Detergent organisation in crystals of monomeric outer membrane phospholipase A

Journal of Structural Biology

Volumn 141, Issue 2, 2003, Pages 122-131

  Snijder, H J ^a,b   Timmins, P A ^a,c   Kalk, K H ^a   Dijkstra, B W ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^c INSTITUT LAUE LANGEVIN   (France)

Author keywords

Contrast variation; Crystallisation; Detergent structure; Membrane proteins; Neutron diffraction; Outer membrane phospholipase

Indexed keywords

DETERGENT; OUTER MEMBRANE PHOSPHOLIPASE A; OUTER MEMBRANE PROTEIN; PHOSPHOLIPASE A; UNCLASSIFIED DRUG; WATER;

ARTICLE; CONTROLLED STUDY; CRYSTAL; CRYSTAL STRUCTURE; CRYSTALLIZATION; DIFFRACTION; DIMERIZATION; ENZYME ACTIVE SITE; HYDROLYSIS; MICELLE; MOLECULE; NEUTRON; NONHUMAN; PRIORITY JOURNAL;

EID: 0037291994     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1047-8477(02)00579-8     Document Type: Article

References (42)

1. Becher P., Trifiletti S.E. Nonionic surface-active agents XIII. The effect of solvent on the thermodynamics of micellization. J. Colloid Interface Sci. 43:1973;485-490.
2. Blaauw M., Dekker N., Verheij H.M., Kalk K.H., Dijkstra B.W. Crystallization and preliminary X-ray analysis of outer membrane phospholipase A from Escherichia coli. FEBS Lett. 373:1995;10-12.
3. Brünger A.T. Free R value: a novel statistical quantity for assessing the accuracy of structures. Nature. 355:1992;472-475.
4. Collaborative Computational Project Number 4, 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-763.
5. Dekker N., Tommassen J., Lustig A., Rosenbusch J.P., Verheij H.M. Dimerization regulates the enzymatic activity of Escherichia coli outer membrane phospholipase A. J. Biol. Chem. 272:1997;3179-3184.
6. Essen L.O., Siegert R., Lehmann W.H., Oesterhelt D. Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex. Proc. Natl. Acad. Sci. USA. 95:1998;11673-11678.
7. Garavito R.M., Markovic-Housley Z., Jenkins J.A. The growth and characterization of membrane protein crystals. J. Crystal Growth. 76:1986;701-709.
8. Iwata S., Ostermeier C., Bernd L., Michel H. Structure at 2.8. Å resolution of cytochrome c oxidase from Paracoccus denitrificans Nature. 376:1995;660-669.
9. Jones T.A., Zou J.-Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119.
10. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26:1993;795-800.
11. Kita Y., Arakawa T., Lin T.-Y., Timasheff S.N. Contribution of the surface free energy perturbation to protein-solvent interactions. Biochemistry. 33:1994;15178-15189.
12. Kleywegt G.J., Jones T.A. xdlMAPMAN and xdlDATMAN - programs for reformatting, analysis and manipulation of biomolecular electron-density maps and reflection data sets. Acta Crystallogr. D. 52:1996;826-828.
13. Lewis B.A., Engelman D.M. Lipid bilayer thickness varies linearly with acyl chain length in fluid phosphatidylcholine vesicles. J. Mol. Biol. 166:1983;211-217.
14. Marone P.A., Thiyagarajan P., Wagner A.M., Tiede D.M. Effect of detergent alkyl chain length on crystallization of a detergent-solubilized membrane protein: correlation of protein-detergent particle size and particle-particle interaction with crystallization of the photosynthetic reaction center from Rhodobacter sphaeroides. J. Crystal Growth. 207:1999;214-225.
15. Michel H. Three-dimensional crystals of a membrane protein complex. The photosynthetic reaction centre from Rhodopseudomonas viridis. J. Mol. Biol. 158:1982;567-572.
16. Michel H. Crystallization of membrane proteins. Trends Biochem. Sci. 8:1983;56-59.
17. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
18. Palczewski K., Kumasaka T., Hori T., Behnke C.A., Motoshima H., Fox B.A., Le Trong I., Teller D.C., Okada T., Stenkamp R.E., Yamamoto M., Miyano M. Crystal structure of rhodopsin: a G protein-coupled receptor. Science. 289:2000;739-745.
19. Papiz M.Z., Hawthornthwaite A.M., Cogdell R.J., Woolley K.J., Wightman P.A., Ferguson L.A., Lindsay J.G. Crystallization and characterization of two crystal forms of the B800-850 light-harvesting complex from Rhodopseudomonas acidophila strain 10050. J. Mol. Biol. 209:1989;833-835.
20. Pautsch A., Schulz G.E. Structure of the outer membrane protein A transmembrane domain. Nat. Struct. Biol. 5:1998;1013-1017.
21. Pautsch A., Vogt J., Model K., Siebold C., Schulz G.E. Strategy for membrane protein crystallization exemplified with OmpA and OmpX. Proteins. 34:1999;167-172.
22. Pebay-Peyroula E., Garavito R.M., Rosenbusch J.P., Zulauf M., Timmins P.A. Detergent structure in tetragonal crystals of OmpF porin. Structure. 3:1995;1051-1059.
23. Penel, S., 1997. Organisation du détergent dans les cristaux de protéines membranaires: analyse des cristaux des porines de Rhodobacter capsulatus et de Escherichia coli. Université Joseph Fourier.
24. Penel S., Legrand J.F. MAINDEX, Manual indexation for area-detector crystallographic data. J. Appl. Crystallogr. 30:1997;206.
25. Penel S., Pebay-Peyroula E., Rosenbusch J., Rummel G., Schirmer T., Timmins P.A. Detergent binding in trigonal crystals of OmpF porin from Escherichia coli. Biochimie. 80:1998;543-551.
26. Pittz E.P., Bello J. Studies on bovine pancreatic ribonuclease A and model compounds in aqueous 2-methyl-2,4-pentanediol. Arch. Biochem. Biophys. 146:1971;513-524.
27. Pollack G.L. Atomic test of the Stokes-Einstein law: diffusion and solubility of Xe. Phys. Rev. A. 23:1981;2660-2663.
28. Pollack G.L., Himm J.F. Solubility of xenon in liquid n-alkanes: temperature dependence and thermodynamic functions. J. Chem. Phys. 77:1982;3221-3229.
29. Roche C.T., Strauss, M.G., Brenner, R., 1985. IEEE Trans. Nucl. Sci. NS-323 73-379.
30. Roth M. Best density maps in low-resolution crystallography with contrast variation. Acta Crystallogr. A. 43:1987;780-787.
31. Roth M. Phasing at low resolution. Moras D., Podjarny A.D., Thierry J.C. Crystallographic Computing. vol. 5:1991;229-248 Oxford Univ. Press, New York.
32. Roth M., Arnoux B., Ducruix A., Reiss-Husson F. Structure of the detergent phase and protein-detergent interactions in crystals of the wild-type (strain Y) Rhodobacter sphaeroides photochemical reaction center. Biochemistry. 30:1991;9403-9413.
33. Roth M., Lewit-Bentley A., Bentley G.A. Scaling and phase-difference determination in solvent contrast variation experiments. J. Appl. Crystallogr. 17:1984;77-84.
34. Roth M., Lewit-Bentley A., Michel H., Deisenhofer J., Huber R., Oesterhelt D. Detergent structure in crystals of a bacterial photosynthetic reaction centre. Nature. 340:1989;659-662.
35. Sauer O., Roth M., Schirmer T., Rummel G., Kratky C. Low-resolution detergent tracing in protein crystals using xenon or krypton to enhance X-ray contrast. Acta Crystallogr. D. 58:2002;60-69.
36. Snijder H.J., Dijkstra B.W. Bacterial phospholipase A, structure and function of an integral membrane phospholipase. Biochim. Biophys. Acta. 1488:2000;91-101.
37. Snijder H.J., Ubarretxena-Belandia I., Blaauw M., Kalk K.H., Verheij H.M., Egmond M.R., Dekker N., Dijkstra B.W. Structural evidence for dimerization-regulated activation of an integral membrane phospholipase. Nature. 401:1999;717-721.
38. Timmins P., Pebay-Peyroula E., Welte W. Detergent organisation in solutions and in crystals of membrane proteins. Biophys. Chem. 53:1994;27-36.
39. Timmins P.A., Hauk J., Wacker T., Welte W. The influence of heptane-1,2,3-triol on the size and shape of LDAO micelles. Implications for the crystallisation of membrane proteins. FEBS Lett. 280:1991;115-120.
40. Vandeputte-Rutten L., Kramer R.A., Kroon J., Dekker N., Egmond M.R., Gros P. Crystal structure of the outer membrane protease OmpT from Escherichia coli suggests a novel catalytic site. EMBO J. 20:2001;5033-5039.
41. Vogt J., Schulz G.E. The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence. Structure. 7:1999;1301-1309.
42. 63rd ed. Weast R.C., Astle M.J. Handbook of Chemistry and Physics. vol. 1:1983;CRC Press, Boca Raton, FL.