Protein crystallization by capillary counterdiffusion for applied crystallographic structure determination

Journal of Structural Biology

Volumn 142, Issue 1, 2003, Pages 218-231

  Ng, Joseph D ^a   Gavira, José A ^a   García Ruíz, Juan M ^b  

^a UNIVERSITY OF ALABAMA IN HUNTSVILLE   (United States)

^b CSIC   (Spain)

Author keywords

Counterdiffusion; Cryocrystallography; Crystallization cassette; High throughput; Protein crystallization

Indexed keywords

CRYOPROTECTIVE AGENT; DETERGENT; INSULIN; LYSOZYME; METAL ION; RECOMBINANT PROTEIN; THAUMATIN;

AB INITIO CALCULATION; ARTICLE; CAPILLARY COUNTERDIFFUSION; CRYSTALLIZATION; FOURIER ANALYSIS; GENOME; HANGING DROP VAPOR DIFFUSION METHOD; INFORMATION PROCESSING; IONIC STRENGTH; ISOELECTRIC POINT; MACROMOLECULE; PH; PRECIPITATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; RADIATION SCATTERING; TECHNIQUE; VAPORIZATION; X RAY ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 0037392851     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1047-8477(03)00052-2     Document Type: Article

References (56)

1. Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.et al. The genome sequence of Drosophila melanogaster. Science. 287:2000;2185-2195.
2. The Arabidopsis Genome Initiative 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
3. Biertümpfel C., Basquin J., Suck D., Sauter C. Crystallization of biological macromolecules using agarose gel. Acta Crystallogr. D. 58:2002;1657-1659.
4. Blundell T.L., Johnson L.N. Protein Crystallography. 1976;Academic Press, New York.
5. Burley S.K., Bonanno J.B. Structural genomics of proteins from conserved biochemical pathways and processes. Curr. Opin. Struct. Biol. 12:2002;383-391.
6. Carotenuto L., Piccolo C., Castagnolo D., Lappa M., Tortora A., Garcia-Ruiz J.M. Experimental observations and numerical modelling of diffusion-driven crystallisation processes. Acta Crystallogr. D. 58:2002;1628-1632.
7. Carter C.W. Jr., Baldwin E.T., Frick L. Statistical design of experiments for protein crystal growth and the use of a precrystallization assay. J. Cryst. Growth. 90:1988;60-73.
8. Carter C.W. Jr., Carter C.W. Protein crystallization using incomplete factorial experiments. J. Biol. Chem. 254:1979;12219-12223.
9. The C. elegans Sequencing Consortium 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018.
10. Chen L., Rose J.P., Breslow E., Yang D., Chang W.R., Furey W.F., Sax M., Wang B.-C. Crystal structure of a bovine neurophysin II dipeptide complex at 2.8. Å determined from the single-wavelength anomalous scattering signal of an incorporated iodine atom Proc. Natl. Acad. Sci. USA. 88:1991;4240-4244.
11. Collaborative Computational Project 4, 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-763.
12. Cudney R., Patel S., Weisgraber K., Newhouse Y., McPherson A. Screening and optimization strategies for macromolecular crystal growth. Acta Crystallogr. D. 50:1994;414-423.
13. Dauter Z., Li M., Wlodawer A. Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics. Acta Crystallogr. D. Biol. Crystallogr. 2001;239-249.
14. Fanchon E., Hendrickson W.A. Crystallographic Computing. vol. 5:1991;IUCr/Oxford Univ. Press, London. Chap. 15.
15. Feigelson R.S. The relevance of small molecule crystal growth theories and techniques to the growth of biological macromolecules. J. Cryst. Growth. 90:1988;1-13.
16. Furey W., Swaminathan S. PHASES-95: a program package for processing and analyzing diffraction data from macromolecules. Methods Enzymol. 277:1997;590-620.
17. Garcia-Ruiz J.M. Uses of crystal growth in gels and other diffusing-reacting systems. Key Eng. Mater. 88:1991;87-106.
18. García-Ruiz J.M., Gavira J.A., Otálora F., Guasch A., Coll M. Reinforced protein crystals. Mater. Res. Bull. 33:1998;1593-1598.
19. Garcia-Ruiz J.M., Moreno A., Viedma C., Coll M. Crystal quality of lysozyme single crystals grown by the gel acupuncture method. Mater. Res. Bull. 28:1993;541-546.
20. García-Ruiz J.M., Otálora F., Novella M.L., Gavira J.A., Sauter C., Vidal O. A supersaturation wave of protein crystallization. J. Cryst. Growth. 232:2001;149-155.
21. Gavira, J.A., 2000. Protein crystallization in gel media using counter-diffusion techniques, Univ. of Granada, Granada. [Ph.D. dissertation].
22. Gavira J.A., Garcia-Ruiz J.M. Agarose as crystallisation media for proteins. II. Trapping of gel fibres into the crystals. Acta Crystallogr. D. 58:2002;1653-1656.
23. Gavira J.A., Toh D., Lopéz-Jaramillo J., García-Ruíz J.M., Ng J.D. Ab initio crystallographic structure determination of insulin from protein to electron density without crystal handling. Acta Crystallogr. D. 58:2002;1147-1154.
24. Green D.W., Ingram V.M., Perutz M.F. Proc. R. Soc. London A. 40:1954;287-307.
25. Harker D. The determination of the phases of the structure factors of noncentro-symmetric crystals by the method of double isomorphous replacement. Acta Crystallogr. 9:1956;1-9.
26. Hendrickson W.A., Teeter M.M. Structure of the hydrophobic protein crambin determined directly from anomalous scattering of sulfur. Nature. 290:1981;107-113.
27. Henisch H.K. Crystal Growth in Gels. 1970;Pennsylvania State Univ. Press, University Park.
28. Henisch H.K., Garcia-Ruiz J.M. Crystal growth in gels and Liesegang ring formation. I. Diffusion relationships. J. Cryst. Growth. 75:1986;195-202. 203-211.
29. Hünefeld, F.L., 1840. Die Chemismus in der Thienschen Organization, Leipzig, p. 160. [Taken from Reichert and Brown, 1909].
30. 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.
31. KalKura S.N., Devanarayanan S. Fibrous crystals of cholesterol in silica gel. J. Cryst. Growth. 83:1987;446-448.
32. Lamzin V.S., Wilson K.S. Automated refinement of protein models. Acta Crystallogr. D. 49:1993;129-147.
33. Liesegang R. Chemische Fernwirkung. Photographisches Arch. 800:1897;305-309.
34. 2+ -regulated photoprotein obelin at 1.7 Å resolution determined directly from its sulfur substructure Protein Sci. 9:2000;2085-2093.
35. López-Jaramillo F.J., García-Ruiz J.M., Gavira J.A., Otálora F. Crystallization and cryocrystallography inside X-ray capillaries. J. Appl. Crystallogr. 34:2001;365-370.
36. Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T. Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences. Genetics. 152:1999;1299-1305.
37. McPherson A. Crystallization Biological Macromolecules. 1999;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
38. McRee, D.E., 1999. Practical Protein Crystallography. second ed., ISBN 0-12-486052-4.
39. Mewes H.W., Albermann K., Bahr M., Frishman D., Gleissner A., Hani J., Heumann K., Kleine, Maierl A., Oliver S.G., Pfeiffer F., Zollner A. Overview of the yeast genome. Nature. 387:1997;7-8.
40. Miers H.A., Isaac F. The spontaneous crystallization of binary mixtures: experiments on salol and betol. Proc. R. Soc. London A. 79:1907;322.
41. Ng J.D. Space grown crystals are more useful for structure determination. Ann. N. Y. Acad. Sci. 974:2002;598-609.
42. Ng, J.D., Gavira, J.A., Garcia-Ruiz, J.M., Wells, M., Jenkins, G., 2003. Crystallization cassette for counter-diffusion crystal growth and X-ray crystallographic analysis. Patent pending.
43. Ostwald W. Besprechung der Arbeit von Liesenganga A-Linien. Z. Phys. Chem. 23:1897;365.
44. Ostwald, W., 1899. Lehrb. D. allgem. Chem., second ed., Leipzig, p. 778.
45. Otálora F., García-Ruiz J.M. Computer model of the diffusion/reaction interplay in the gel acupuncture method. J. Cryst. Growth. 169:1996;361-367.
46. Otálora F., García-Ruiz J.M. Crystal growth studies in microgravity with the APCF. I. Computer simulation of transport dynamics. J. Cryst. Growth. 182:1997;141-154.
47. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
48. Perutz M.F., Rossmann M.G., Cullis A.F., Muirhead H., Will G., North A.C.T. Structure of haemoglobin. A three-dimensional Fourier synthesis at 5.5. Å resolution, obtained by X-ray analysis Nature. 185:1960;416-422.
49. Robert M.C., Lefaucheux F. Crystal growth in gels: principle and applications. J. Cryst. Growth. 90:1988;358-367.
50. Salemne F.R. A free interface diffusion technique for the crystallization of proteins for X-ray crystallography. Arch. Biochem. Biophys. 151:1972;533-539.
51. Smith J.L., Hendrickson W.A. Structure of trimeric haemerythrin. Nature. 303:1983;86-88.
52. Terwilliger T.C., Berendzen J. Automated structure solution for MIR and MAD. Acta Crystallogr. D. 55:1999;849-861.
53. Venter J.C., Adams M.D., Myers E.W.et al. The sequence of the human genome. Science. 291:2001;1304-1351.
54. Wang B.-C. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115:1985;90-112.
55. Zeppezauer M.E.H., Zeppezauer E.S. Micro diffusion cells for the growth of single protein crystals by means of equilibrium dialysis. Arch. Biochem. Biophys. 19:1968;564-573.
56. Lopéz-Jaramillo J., Otálora F., Gavira J.A. Protein crystal quality in diffusive environments and its evaluation. J. Cryst. Growth. 247:2003;177-184.