Five years of increasing structural biology throughput - A retrospective analysis

Structure-Based Drug Discovery

Volumn , Issue , 2007, Pages 1-26

  Abola, Enrique ^a   Carlton, Dennis D ^a   Kuhn, Peter ^a   Stevens, Raymond C ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84865473629     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/1-4020-4407-0_1     Document Type: Chapter

References (41)

1. Abola E., Kuhn P., Earnest T. and Stevens R. C. 2000. Automation of X-ray crystallography. Nat. Struct. Biol. 7, 973-977.
2. Adams M. D., Celniker S. E., Holt R. A., Evans C. A., Gocayne J. D., Amanatides P. G., Scherer S. E., Li P. W., Hoskins R. A., Galle R. F. et al. 2000. The genome sequence of Drosophila melanogaster. Science 287, 2185-2195.
3. Bertone P., Kluger Y., Zheng D., Edwards A. M., Arrowsmith C. H., Montelione G. T., and Gerstein M. 2001. SPINE: An integrated tracking database and data mining approach for prioritizing feasible targets in high-throughput structural proteomics. Nucleic Acids Res. 29, 2884-2898.
4. Canaves J. M., Page R., Wilson I. A. and Stevens R. C. 2004. Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: Maximum clustering strategy for structural genomics. J. Mol. Biol. 344, 977-991.
5. Carter D. C., Rhodes P., McRee D. E., Tari L. W., Dougan D. R., Snell G., Abola E. and Stevens R. C. 2005. Reduction in diffuse-convective disturbances in nanovolume protein crystallization experiments. J. Appl. Cryst. 38, 87-90.
6. Choi K. H., Groarke J. M., Young D. C., Rossmann M. G., Pevear D. C., Kuhn R. J. and Smith J. L. 2004. Design, expression, and purification of a Flaviviridae polymerase using a high-throughput approach to facilitate crystal structure determination. Protein Sci. 13, 2685-92.
7. Cohen A. E., Ellis P. J., Miller M. D., Deacon A. M. and Phizackerley R. P. 2002. An automated system to mount cryocooled protein crystals on a synchrotron beam line, using compact sample cassettes and a small-scale robot. J. Appl. Crystallogr. 35, 720-726.
8. Derewenda Z. 2004. Rational protein crystallization by mutational surface engineering structure. 12, 529-35.
9. Hansen C. L., Skordalakes E., Berger J. M. and Quake S. R. 2002. A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion. PNAS 99, 16531-16536.
10. Hosfield D., Palan J., Hilgers M., Scheibe D., McRee D. E. and Stevens R. C. 2003. A fully integrated protein crystallization platform for small-molecule drug discovery. J. Struct. Biol. 142, 207-217.
11. Jancarik J., Pufan R., Hong C., Kim S. H. and Kim R. 2004. Optimum solubility (OS) screening: An efficient method to optimize buffer conditions for homogeneity and crystallization of proteins. Acta Crystallogr. D 60, 1670-1673.
12. Kigawa T., Yabuki T., Matsuda N., Matsuda T., Nakajima R., Tanaka A. and Yokoyama S. 2004. Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J. Struct. Funct. Genomics 5, 63-68.
13. Klock H. E., White A., Koesema E. and Lesley S. A. 2005. Methods and results for semiautomated cloning using integrated robotics. 2005. J. Struct. Funct. Genomics., 6, 89-94.
14. Lander E. S., Linton L. M., Birren B., Nusbaum C., Zody M. C., Baldwin J., Devon K., Dewar K., Doyle M., Fitz Hugh W. et al. 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921.
15. Lesley S. A., Kuhn P., Godzik A., Deacon A. M., Mathews I., Kreusch A., Spraggon G., Klock H. E., McMullan D., Shin T. 2002. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc. Natl. Acad. Sci. 99, 11664-11669.
16. Longenecker K. L., Garrard S. M., Sheffield P. J. and Derewenda Z. S. 2001. Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI. Acta. Crystallogr. D. Biol. Crystallogr. 57, 679-88.
17. Markley J. L., Ulrich E. L., Westler W. M. and Volkman B. F. 2003. Macromolecular structure determination by NMR spectroscopy. Methods Biochem. Anal. 44, 89-113.
18. Marra M. A., Jones S. J. M., Astell C. R., Holt R. A., Brooks-Wilson A., Butterfield Y. S. N., Khattra J., Asano J. K., Barber S. A., Chan S. Y. 2003. The genome sequence of the SARS-Associated Coronavirus. Science 300, 1399-1404.
19. McPhillips T. M., McPhillips S. E., Chiu H.-J., Cohen A. E., Deacon A. M., Ellis P. J., Garman E., Gonzalez A., Sauter N. K., Phizackerley R. P. et al. 2002. Blu-Ice and the distributed control system: Software for data acquisition and instrument control at macromolecular crystallography beamlines. J. Synchrotron Rad. 9, 401-406.
20. Monleon D., Colson K., Moseley H. N. B., Anklin C., Oswald R., Szyperski T. and Montelione G. T. J. 2002. Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture and a set of semi-automated spectral analysis tools. J. Struct. Funct. Genomics 2, 93-101.
21. Muchmore S. W., Olson J., Jones R., Pan J., Blum M., Greer J., Merrick S. M., Magdalinos P. and Nienaber V. 2000. Automated crystal mounting and data collection for protein crystallography. Structure 8, R243-R246.
22. NIH press release 2005. http://www.nih.gov/news/pr/jul2005/nigms-01.htm.
23. Olson D. L., Peck T. L., Webb A., Magin R. L. and Sweedler J. V. 1995. High-resolution microcoil 1H-NMR for mass-limited, nanoliter-volume samples. Science 270, 1967-1970.
24. Page R., Moy K., Sims E. C., Velasquez J., McManus B., Grittini C., Clayton T. L. and Stevens R. C. 2004. Scalable high-throughput micro-expression device for recombinant proteins. Biotechniques 37, 364-370.
25. Page R., Peti W., Wilson I. A., Stevens R. C. and Wuthrich K. 2005. NMR screening and crystal quality of bacterially expressed prokaryotic and eukaryotic proteins in a structural genomics pipeline. Proc. Natl. Acad. Sci. U. S. A. 102, 1901-1905.
26. Page R. and Stevens R. C. 2004. Crystallization data mining in structural genomics: using positive and negative results to optimize protein crystallization screens. Methods 34, 373.
27. Page R., Grzechnik S. K., Canaves J. M., Spraggon G., Kreusch A., Kuhn P., Stevens R. C. and Lesley S. A. 2003. Shotgun crystallization strategy for structural genomics: An optimized two-tiered crystallization screen against the thermotoga maritima proteome. Acta Crystallogr. D 59, 1028-1037.
28. Pantazatos D., Kim J. S., Klock H. E., Stevens R. C., Wilson I. A., Lesley S. A. and Woods V. L., Jr. 2004. Raid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS. Proc. Natl. Acad. Sci. U. S. A. 101, 751-756.
29. Peti W., Norcross J., Eldridge G., O'Neil-Johnson M. 2004. Biomolecular NMR using a microcoil NMR probe-new technique for the chemical shift assignment of aromatic side chains in proteins. J. Am. Chem. Soc. 126, 5873-5878.
30. Peti W., Page R., Moy K., O'Neil-Johnson M., Wilson I. A., Stevens R. C. and Wuthrich K. 2005. Towards miniaturization of a structural genomics pipeline using microexpression and microcoil NMR. J. Struct. Funct. Genomics 6, 259-67.
31. Rota P. A., Oberste M. S., Monroe S. S., Nix W. A., Campagnoli R., Icenogle J. P., Peñaranda S., Bankamp B., Maher K., Chen M. 2003. Characterization of a Novel Coronavirus associated with severe acute respiratory syndrome. Science 300, 1394-1399.
32. Santarsiero B. D., Yegian D. T., Lee C. C., Spraggon G., Gu J., Scheibe D., Uber D. C., Cornell E. W., Nordmeyer R. A., Kolbe W. F. et al. 2002. J. Appl. Cryst. 35, 278.
33. Snell G., Cork C., Nordmeyer R., Cornell E., Meigs G., Yegian D., Jaklevic J., Jin J., Stevens R. C. and Earnest T. 2004. Automated sample mounting and alignment system for biological crystallography at a synchrotron source. Structure 12, 537-545.
34. Stevens R. C. 2000. High-throughput protein crystallization. Curr. Opin. Struct. Biol. 10, 558-563.
35. Stevens R. C. 2004. Long live structural biology. Nat. Struct. Mol. Biol. 11, 293-295.
36. Stewart L. and Burgin A. B. 2005. Whole gene synthesis: A Gene-O-Matic future. In Frontiers in Drug Design and Discovery. Bentham Science Publishers, Ltd, Co-Editors Atta-ur-Rahman, B. A. Springer, G. W. Caldwell.
37. Studier F. W. 2005. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207-34.
38. Venter J. C., Adams M. D., Myers E. W., Li P. W., Mural R. J., Sutton G. G., Smith H. O., Yandell M., Evans C. A., Holt R. A. et al. 2001. The sequence of the human genome. Science. 291, 1304-1351.
39. Wüthrich K. 2003. NMR studies of structure and function of biological macromolecules. J. Biomol. NMR 27, 13-39.
40. Wüthrich K. 1986. NMR of proteins and nucleic acids. New York, Wiley.
41. Zolnai Z., Lee P. T., Li J., Chapman M. R., Newman C. S., Phillips G. N., Jr., Rayment I., Ulrich E. L., Volkman B. F. and Markley J. L. 2003. Project management system for structural and functional proteomics: Sesame. J. Struct. Funct. Genomics 4, 11-23.