Organic Solvents Identify Specific Ligand Binding Sites on Protein Surfaces

Nature Biotechnology

Volumn 15, Issue 3, 1997, Pages 264-268

  Liepinsh, Edvards ^a   Otting, Gottfried ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Nuclear magnetic resonance; Nuclear overhauser effect; Protein salvation

Indexed keywords

ORGANIC SOLVENT;

ARTICLE; BACTERIAL CELL WALL; BINDING SITE; COMPLEX FORMATION; CRYSTAL STRUCTURE; DIPOLE; ENZYME SUBSTRATE; GENE MAPPING; LIGAND BINDING; NONHUMAN; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY;

ANIMALS; BINDING SITES; CHICKENS; CRYSTALLOGRAPHY, X-RAY; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; MURAMIDASE; PROTEIN BINDING; SOLVENTS; UREA;

BACTERIA (MICROORGANISMS);

EID: 0030965629     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt0397-264     Document Type: Article

References (30)

1. Allen, K.N., Bellamacina, C.R., Ding, X., Jeffery, C.J., Mattos, C, Petsko, G.A., et al. 1996. An experimental approach to mapping the binding surfaces of crystalline proteins. J. Phys. Chem. 100:2605-2611.
2. Mattos, C. and Ringe, D. 1996. Locating and characterizing binding sites on proteins. Nature Biotechnology 14:595-599.
3. Wescott, CR. and Klibanov, A.M. 1994. The solvent dependence of enzyme specificity. Biochim. Biophys. Acta 1286:1-9.
4. 1H nuclear magnetic resonance studies of hen lysozyme-N-acetylglucosamine oligosaccharide complexes in solution. Application of chemical shifts for the comparison of conformational changes in solution and in the crystal. J. Mol. Biol. 235:1072-1087.
5. Kelly, J.A., Sielecki, A.R., Sykes, B.D., James, M.N., and Phillips, D.C. 1970. X-ray crystallography of the binding of the bacterial cell wall trisaccharide NAM-NAG-NAM to lysozyme. Nature 282:875-878.
6. Cheetham, J.C, Artymiuk, P.J., and Phillips, D.C 1992. Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-acetylchitotriose at 1.75 Å resolution. J. Mol. Biol. 224:613-628.
7. Hadfield, A.T., Harvey, D.J., Archer, D.B., MacKenzie, O.A., Jeenes, D.J., Radford, S.E., et al. 1994. Crystal structure or the mutant D52S hen egg white lysozyme with an oligosaccharide product. J. Mol. Biol. 243:856-872.
8. Maenaka, K., Matsushima M., Song, H., Sunada, F., Watanabe, K., and Kumagai, I. 1995. Dissection of protein-carbohydrate interactions in mutant hen egg-white lysozyme complexes and their hydrolytic activity. J. Mol. Biol. 247:281-293.
9. Ernst, R.R., Bodenhausen, G., and Wokaun, A. 1987. Principles of Nuclear Magnetic Resonance in One and Two Dimensions. Clarendon Press, Oxford.
10. Yonath, A., Podjarny, A., Honig, B., Traub, W., Sielecki, A., Herzberg, O., et al. 1978. Structural analysis of denaturant-protein interactions: comparison between the effects of bromoethanol and SDS on denaturation and renaturation of triclinic lysozyme. Biophys. Struct. Mech. 4:27-36.
11. Lehmann, M.S., Mason, S.A., and Mclntyre, G.J. 1985. Study of ethanol-lysozyme interactions using neutron diffraction. Biochemistry 24:5862-5869.
12. Lehmann, M.S. and Stansfield, R.F.D. 1989. Binding of dimethyl sulfoxide to lysozyme In crystals, studied with neutron diffraction. Biochemistry 28:7028-7033.
13. Pike, A.C. and Acharya, K.R. 1994. A structural basis for the interaction of urea with lysozyme. Protein Science 3:706-710.
14. Imoto, T., Johnson, L.N., North, A.C.T., Phillips, D.C, and Rupley, J.A. 1972. Vertebrate Enzymes, pp. 665-864 in The Enzymes Vol. 7, Boyer, P.D. (ed.). Academic Press, New York.
15. 1H nuclear magnetic resonance studies of the interaction of urea with hen lysozyme. Origins of the conformational change induced in hen lysozyme by N-acetylglucosamine oligosaccharides. J. Mol. Biol. 227:9-14.
16. Smith, R.J., Williams, D.H., and James, K. 1989. Analysis of the rotational motions of the guanidino group in arginine. J. Chem. Soc. Chem. Commun. 682-683.
17. Kundrot, CE. and Richards, F.M. 1987. Crystal structure of hen egg-white lysozyme at a hydrostatic pressure of 1000 atmospheres. J. Mol. Biol. 193:157-170.
18. Bernstein, F.C, Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Jr., Brice, M.D., Rodgers, J.R., et al. 1977. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542.
19. Otting, G., Liepinsh, E., and Wüthrich, K. 1991. Protein hydration in aqueous solution. Science 254:974-980.
20. Otting, G. and Liepinsh, E. 1995. Protein hydration by high-resolution NMR spectroscopy—Implications for MR image contrast, Acc. Chem. Res. 28:171-177.
21. Eigen, M. and Hammes, G.G. 1963. Elementary steps in enzyme reactions. Adv. Enzym. 25:1-38.
22. Briand, J. and Ernst, R.R. 1991. Computer-optimized homonuclear TOCSY experiments with suppression of cross relaxation. Chem. Phys. Lett. 185:276-285.
23. 1H NMR assignments and secondary structure of hen egg white lysozyme in solution. Biochemistry 27:122-136.
24. Bodenhausen, G., Kogler, H., and Ernst, R.R. 1984. Selection of coherence-transfer pathways in NMR pulse experiments. J. Magn. Reson. 58:370-388.
25. Geen, H. and Freeman, R. 1991. Band-selective radiofrequency pulses. J. Magn. Reson. 93:93-141.
26. 1H NMR experiments. J. Biomol. NMR 1:209-215.
27. Otting, G., Liepinsh, E., and Wüthrich, K. 1992. Protein hydration in mixed solvents at low temperatures. J. Am. Chem. Soc. 114:7093-7095.
28. Liepinsh, E. and Otting, G. 1994. Specificity of urea binding to proteins. J. Am. Chem. Soc. 116:9670-9674.
29. Xia, T.H 1992. Ph.D. Thesis no. 9831, ETH Zürich, Switzerland.
30. Ferrin, T.E., Huang, C.C, Jarvis, L.E., and Langridge, R. 1988. The MIDAS display system. J. Mol. Graphics 6:13-27.