An approach to quality management in structural biology: Biophysical selection of proteins for successful crystallization

Journal of Structural Biology

Volumn 162, Issue 3, 2008, Pages 451-459

  Niesen, Frank H ^a   Koch, Anja ^a   Lenski, Ulf ^b,c   Harttig, Ulrich ^c   Roske, Yvette ^b   Heinemann, Udo ^b,d   Hofmann, Klaus Peter ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^c German Genome Resource Center RZPD   (Germany)

^d FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

Differential scanning calorimetry (DSC); Dynamic light scattering (DLS); Fourier transform infrared spectroscopy (FTIR); Protein crystallization; Protein fold; Structural genomics

Indexed keywords

ARTICLE; CRYSTALLIZATION; DIFFERENTIAL SCANNING CALORIMETRY; INFRARED SPECTROSCOPY; LIGHT SCATTERING; PRIORITY JOURNAL; PROTEIN ANALYSIS; TOTAL QUALITY MANAGEMENT;

BIOPHYSICS; CALORIMETRY, DIFFERENTIAL SCANNING; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; FOURIER ANALYSIS; LIGHT; PICHIA; PROTEIN FOLDING; PROTEINS; QUALITY CONTROL; SACCHAROMYCES CEREVISIAE; SCATTERING, RADIATION; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; THERMODYNAMICS;

EID: 44549086572     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2008.03.007     Document Type: Article

References (41)

1. Bergfors, T.M. 1999. Protein crystallization techniques strategies and tips. A Laboratory Manual International University Line La Jolla.
2. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The protein data bank. Nucleic Acids Res. 28 (2000) 235-242
3. Berman H.M., Battistuz T., Bhat T.N., Bluhm W.F., Bourne P.E., Burkhardt K., Feng Z., Gilliland G.L., Iype L., Jain S., Fagan P., Marvin J., Padilla D., Ravichandran V., Schneider B., Thanki N., Weissig H., Westbrook .J.D., and Zardecki C. The protein data bank. Acta Crystallogr. D 58 (2002) 899-907
4. Boettner M., Prinz B., Holz C., Stahl U., and Lang C. High-throughput screening for expression of heterologous proteins in the yeast Pichia pastoris. J. Biotechnol. 99 (2002) 51-62
5. Bourne P.E., Allerston C.K., Krebs W., Li W., Shindyalov I.N., Godzik A., Friedberg I., Liu T., Wild D., Hwang S., Ghahramani Z., Chen L., and Westbrook J. The status of structural genomics defined through the analysis of current targets and structures. Pac. Symp. Biocomput. (2004) 375-386
6. Büssow K., Quedenau C., Sievert V., Tischer J., Scheich C., Seitz H., Hieke B., Niesen F.H., Gotz F., Harttig U., and Lehrach H. A catalog of human cDNA expression clones and its application to structural genomics. Genome Biol. 5 (2004) R71
7. Büssow K., Scheich C., Sievert V., Harttig U., Schultz J., Simon B., Bork P., Lehrach H., and Heinemann U. Structural genomics of human proteins-target selection and generation of a public catalogue of expression clones. Microb. Cell Fact. 4 (2005) 21
8. Chandonia J.M., and Brenner S.E. The impact of structural genomics: expectations and outcomes. Science 311 (2006) 347-351
9. Cooper E.A., and Knutson K. Fourier transform infrared spectroscopy investigations of protein structure. Pharm. Biotechnol. 7 (1995) 101-143
10. Fernandez-Ballester G., Castresana J., Arrondo J.L., Ferragut J.A., and Gonzalez-Ros J.M. Protein stability and interaction of the nicotinic acetylcholine receptor with cholinergic ligands studied by Fourier-transform infrared spectroscopy. Biochem. J. 288 (1992) 421-426
11. Ferré-D'Amaré A.R., and Burley S.K. Use of dynamic light scattering to assess crystallizability of macromolecules and macromolecular assemblies. Structure 2 (1994) 357-359
12. Fink A.L. Protein aggregation: folding aggregates, inclusion bodies and amyloid. Fold. Des. 3 (1998) R9-R23
13. Franks F. Protein stability: the value of 'old literature'. Biophys. Chem. 96 (2002) 117-127
14. Gileadi O., Knapp S., Lee W.H., Marsden B.D., Müller S., Niesen F.H., Kavanagh K.L., Ball L.J., von Delft F., Doyle D.A., Oppermann U.C.T., and Sundström M. The scientific impact of the structural genomics consortium: a protein family and ligand-centered approach to medically-relevant human proteins. J. Struct. Funct. Genomics 8 (2007) 107-119
15. Heinemann U., Frevert J., Hofmann K., Illing G., Maurer C., Oschkinat H., and Saenger W. An integrated approach to structural genomics. Prog. Biophys. Mol. Biol. 73 (2000) 347-362
16. Heinemann U., Bussow K., Mueller U., and Umbach P. Facilities and methods for the high-throughput crystal structural analysis of human proteins. Acc. Chem. Res. 36 (2003) 157-163
17. Holz C., Hesse O., Bolotina N., Stahl U., and Lang C. A micro-scale process for high-throughput expression of cDNAs in the yeast Saccharomyces cerevisiae. Protein Expr. Purif. 25 (2002) 372-378
18. Holz C., Prinz B., Bolotina N., Sievert V., Büssow K., Simon B., Stahl U., and Lang C. Establishing the yeast Saccharomyces cerevisiae as a system for expression of human proteins on a proteome-scale. J. Struct. Funct. Genomics 4 (2003) 97-108
19. Ismail A.A., Mantsch H.H., and Wong P.T. Aggregation of chymotrypsinogen: portrait by infrared spectroscopy. Biochim. Biophys. Acta 1121 (1992) 183-188
20. Manjasetty B.A., Delbrück H., Pham D.T., Mueller U., Fieber-Erdmann M., Scheich C., Sievert V., Büssow K., Niesen F.H., Weihofen W., Loll B., Saenger W., and Heinemann U. Crystal structure of Homo sapiens protein hp14.5. Proteins 54 (2004) 797-800
21. Manjasetty B.A., Quedenau C., Sievert V., Büssow K., Niesen F., Delbrück H., and Heinemann U. X-ray structure of human gankyrin, the product of a gene linked to hepatocellular carcinoma. Proteins 55 (2004) 214-217
22. Martin S.R., and Schilstra M.J. Circular dichroism and its application to the study of biomolecules. Methods Cell. Biol. 84 (2008) 263-293
23. McPherson A. Protein crystallization in the structural genomics era. J. Struct. Funct. Genomics 5 (2004) 3-12
24. Middaugh C.R., Mach H., Ryan J.A., Sanyal G., and Volkin D.B. Infrared spectroscopy. Methods Mol. Biol. 40 (1995) 137-156
25. Mueller U., Büssow K., Diehl A., Bartl F.J., Niesen F.H., Nyarsik L., and Heinemann U. Rapid purification and crystal structure analysis of a small protein carrying two terminal affinity tags. J. Struct. Funct. Genomics 4 (2003) 217-225
26. Niesen F.H., Berglund H., and Vedadi M. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat. Protoc. 2 (2007) 2212-2221
27. Pace C.N., Vajdos F., Fee L., Grimsley G., and Gray T. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4 (1995) 2411-2423
28. Plotnikov V., Rochalski A., Brandts M., Brandts J.F., Williston S., Frasca V., and Lin L.N. An autosampling differential scanning calorimeter instrument for studying molecular interactions. Assay Drug Dev. Technol. 1 (2002) 83-90
29. Pusey M.L., Liu Z.J., Tempel W., Praissman J., Lin D., Wang B.C., Gavira J.A., and Ng J.D. Life in the fast lane for protein crystallization and X-ray crystallography. Prog. Biophys. Mol. Biol. 88 (2005) 359-386
30. Scheich C., Sievert V., and Büssow K. An automated method for high-throughput protein purification applied to a comparison of His-tag and GST-tag affinity chromatography. BMC Biotechnol. 3 (2003) 12
31. Scheich C., Leitner D., Sievert V., Leidert M., Schlegel B., Simon B., Letunic I., Bussow K., and Diehl A. Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis. BMC Struct. Biol. 4 (2004) 4
32. Schein C.H. Solubility as a function of protein structure and solvent components. Biotechnology 8 (1990) 308-317
33. Schmitz K.S. An Introduction to Dynamic Light Scattering by Macromolecules (1990), Academic Press, Boston, London
34. Terwilliger T.C. Structural genomics in North America. Nat. Struct. Biol. 7 Suppl. (2000) 935-939
35. Todd A.E., Marsden R.L., Thornton J.M., and Orengo C.A. Progress of structural genomics initiatives: an analysis of solved target structures. J. Mol. Biol. 348 (2005) 1235-1260
36. Vedadi M., Niesen F.H., Allali-Hassani A., Fedorov O.Y., Finerty Jr. P.J., 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. Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination. Proc. Natl. Acad. Sci. USA 103 (2006) 15835-15840
37. Veesler S., Marcq S., Lafont S., Astier J.P., and Boistelle R. Influence of polydispersity on protein crystallization: a quasi-elastic light-scattering study applied to alpha-amylase. Acta Crystallogr. D 50 (1994) 355-360
38. Wilson W.W. Light scattering as a diagnostic for protein crystal growth-a practical approach. J. Struct. Biol. 142 (2003) 56-65
39. Yokoyama S., Hirota H., Kigawa T., Yabuki T., Shirouzu M., Terada T., Ito Y., Matsuo Y., Kuroda Y., Nishimura Y., Kyogoku Y., Miki K., Masui R., and Kuramitsu S. Structural genomics projects in Japan. Nat. Struct. Biol. 7 Suppl. (2000) 943-945
40. Zhang C., and Kim S.H. Overview of structural genomics: from structure to function. Curr. Opin. Chem. Biol. 7 (2003) 28-32
41. Zulauf M., and D'Arcy A. Light scattering of proteins as a criterion for crystallization. J. Cryst. Growth 122 (1992) 102-106