Pipelines, robots, crystals and biology: What use high throughput solving structures of challenging targets?

Current Protein and Peptide Science

Volumn 8, Issue 2, 2007, Pages 205-217

  Kambach, Christian ^a  

^a PAUL SCHERRER INSTITUTE   (Switzerland)

Author keywords

Cloning; Crystallography; Expression; High throughput; Screening; Structural biology; Structural genomics

Indexed keywords

COMPLEMENTARY DNA; MEMBRANE PROTEIN;

ANALYTIC METHOD; ANALYTICAL PARAMETERS; AUTOMATION; CISTRON; COMPLEX FORMATION; COMPUTER INTERFACE; COMPUTER PROGRAM; COST BENEFIT ANALYSIS; CRYSTAL STRUCTURE; DIFFRACTION; ENZYME LINKED IMMUNOSORBENT ASSAY; EUKARYOTE; HIGH THROUGHPUT SCREENING; HUMAN; HYPOTHESIS; IMAGING SYSTEM; MEDICAL TECHNOLOGY; MOLECULAR CLONING; NONHUMAN; POLYMERASE CHAIN REACTION; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; QUALITY CONTROL; REVIEW; ROBOTICS; SEQUENCE ANALYSIS; SOLUBILITY; STRUCTURAL GENOMICS; THERMAL SHIFT ASSAY; X RAY CRYSTALLOGRAPHY;

CRYSTALLIZATION; PROTEIN CONFORMATION; PROTEINS; ROBOTICS;

EID: 34247617865     PISSN: 13892037     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920307780363442     Document Type: Review

References (72)

1. Brenner, S.E. (2001) Nat. Rev. Genet., 2, 801-809.
2. Burley, S.K. (2000) Nat. Struct. Biol., 7 Suppl, 932-934.
3. Stevens, R.C., Yokoyama, S. and Wilson, I.A. (2001) Science, 294, 89-92.
4. Chandonia, J.M. and Brenner, S.E. (2006) Science, 311, 347-351.
5. Todd, A.E., Marsden, R.L., Thornton, J.M. and Orengo, C.A. (2005) J. Mol. Biol., 348, 1235-1260.
6. Stevens, R.C. and Wilson, I.A. (2001) Science, 293, 519-520.
7. Terwilliger, T.C. (2004) Nat. Struct. Mol. Biol., 11, 296-297.
8. Thornton, J. (2001) Trends Biochem. Sci., 26, 88-89.
9. Moreland, N., Ashton, R., Baker, H.M., Ivanovic, I., Patterson, S., Arcus, V.L., Baker, E.N. and Lott, J.S. (2005) Acta Crystallogr. D. Biol. Crystallogr., 61, 1378-1385.
10. Berry, I.M., Dym, O., Esnouf, R.M., Harlos, K., Meged, R., Perrakis, A., Sussman, J.L., Walter, T.S., Wilson, J. and Messerschmidt, A. (2006) Acta Crystallogr. D. Biol. Crystallogr., 62, 1137-1149.
11. Lesley, S.A., Kuhn, P., Godzik, A., Deacon, A.M., Mathews, I., Kreusch, A., Spraggon, G., Klock, H.E., McMullan, D., Shin, T., Vincent, J., Robb, A., Brinen, L.S., Miller, M.D., McPhillips, T.M., Miller, M.A., Scheibe, D., Canaves, J.M., Guda, C., Jaroszewski, L., Selby, T.L., Elsliger, M.A., Wooley, J., Taylor, S.S., Hodgson, K.O., Wilson, I.A., Schultz, P.G. and Stevens, R.C. (2002) Proc. Natl. Acad. Sci. USA, 99, 11664-11669.
12. Stevens, R.C. (2004) Nat. Struct. Mol. Biol., 11, 293-295.
13. Stock, D., Perisic, O. and Lowe, J. (2005) Prog. Biophys. Mol. Biol., 88, 311-327.
14. Su, X.D., Liang, Y., Li, L., Nan, J., Brostromer, E., Liu, P., Dong, Y. and Xian, D. (2006) Acta Crystallogr. D. Biol. Crystallogr., 62, 843-851.
15. Rupp, B. (2003) Acc. Chem. Res., 36, 173-181.
16. Vincentelli, R., Bignon, C., Gruez, A., Canaan, S., Sulzenbacher, G., Tegoni, M., Campanacci, V. and Cambillau, C. (2003) Acc. Chem. Res., 36, 165-172.
17. Geerlof, A., Brown, J., Coutard, B., Egloff, M.P., Enguita, F.J., Fogg, M.J., Gilbert, R.J.C., Groves, M.R., Haouz, A., Nettleship, J.E., Nordlund, P., Owens, R.J., Ruff, M., Sainsbury, S., Svergun, D.I. and Wilmanns, M. (2006) Acta Crystallogr. D. Biol. Crystallogr., D62, 1125-1136.
18. O'Toole, N., Grabowski, M., Otwinowski, Z., Minor, W. and Cygler, M. (2004) Proteins, 56, 201-210.
19. Albeck, S., Alzari, P., Andreini, C., Banci, L., Berry, I.M., Bertini, I., Cambillau, C., Canard, B., Carter, L., Cohen, S.X., Diprose, J.M., Dym, O., Esnouf, R.M., Felder, C., Ferron, F., Guillemot, F., Hamer, R., Ben Jelloul, M., Laskowski, R.A., Laurent, T., Longhi, S., Lopez, R., Luchinat, C., Malet, H., Mochel, T., Morris, R.J., Moulinier, L., Oinn, T., Pajon, A., Peleg, Y., Perrakis, A., Poch, O., Prilusky, J., Rachedi, A., Ripp, R., Rosato, A., Silman, I., Stuart, D.I., Sussman, J.L., Thierry, J.C., Thompson, J.D., Thornton, J.M., Unger, T., Vaughan, B., Vranken, W., Watson, J.D., Whamond, G. and Henrick, K. (2006) Acta Crystallogr. D. Biol. Crystallogr., D62, 1184-1195.
20. Dale, G.E., Oefner, C. and D'Arcy, A. (2003) J. Struct. Biol., 142, 88-97.
21. Hart, D.J. and Tarendeau, F. (2006) Acta Crystallogr. D. Biol. Crystallogr., 62, 19-26.
22. Cornvik, T., Dahlroth, S.L., Magnusdottir, A., Herman, M.D., Knaust, R., Ekberg, M. and Nordlund, P. (2005) Nat. Methods, 2, 507-509.
23. Gillette, W.K., Esposito, D., Frank, P.H., Zhou, M., Yu, L.R., Jozwik, C., Zhang, X., McGowan, B., Jacobowitz, D.M., Pollard, H.B., Hao, T., Hill, D.E., Vidal, M., Conrads, T.P., Veenstra, T.D. and Hartley, J.L. (2005) Mol. Cell Proteomics., 4, 1647-1652.
24. Banci, L., Bertini, I., Cusack, S., de Jong, R.N., Heinemann, U., Jones, E.Y., Kozielski, F., Maskos, K., Messerschmidt, A., Owens, R., Perrakis, A., Poterszman, A., Schneider, G., Siebold, C., Silman, I., Sixma, T., Stewart-Jones, G., Sussman, J.L., Thierry, J.C. and Moras, D. (2006) Acta Crystallogr. D. Biol. Crystallogr., D62, 1208-1217.
25. Busso, D., Poussin-Courmontagne, P., Rose, D., Ripp, R., Litt, A., Thierry, J.C. and Moras, D. (2005) J. Struct. Funct. Genomics, 6, 81-88.
26. Klock, H.E., White, A., Koesema, E. and Lesley, S.A. (2005) J. Struct. Funct. Genomics, 6, 89-94.
27. Hartley, J.L. (2006) Curr. Opin. Biotechnol., 17, 359-366.
28. Alzari, P.M., Berglund, H., Berrow, N.S., Blagova, E., Busso, D., Cambillau.C., Geerlof, A., Hart, D.J., Nordlund, P., Perrakis, A., Tarendeau, F., Unger, T., Willmanns, M. and Owens, R.J. (2006) Acta Crystallogr. D. Biol. Crystallogr., D62, 1103-1113.
29. Li, M.Z. and Elledge, S.J. (2005) Nat Genet, 37, 311-319.
30. Marsischky, G. and Labaer, J. (2004) Genome Res., 14, 2020-2028.
31. Esposito, D. and Chatterjee, D.K. (2006) Curr. Opin. Biotechnol., 17, 353-358.
32. Butt, T.R., Edavettal, S.C., Hall, J.P. and Mattern, M.R. (2005) Protein Expr. Purif., 43, 1-9.
33. Malakhov, M.P., Mattern, M.R., Malakhova, O.A., Drinker, M., Weeks, S.D. and Butt, T.R. (2004) J. Struct. Funct. Genomics, 5, 75-86.
34. Marblestone, J.G., Edavettal, S.C., Lim, Y., Lim, P., Zuo, X. and Butt, T.R. (2006) Protein Sci., 15, 182-189.
35. Prinz, B., Schultchen, J., Rydzewski, R., Holz, C., Boettner, M., Stahl, U. and Lang, C. (2004) J. Struct. Funct. Genomics, 5, 29-44.
36. Kapust, R.B., Tozser, J., Copeland, T.D. and Waugh, D.S. (2002) Biochem. Biophys. Res. Commun., 294, 949-955.
37. Hearn, M.T. and Acosta, D. (2001) J. Mol. Recognit., 14, 323-369.
38. Zuo, X., Li, S., Hall, J., Mattern, M.R., Tran, H., Shoo, J., Tan, R., Weiss, S.R. and Butt, T.R. (2005) J. Struct. Funct. Genomics, 6, 103-111.
39. Studier, F.W. (2005) Prot. Exp. Purif., 41, 207-234.
40. Boettner, M., Prinz, B., Holz, C., Stahl, U. and Lang, C. (2002) J. Biotechnol., 99, 51-62.
41. Holz, C., Prinz, B., Bolotina, N., Sievert, V., Bussow, K., Simon, B., Stahl, U. and Lang, C. (2003) J. Struct. Funct. Genomics, 4, 97-108.
42. Bahia, D., Cheung, R., Buchs, M., Geisse, S. and Hunt, I. (2005) Protein Exp. Purif., 39, 61-70.
43. Gao, M., Brufatto, N., Chen, T., Murley, L.L., Thalakada, R., Domagala, M., Beattie, B., Mamelak, D., Athanasopoulos, V., Johnson, D., McFadden, G., Burks, C. and Frappier, L. (2005) J. Proteome. Res., 4, 2225-2235.
44. Schlaeppi, J.M., Henke, M., Mahnke, M., Hartmann, S., Schmitz, R., Pouliquen, Y., Kerins, B., Weber, E., Kolbinger, F. and Kocher, H.P. (2006) Protein Expr. Purif., 50, 185-195.
45. Geisse, S. and Henke, M. (2005) J. Struct. Funct. Genomics, 6, 165-170.
46. Aricescu, A.R., Lu, W. and Jones, E.Y. (2006) Acta Crystallogr. D. Biol. Crystallogr., D62, 1243-1250.
47. Durocher, Y., Perret, S. and Kamen, A. (2002) Nucleic Acids Res., 30, E9.
48. Endo, Y. and Sawasaki, T. (2006) Curr. Opin. Biotechnol., 17, 373-380.
49. Yokoyama, S. (2003) Curr. Opin. Chem. Biol., 7, 39-43.
50. Romier, C., Ben Jelloul, M., Albeck, S., Buchwald, G., Busso, D., Moras, D., Sixma, T.K. and Perrakis, A. (2006) Acta Crystallogr. D. Biol. Crystallogr., D62, 1232-1242.
51. Tan, S. (2001) Protein Expr. Purif., 21, 224-234.
52. Kim, K.J., Kim, H.E., Lee, K.H., Han, W., Yi, M.J., Jeong, J. and Oh, B.H. (2004) Protein Sci., 13, 1698-1703.
53. Berger, I., Fitzgerald, D.J. and Richmond, T.J. (2004) Nat. Biotechnol., 22, 1583-1587.
54. Fitzgerald, D.J., Berger, P., Schaffitzel, C., Yamada, K., Richmond, T.J. and Berger, I. (2006) Nat. Methods, 3, 1021-1032.
55. Knaust, R.K. and Nordlund, P. (2001) Anal. Biochem., 297, 79-85.
56. Lindwall, G., Chau, M., Gardner, S.R. and Kohlstaedt, L.A. (2000) Protein Eng., 13, 67-71.
57. Vincentelli, R., Canaan, S., Campanacci, V., Valencia, C., Maurin, D., Frassinetti, F., Scappucini-Calvo, L., Bourne, Y., Cambillau, C. and Bignon, C. (2004) Protein Sci., 13, 2782-2792.
58. Cull, M.G. and Schatz, P.J. (2000) Methods Enzymol., 326, 430-440.
59. Raines, R.T., McCormick, M., Van Oosbree, T.R. and Mierendorf, R.C. (2000) Methods Enzymol., 326, 362-376.
60. Cabantous, S., Terwilliger, T.C. and Waldo, G.S. (2005) Nat. Biotechnol., 23, 102-107.
61. Hedren, M., Ballagi, A., Mortsell, L., Rajkai, G., Stenmark, P., Sturesson, C. and Nordlund, P. (2006) Acta Crystallogr. D. Biol. Crystallogr., D62, 1227-1231.
62. Page, R., Moy, K., Sims, E.C., Velasquez, J., McManus, B., Grittini, C., Clayton, T.L. and Stevens, R.C. (2004) Biotechniques, 37, 364, 366, 368.
63. Bhikhabhai, R., Sjoberg, A., Hedkvist, L., Galin, M., Liljedahl, P., Frigard, T., Pettersson, N., Nilsson, M., Sigrell-Simon, J.A. and Markeland-Johansson, C. (2005) J. Chromatogr. A, 1080, 83-92.
64. Bondos, S.E. and Bicknell, A. (2003) Anal. Biochem., 316, 223-231.
65. Golovanov, A.P., Hautbergue, G.M., Wilson, S.A. and Lian, L.Y. (2004) J. Am. Chem. Soc., 126, 8933-8939.
66. Jancarik, J., Pufan, R., Hong, C., Kim, S.H. and Kim, R. (2004) Acta Crystallogr. D. Biol. Crystallogr., 60, 1670-1673.
67. Pantoliano, M.W., Petrella, E.C., Kwasnoski, J.D., Lobanov, V.S., Myslik, J., Graf, E., Carver, T., Asel, E., Springer, B.A., Lane, P. and Salemme, F.R. (2001) J. Biomol. Screen., 6, 429-440.
68. Ignatova, Z. and Gierasch, L.M. (2006) Proc. Natl. Acad. Sci. USA, 103, 13357-13361.
69. Ericsson, U.B., Hallberg, B.M., Detitta, G.T., Dekker, N. and Nordlund, P. (2006) Anal. Biochem., 357, 289-298.
70. Vedadi, M., Niesen, F.H., lali-Hassani, A., Fedorov, O.Y., Finerty, P.J., Jr., Wasney, G.A., Yeung, R., Arrowsmith, C., Ball, L.J., Berglund, H., Hui, R., Marsden, B.D., Nordlund, P., Sundstrom, M., Weigelt, J. and Edwards, A.M. (2006) Proc. Natl. Acad. Sci. USA, 103, 15835-15840.
71. Page, R., Peti, W., Wilson, I.A., Stevens, R.C. and Wuthrich, K. (2005) Proc. Natl. Acad. Sci. USA, 102, 1901-1905.
72. Peti, W., Page, R., Moy, K., O'neil-Johnson, M., Wilson, I.A., Stevens, R.C. and Wuthrich, K. (2005) J. Struct. Funct. Genomics, 6, 259-267.