Automation in biological crystallization

Acta Crystallographica Section F:Structural Biology Communications

Volumn 70, Issue 6, 2014, Pages 686-696

  Shaw Stewart, Patrick ^a   Mueller Dieckmann, Jochen ^b  

^a Douglas Instruments Ltd   (United Kingdom)

^b UNIVERSITY OF HAMBURG   (Germany)

Author keywords

automation; crystallization

Indexed keywords

AUTOMATION; CRYSTALLIZATION; INFORMATION RETRIEVAL;

AUTOMATION; CRYSTALLIZATION; INFORMATION STORAGE AND RETRIEVAL;

EID: 84905484118     PISSN: None     EISSN: 2053230X     Source Type: Journal    
DOI: 10.1107/S2053230X14011601     Document Type: Article

References (58)

1. Albeck, S., Burstein, Y., Dym, O., Jacobovitch, Y., Levi, N., Meged, R., Michael, Y., Peleg, Y., Prilusky, J., Schreiber, G., Silman, I., Unger, T. & Sussman, J. L. (2005). Three-dimensional structure determination of proteins related to human health in their functional context at The Israel Structural Proteomics Center (ISPC). Acta Cryst. D61, 1364-1372.
2. Atkinson, A. C., Donev, A. N. & Tobias, R. D. (2007). Optimum Experimental Designs, With SAS. Oxford University Press.
3. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
4. Bern, M., Goldberg, D., Stevens, R. C. & Kuhn, P. (2004). Automatic classification of protein crystallization images using a curve-tracking algorithm. J. Appl. Cryst. 37, 279-287.
5. Box, G. E. P. & Hunter, J. S. (1957). Multi-factor experimental designs for exploring response surfaces. Ann. Math. Statist. 28, 195-241.
6. Carter, C. W. & Yin, Y. (1994). Quantitative analysis in the characterization and optimization of protein crystal growth. Acta Cryst. D50, 572-590.
7. Cherezov, V. (2011). Lipidic cubic phase technologies for membrane protein structural studies. Curr. Opin. Struct. Biol. 21, 559-566.
8. Cumbaa, C. A., Lauricella, A., Fehrman, N., Veatch, C., Collins, R., Luft, J. R., DeTitta, G. & Jurisica, I. (2003). Automatic classification of sub-microlitre protein-crystallization trials in 1536-well plates. Acta Cryst. D59, 1619-1627.
9. D'Arcy, A., Elmore, C., Stihle, M. & Johnston, J. E. (1996). A novel approach to crystallising proteins under oil. J. Cryst. Growth, 168, 175-180.
10. D'Arcy, A., Villard, F. & Marsh, M. (2007). An automated microseed matrix-screening method for protein crystallization. Acta Cryst. D63, 550-554.
11. Deller, M. C. & Rupp, B. (2014). Approaches to automated protein crystal harvesting. Acta Cryst. F70, 133-155.
12. Dierks, K., Meyer, A., Oberthür, D., Rapp, G., Einspahr, H. & Betzel, C. (2010). Efficient UV detection of protein crystals enabled by fluorescence excitation at wavelengths longer than 300 nm. Acta Cryst. F66, 478-484.
13. Elsliger, M.-A., Deacon, A. M., Godzik, A., Lesley, S. A., Wooley, J., Wüthrich, K. & &Wilson, I. A. (2010). The JCSG high-throughput structural biology pipeline. Acta Cryst. F66, 1137-1142.
14. Fulton, K. F., Ervine, S., Faux, N., Forster, R., Jodun, R. A., Ly, W., Robilliard, L., Sonsini, J., Whelan, D., Whisstock, J. C. & Buckle, A. M. (2004). CLIMS: Crystallography Laboratory Information Management System. Acta Cryst. D60, 1691-1693.
15. García-Ruiz, J. M., González-Ramírez, L. A., Gavira, J. A. & Otálora, F. (2002). Granada Crystallisation Box: a new device for protein crystallisation by counter-diffusion techniques. Acta Cryst. D58, 1638-1642.
16. Gilliland, G. L., Tung, M. & Ladner, J. E. (2002). The biological macromolecule crystallization database: crystallization procedures and strategies. Acta Cryst. D58, 916-920.
17. Groves, M. R., Müller, I. B., Kreplin, X. & Müller- Dieckmann, J. (2007). A method for the general identification of protein crystals in crystallization experiments using a noncovalent fluorescent dye. Acta Cryst. D63, 526-535.
18. Haebel, P. W., Arcus, V. L., Baker, E. N. & Metcalf, P. (2001). LISA: an intranet-based flexible database for protein crystallography project management. Acta Cryst. D57, 1341-1343.
19. Harris, M. & Jones, T. A. (2002). Xtrack-a web-based crystallographic notebook. Acta Cryst. D58, 1889-1891.
20. Heinemann, U., Frevert, J., Hofmann, K.-P., Illing, G., Maurer, C., Oschkinat, H. & Saenger, W. (2000). An integrated approach to structural genomics. Prog. Biophys. Mol. Biol. 73, 347-362.
21. Hosfield, D., Palan, J., Hilgers, M., Scheibe, D., McRee, D. E. & Stevens, R. C. (2003). A fully integrated protein crystallization platform for small-molecule drug discovery. J. Struct. Biol. 142, 207-217.
22. Hünefeld, F. L. (1840). Der Chemismus in der thierischen Organisation, p.160. Leipzig University, Germany.
23. Kendrew, J. C., Bodo, G., Dintzis, H. M., Parrish, R. G., Wyckhoff, H. & Phillips, D. C. (1958). A three dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature (London), 199, 662-666.
24. Kurgan, L., Razib, A. A., Aghakhani, S., Dick, S., Mizianty, M. & Jahandideh, S. (2009). CRYSTALP2: sequence-based protein crystallization propensity prediction. BMC Struct. Biol. 9, 50.
25. Luft, J. R., Collins, R. J., Fehrman, N. A., Lauricella, A. M., Veatch, C. K. & DeTitta, G. T. (2003). A deliberate approach to screening for initial crystallization conditions of biological macromolecules. J. Struct. Biol. 142, 170-179.
26. Luft, J. R. & DeTitta, G.T. (1995). Chaperone Salts, Polyethylene Glycol and Rates of Equilibration in Vapor Diffusion Crystallization. Acta Cryst. D51, 780-785.
27. McPherson, A., Cudney, R. & Patel, S. (2003). The Crystallization of Proteins, Nucleic Acids and Viruses for X-ray Diffraction Analysis. Biopolymers, Vol. 8, edited by S. R. Fahnenstock & A. Steinbüchel, pp. 427-468. Berlin: Wiley-VCH.
28. McPherson, A. & Gavira, J. A. (2014). Introduction to protein crystallization. Acta Cryst. F70, 2-20.
29. Meijers, R. & Mueller-Dieckmann, J. (2011). Advances in High-Throughput Crystallization. eLS. Chichester: John Wiley & Sons. doi:10.1002/9780470015902.a0023171.
30. Ménétrey, J., Perderiset, M., Cicolari, J., Houdusse, A. & Stura, E. A. (2007). Improving Diffraction from 3 to 2 A for a Complex between a Small GTPase and Its Effector by Analysis of Crystal Contacts and Use of Reverse Screening. Cryst. Growth Des. 7, 2140-2146.
31. Morris, C. et al. (2011). The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory. Acta Cryst. D67, 249-260.
32. Morris, C., Wood, P., Griffiths, S. L., Wilson, K. S. & Ashton, A. W. (2005). MOLE: a data management application based on a protein production data model. Proteins, 58, 285-289.
33. Mueller, U., Darowski, N., Fuchs, M. R., Fö rster, R., Hellmig, M., Paithankar, K. S., Pühringer, S., Steffien, M., Zocher, G. & Weiss, M. S. (2012). Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin. J. Synchrotron Rad. 19, 442-449.
34. Mueller-Dieckmann, J. (2006). The open-access high-throughput crystallization facility at EMBL Hamburg. Acta Cryst. D62, 1446-1452.
35. Newman, J., Xu, J. & Willis, M. C. (2007). Initial evaluations of the reproducibility of vapor-diffusion crystallization. Acta Cryst. D63, 826-832.
36. Obmolova, G., Malia, T. J., Teplyakov, A., Sweet, R. & Gilliland, G. L. (2010). Promoting crystallization of antibody-antigen complexes via microseed matrix screening. Acta Cryst. D66, 927-933.
37. Peat, T., de La Fortelle, E., Culpepper, J. & Newman, J. (2002). From information management to protein annotation: preparing protein structures for drug discovery. Acta Cryst. D58, 1968-1970.
38. Prilusky, J., Felder, C. E., Zeev-Ben-Mordehai, T., Rydberg, E. H., Man, O., Beckmann, J. S. & Sussman, J. L. (2005). FoldIndex#: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinfor-matics, 21, 3435-3438.
39. Prilusky, J., Oueillet, E., Ulryck, N., Pajon, A., Bernauer, J., Krimm, I., Quevillon-Cheruel, S., Leulliot, N., Graille, M., Liger, D., Trésaugues, L., Sussman, J. L., Janin, J., van Tilbeurgh, H. & Poupon, A. (2005). HalX: an open-source LIMS (Laboratory Information Management System) for small-to large-scale laboratories. Acta Cryst. D61, 671-678.
40. Rupp, B. & Wang, J. (2004). Predictive models for protein crystallization. Methods, 34, 390-407.
41. Salemme, F. R. (1972). A free interface diffusion technique for the crystallization of proteins for X-ray crystallography. Arch. Biochem. Biophys. 151, 533-539.
42. Savitsky, M., Diprose, J. M., Morris, C., Griffiths, S. L., Daniel, E., Lin, B., Daenke, S., Bishop, B., Siebold, C., Wilson, K. S., Blake, R., Stuart, D. I. & Esnouf, R. M. (2011). Recording information on protein complexes in an information management system. J. Struct. Biol. 175, 224-229.
43. Shah, A. K., Liu, Z.-J., Stewart, P. D., Schubot, F. D., Rose, J. P., Newton, M. G. & Wang, B.-C. (2005). On increasing protein-crystallization throughput for X-ray diffraction studies. Acta Cryst. D61, 123-129.
44. Shaw Stewart, P. D. & Baldock, P. F. M. (1999). Practical experimental design techniques for automatic and manual protein crystallization. J. Cryst. Growth, 196, 665-673.
45. Shaw Stewart, P. D., Kolek, S. A., Briggs, R. A., Chayen, N. E. & Baldock, P. F. M. (2011). Random microseeding: a theoretical and practical exploration of seed stability and seeding techniques for successful protein crystallization. Cryst. Growth Des. 11, 3432-3441.
46. Sigdel, M., Pusey, M. L. & Aygun, R. S. (2013). Real-Time Protein Crystallization Image Acquisition and Classification System. Cryst. Growth Des. 13, 2728-2736.
47. Slabinski, L., Jaroszewski, L., Rychlewski, L., Wilson, I. A., Lesley, S. A. & Godzik, A. (2007). XtalPred: a web server for prediction of protein crystallizability. Bioinformatics, 23, 3403-3405.
48. Soliman, A. S. M., Warkentin, M., Apker, B. & Thorne, R. E. (2011). Development of high-performance X-ray transparent crystallization plates for in situ protein crystal screening and analysis. Acta Cryst. D67, 646-656.
49. Spraggon, G., Lesley, S. A., Kreusch, A. & Priestle, J. P. (2002). Computational analysis of crystallization trials. Acta Cryst. D58, 1915-1923.
50. St John, F. J., Feng, B. & Pozharski, E. (2008). The role of bias in crystallization conditions in automated microseeding. Acta Cryst. D64, 1222-1227.
51. Till, M., Robson, A., Byrne, M. J., Nair, A. V., Kolek, S. A., Shaw Stewart, P. D. & Race, P. R. (2013). Improving the success rate of protein crystallization by random microseed matrix screening. J. Vis. Exp., doi:10.3791/50548.
52. Vekilov, P. G. & Vorontsova, M. A. (2014). Nucleation precursors in protein crystallization. Acta Cryst. F70, 271-282.
53. Watanabe, N., Murai, H. & Tanaka, I. (2002). Semi-automatic protein crystallization system that allows in situ observation of X-ray diffraction from crystals in the drop. Acta Cryst. D58, 1527-1530.
54. Watts, D., Cowtan, K. & Wilson, J. (2008). Automated classification of crystallization experiments using wavelets and statistical texture characterization techniques. J. Appl. Cryst. 41, 8-17.
55. Watts, D., Müller-Dieckmann, J., Tsakanova, G., Lamzin, V. S. & Groves, M. R. (2010). Quantitive evaluation of macromolecular crystallization experiments using 1, 8-ANS fluorescence. Acta Cryst. D66, 901-908.
56. Weber, P. C. (1990). A protein crystallization strategy using automated grid searches on successively finer grids. Methods, 1, 31-37.
57. Zolnai, Z., Lee, P. T., Li, J., Chapman, M. R., Newman, C. S., Phillips, G. N., Rayment, I., Ulrich, E. L., Volkman, B. F. & Markley, J. L. (2003). Project management system for structural and functional proteomics: Sesame. J. Struct. Funct. Genomics, 4, 11-23.
58. Zuk, W. M. & Ward, K. B. (1991). Methods of analysis of protein crystal images. J. Cryst. Growth, 110, 148-155.