis (African black-necked spitting cobra). Biochemistry 14: 2865-2871.
7. Gordon, D., Savarin, P., Gurevitz, M., and Zinn-Justin, S. 1998. Functional anatomy of scorpion toxins affecting sodium channels. J. Toxicol. 17: 131-159.
8. Guenneugues, M., Gilquin, B., Wolff. N., Ménez, A., and Zinn-Justin, S. 1999. Internal motion time scales of a small, highly stable and disulfide-rich protein: A 15N, 13C NMR and molecular dynamics study. J. Biomol. NMR 14: 47-66.
9. Guidebook. 1997. Guidebook to protein toxins and their use in cell biology (eds. R. Rapuolli and C. Montecucco). Sambrook & Tooze Publication (Oxford University Press), Oxford, UK.
10. Jorgensen, W.L. 1981. Transferable intermolecular potentiel function for water, alcohols and ethers. J. Am. Chem. Soc. 103: 335-340.
11. Kabsch, W. and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
12. Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crysallogr. 26: 283-291.
13. Laskowski, R.A., Rullmann, J.A., MacArthur, M.W., Kaptein, R., and Thomton, J.M. 1996. AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR. 8: 477-486.
14. Le Du, M.H., Ricciardi, A., Khayati, M., Menez, R., Boulain, J.C., Ménez, A., and Ducancel, F. 2000. Stability of a structural scaffold upon activity transfer: X-ray structure of a three fingers chimeric protein. J. Mol. Biol. 296: 1017-1026.
15. Lipari, G. and Szabo, A. 1996. Model free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules, 1. Theory and range of validity. J. Am. Chem. Soc. 104: 4546-4559.
16. MacKerell, A.D., Bashford, D., Bellott, M., Dunbrack, R.L., Evansek, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B102: 3586-3616.
17. Ménez, A. 1998. Functional architecture of animal toxins: A clue to drug design? Toxicon 36: 1557-1572.
18. Met, G., Kellenberger, E., and Lefevre. J.F. 1998. α-helix mimicry of a β-turn. J. Mol. Biol. 281: 235-240.
19. Mourier, G., Servent, D., Zinn-Justin, S., and Ménez, A. 2000. Chemical engineering of a three-fingered toxin with anti-α7 neuronal acetylcholine receptor activity. Protein Eng. 13: 217-225.
20. Navaza, J. 1994. AMoRe: An automated package for molecular replacement. Acta Crysallogr. A50: 157-163.
21. Ohno, M., Ménez, R., Ogawa, T., Danse, J.M., Shimohigashi, Y., Fromen, C., Ducancel, F., Zinn-Justin, S., Le Du, M.H., Boulain, J.C., et al. 1998. Molecular evolution of snake toxins: Is the functional diversity of snake toxins associated with a mechanism of accelerated evolution. Prog. Nucleic Acid Res. Mol. Biol. 59: 307-354.
22. Otwinowski, Z. and Minor, W. 1997. Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307-326.
23. Philippopoulos, M., Mandel, A.M., Palmer, A.G., and Lim, C. 1997. Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics. Proteins 28: 481-493.
24. Ricciardi, A., le Du, M.H., Khayati, M., Dajas, F., Boulain, J.C., Menez, A., and Ducancel, F. 2000. Do structural deviations between toxins adopting the same fold reflect functional differences? J. Biol. Chem. 275: 18302-18310.
25. Roussel, A. and Cambillau, C. 1989. Silicon graphics geometry partner directory, pp. 77-78. Silicon Graphics, Mountain View, CA.
26. Schneider, T.R., Brunger, A.T., and Nilges, M. 1999. Influence of internal dynamics on accuracy of protein NMR structures: Derivation of realistic model distance data from a long molecular dynamics trajectory. J. Mol. Biol. 285: 727-740.
27. Servent, D. and Ménez, A. 2001. Snake neurotoxins that interact with nicotine acetylcholine receptors. In Natural toxins of animal origin (ed. E.J. Massaro), vol. 1, chap. 20. Humana Press Inc., Clifton, NJ.
28. Vita, C., Roumestand, C., Toma, F., and Ménez, A. 1995. Scorpion toxins as natural scaffolds for protein engineering. Proc. Natl. Acad. Sci. 92: 6404-6408.
29. Vita, C., Drakopoulou, E., Vizzavona, J., Rochette, S., Martin, L., Ménez, A., Roumestand, C., Yang, Y.S., Ylisastigui, L., Benjouad, A., et al. 1999. Rational engineering of a miniprotein that reproduces the core of the CD4 site interacting with HIV-1 envelope glycoprotein. Proc. Natl. Acad. Sci. 96: 13091-13096.
30. Wolff, N., Guenneugues, M., Gilquin, B., Drakopoulou, E., Vita, C., Ménez, A., and Zinn-Justin, S. 2000. Characterization of the internal motions of a chimeric protein by 13C NMR highlights the important dynamic consequences of the engineering on a millisecond time scale. Eur. J. Biochem. 267:6519-6533.
31. Yang, Y.S., Mitta, G., Chavanieu, A., Calas, B., Sanchez, J.F., Roch, P., and Aumelas, A. 2000. Solution structure and activity of the synthetic fourdisulfide bond Mediterranean mussel defensin (MGD-1). Biochemistry 39:14436-14447.
32. Zinn-Justin, S., Roumestand, C., Gilquin, B., Bontems, F., Ménez, A., and Toma, F. 1992. Three-dimensional solution structure of a curaremimetic toxin from Naja nigricollis venom: A proton NMR and molecular modeling study. Biochemistry 31: 11335-11347.
33. Zinn-Justin, S., Berthault, P., Guenneugues, M., and Desvaux, H. 1997. Off-resonance rf fields in heteronuclear NMR: Application to the study of slow motions. J. Biomol. NMR 10: 363-372.