Protein production and purification

Nature Methods

Volumn 5, Issue 2, 2008, Pages 135-146

  Gräslund, Susanne ^a   Nordlund, Pär ^a   Weigelt, Johan ^a   Hallberg, B Martin ^a   Bray, James ^b   Gileadi, Opher ^b   Knapp, Stefan ^b   Oppermann, Udo ^b   Arrowsmith, Cheryl ^c   Hui, Raymond ^c   Ming, Jinrong ^c   dhe Paganon, Sirano ^c   Park, Hee Won ^c   Savchenko, Alexei ^c   Yee, Adelinda ^c   Edwards, Aled ^c   Vincentelli, Renaud ^d   Cambillau, Christian ^d   Kim, Rosalind ^e   Kim, Sung Hou ^e   Rao, Zihe ^f   Shi, Yunyu ^g   Terwilliger, Thomas C ^h   Kim, Chang Yub ^h   Hung, Li Wei ^h   Waldo, Geoffrey S ^h   Peleg, Yoav ⁱ   Albeck, Shira ⁱ   Unger, Tamar ⁱ   Dym, Orly ⁱ   Prilusky, Jaime ⁱ   Sussman, Joel L ⁱ   Stevens, Ray C ^j   Lesley, Scott A ^j,k   Wilson, Ian A ^j,k   Joachimiak, Andrzej ^l   Collart, Frank ^l   Dementieva, Irina ^l   Donnelly, Mark I ^l   Eschenfeldt, William H ^l   Kim, Youngchang ^l   Stols, Lucy ^l   Wu, Ruying ^l   Zhou, Min ^l   Burley, Stephen K ^m   Emtage, J Spencer ^m   Sauder, J Michael ^m   Thompson, Devon ^m   Bain, Kevin ^m   Luz, John ^m   Gheyi, Tarun ^m   Zhang, Fred ^m   Atwell, Shane ^m   Almo, Steven C ⁿ   Bonanno, Jeffrey B ⁿ   Fiser, Andras ⁿ   Swaminathan, Sivasubramanian ^o   Studier, F William ^o   Chance, Mark R ^p   Sali, Andrej ^q   Acton, Thomas B ^r   Xiao, Rong ^r   Zhao, Li ^r   Ma, Li Chung ^r   Hunt, John F ^s   Tong, Liang ^s   Cunningham, Kellie ^r   Inouye, Masayori ^r   Anderson, Stephen ^r   Janjua, Heleema ^r   Shastry, Ritu ^r   Ho, Chi Kent ^r   Wang, Dongyan ^r   Wang, Huang ^r   Jiang, Mei ^r   Montelione, Gaetano T ^r   Stuart, David I ^t   Owens, Raymond J ^t   Daenke, Susan ^t   Schütz, Anja ^u   Heinemann, Udo ^u   Yokoyama, Shigeyuki ^v   Büssow, Konrad ^u,w   Gunsalus, Kristin C ^r,x   more..

^a KAROLINSKA INSTITUTE   (Sweden)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF TORONTO   (Canada)

^d CNRS   (France)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f TSINGHUA UNIVERSITY   (China)

^g UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^h LOS ALAMOS NATIONAL LABORATORY   (United States)

ⁱ WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^j SCRIPPS RESEARCH INSTITUTE   (United States)

^k GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^l ARGONNE NATIONAL LABORATORY   (United States)

^m SGX Pharmaceuticals Inc   (United States)

ⁿ ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^o BROOKHAVEN NATIONAL LABORATORY   (United States)

^p CASE WESTERN RESERVE UNIVERSITY   (United States)

^q UNIVERSITY OF CALIFORNIA   (United States)

^r RUTGERS UNIVERSITY   (United States)

^s Och Spine at New York Presbyterian Hospitals   (United States)

^t UNIVERSITY OF OXFORD   (United Kingdom)

^u MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^v Yokohama Institute   (Japan)

^w HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^x NEW YORK UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID DERIVATIVE; BACTERIAL PROTEIN; BACTERIUM LYSATE; CHAPERONE; COMPLEMENTARY DNA; ESCHERICHIA COLI PROTEIN; GENOMIC DNA; HISTIDINE; HYBRID PROTEIN; MUTANT PROTEIN; RECOMBINANT PROTEIN; RNA POLYMERASE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANALYTIC METHOD; BACTERIAL STRAIN; CARBOXY TERMINAL SEQUENCE; ESCHERICHIA COLI; EXPRESSION VECTOR; GEL FILTRATION CHROMATOGRAPHY; GENETIC SELECTION; HUMAN; MOLECULAR CLONING; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRECIPITATION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; PROTEIN VARIANT; REVIEW; STRUCTURAL GENOMICS; STRUCTURAL PROTEOMICS; ULTRAVIOLET SPECTROSCOPY; FRACTIONATION; ISOLATION AND PURIFICATION; METABOLISM; PHYSICAL CHEMISTRY; PROCEDURES; PROTEIN ENGINEERING; PROTEOMICS;

CHEMICAL FRACTIONATION; CHEMISTRY, PHYSICAL; PROTEIN ENGINEERING; PROTEOMICS; RECOMBINANT PROTEINS;

EID: 38749142906     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth.f.202     Document Type: Review

References (90)

1. Sauder, J.M. et al. High throughput protein production and crystallization at NYSGXRC. in Structural Proteomics: High-Throughput Methods, Vol. 426 (eds. B. Kobe, M.Guss & H. Thomas) 561-575 (Humana Press, Totowa, New Jersey, USA, 2008).
2. Büssow, K. et al. Structural genomics of human proteins-target selection and generation of a public catalogue of expression clones. Microb. Cell Fact. 4, 21 (2005).
3. Heinemann, U., Büssow, K., Mueller, U. & Umbach, P. Facilities and methods for the high-throughput crystal structural analysis of human proteins. Accounts Chem. Res. 36, 157-103 (2003).
4. Banci, L. et al. First step's towards effective methods in exploiting high-throughput technologies for the determination of human protein structures of high-biomedical value. Acta Crystallogr. D62, 1208-1217 (2006).
5. Aricescu, A.R. et al. Eukaryotic expression: Developments for structural proteomics. Acta Crystallogr. D62, 1114-1124 (2006).
6. Heinemann, U. Establishing a structural genomics platform: The Berlin-based Protein Structure Factory. Gene Funct. Dis. 3, 25-32 (2002).
7. Scheich, C., Kummel, D., Soumailakakis, D., Heinemann, U. & Büssow, K. Vectors for co-expression of an unrestrictgd number of proteins. Nucleic Acids Res. 35, e43 (2007).
8. Bartlam, M., Xu, Y. & Rao, Z. Structural proteomics of the SARS coronavirus: A model response to emerging infectious diseases. J. Struct. Funct. Genomics 8, 85-97 (2007).
9. Gong, W.M. et al. Structural genomics efforts at the Chinese Academy of Sciences and Peking University. J. Struct. Funct. Genomics 4, 137-139 (2003).
10. Albeck, S. et al. Three-dimensional structure determination of proteins related to human health in their functional context at The Israel Structural Proteomics Center (ISPC). Acta Crystallogr. D61, 1364-1372 (2005).
11. Lesley, S.A. et al. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc. Natl. Acad. Sci. USA 99, 11664-11669 (2002).
12. Montelione, G.T., Zheng, D., Huang, Y.J., Gunsalus, K.C. & Szyperski, T. Protein NMR spectroscopy in stuctural genomics. Nat. Struct. Biol. 7 (Suppl.), 982-985 (2000).
13. Acton, T.B. et al. Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium. Methods Enzymol. 394, 210-243 (2005).
14. Alzari, P.M. et al. Implementation of semi-automated cloning and prokaryotic expression screening: The impact of SPINE. Acta Crystallogr. D62, 1103-1113 (2006).
15. Gileadi, O. The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-retevant human proteins. J. Struct. Funct. Genomics 8, 107-119 (2007).
16. Gileadi, O. et al. Methods in Molecular Biology. in Structural Proteomics: High-Throughput Methods. Vol. 426 (eds., B. Kobe, M. Guss & T. Huber) 222-246 (Humana Press, Totowa, New Jersey, USA, 2008).
17. You, J., Cohen, R.E. & Pickart, C.M. Construct for high-level expression and low misincorporation of lysine for arginine during expression of pET-encoded eukaryotic proteins in Escherichia coli. Biotechniques 27, 950-954 (1999).
18. Klock, H.E., Koesema, E.J., Knuth, M.W. & Lesley, S.A. Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts. Proteins published online, doi: 10.1002/prot.21786 (14 November 2007).
19. Gräslund, S. et al. The use of systematic N- and C-terminal deletions to promote production and structural studies of recombinant proteins. Protein Expr. Purif. (in the press).
20. Ginalski, K., Elofsson, A., Fischer, D. & Rychlewski, L. 3D-Jury: A simple approach to improve protein structure predictions. Bioinformatics 19, 1015-1018 (2003).
21. Ward, J.J., McGuffin, L.J., Bryson, K., Buxton, B.F. & Jones, D.T. The DISOPRED server for the prediction of protein disorder. Bioinformatics 20, 2138-2139 (2004).
22. Yang, Z.R., Thomson, R., McNeil, P. & Esnouf, R.M. RONN: The bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21, 3369-3376 (2005).
23. Cornvik, T. et al. An efficient anod generic strategy for producing soluble human proteins and domains in E. coli by screening construct libraries. Proteins 65, 266-273 (2006).
24. Gao, X. et al. High-throughput limited proteolysis/mass spectrometry for protein domain elucidation. J. Struct. Funct. Genomics 5, 129-134 (2005).
25. Hartley, J.L., Temple, G.F. & Brasch, M.A. DNA cloning using in vitro site-specific recombination. Genome Res. 10, 1788-1795 (2000).
26. Aslanidis, C. & de Jong, P.J. Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res. 18, 6069-6074 (1990).
27. Landy, A. Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu. Rev. Biochem. 58, 913-949 (1989).
28. Guo, F., Gopaul, D.N. & Van Duyne, G.D. Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse. Proc. Natl. Acad. Sci. USA 96, 7143-7148 (1999).
29. Hammarström, M., Hellgren, N., van Den Berg, S., Berglund, H. & Härd, T. Rapid screening for improved solubility of small human proteins produced as fusion proteins in Escherichia coli. Protein Sci. 11, 313-321 (2002).
30. Peti, W. & Page, R. Strategies to maximize heterotogous protein expression in Escherichia coli with minimal cost. Protein Expr. Purif. 51, 1-10 (2007).
31. Braun, P. & LaBaer, J. High throughput protein production for functional proteomics. Trends Biotechnol. 21, 383-388 (2003).
32. Vincentelli, R. et al. Medium-scate structural genomics: strategies for protein expression and crystallization. Accounts Chem. Res. 36, 165-172 (2003).
33. Studier, F.W., Rosenberg, A.H., Dunn, J.J. & Dubendorff, J.W. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 185, 60-89 (1990).
34. Uhlen, M., Forsberg, G., Moks, T., Hartmanis, M. & Nilsson, B. Fusion proteins in biotechnology. Curr. Opin. Biotechnol. 3, 363-369 (1992).
35. Arnau, J., Lauritzen, C., Petersen, G.E. & Pedersen, J. Current strategies for the use of affinity tags and tag removal for the purification of recombinant proteins. Protein Expr. Purif. 48 1-13 (2006).
36. Carrington, J.C. & Dougherty, W.G. A viral cleavage site cassette: identification of amino acid sequences required for tobacco etch virus polyprotein processing. Proc. Natl. Acad. Sci. USA 85, 3391-3395 (1988).
37. Porath, J. Immobilized metal ion affinity chromatography. Protein Expr. Purif. 3, 263-281 (1992).
38. Nallamsetty, S. & Waugh, D. Solubility-enhancing proteins MBP and NusA play a passive rote in the folding of their fusion partners. Protein Expr. Purif. 45, 175-182 (2006).
39. 6-maltose binding protein fusion tag. Nat. Protoc. 2, 383-391 (2007).
40. Waugh, D.S. Making the most of affinity tags. Trends Biotechnol. 23, 316-320 (2005).
41. Carson, M., Johnson, D.H., McDonald, H., Brouillette, C. & Delucas, L.J. Histag impact on structure. Acta Crystallogr. 63, 295-301 (2007).
42. Dubendorff, J.W. & Studier, F.W. Controlling basal expression in an inducible T7 expression system by blocking the target T7 promoter with lac repressor. J. Mol. Biol. 219, 45-59 (1991).
43. Wycuff, D.R. & Matthews, K.S. Generation of an AraC-araBAD promoter-regulated T7 expression system. Anal. Biochem. 277, 67-73 (2000).
44. Shimizu, Y. et al. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19, 751-755 (2001).
45. Guzman, L.M., Belin, D., Carson, M.J. & Beckwith, J. Tight regulation, modulation, and high-level expression by vectors containing the arabinose pBAD promoter. J. Bocteriol. 177, 4121-4130 (1995).
46. Studier, F.W. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207-234 (2005).
47. Lesley, S.A. High-throughput proteomics: Protein expression and purification in the postgenomic world. Protein Expr. Purif. 22 159-164 (2001).
48. Tunac, J. A new high-aeration capacity shake-flask system. J. Ferm. Bioeng. 68, 15-159 (1989).
49. Brodsky, O. & Cronin, C.N. Economical parallel protein expression screening and scale-up in Escherichia coli. J. Struct. Funct. Genomics 7, 101-108 (2006).
50. Vera, A., Gonzalez-Montalban, N., Aris, A. & Villaverde, A. The conformational quality of insoluble recombinant proteins is enhanced at low growth temperatures. Biotechnol. Bioeng. 96, 1101-1106 (2007).
51. Berrow, N.S. et al. Recombinant protein expression and solubility screening in Escherichia coli: A comparative study. Acta Crystallogr. D62, 1218-1226 (2006).
52. Page, R. et al. Scalable high-throughput micro-expression device for recombinant proteins. Biotechniques 37, 364-370 (2004).
53. Bradford, M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254 (1976).
54. Bolanos-Garcia, V.M. & Davies, O.R. Structural analysis and classification of native proteins from E. coli commonly co-purified by immobilised metal affinity chromatography. Biochim. Biophys. Acta 1760, 1304-1313 (2006).
55. Howell, J.M., Winstone, T.L., Coorssen, J.R. & Turner, R.J. An evaluation of in vitro protein-protein interaction techniques: Assessing contaminating background proteins. Proteomics 6, 2050-2069 (2006).
56. Bullock, A.N., Debreczeni, J., Amos, A.L., Knapp, S. & Turk, B.E. Structure and substrate specificity of the Pim-1 kinase. J. Biol. Chem. 280, 41675-41682 (2005).
57. Alam, M., Ho, S., Vance, D.E. & Lehner, R. Heterologous expression, purification, and characterization of human triacylglycerol hydrolase. Protein Expr. Purif. 24, 33-42 (2002).
58. Kapust, R.B. & Waugh, D.S. Escherichia coli maltose-binding protein is uncommonly effective at promoting the solubility of polypeptides to which it is fused. Protein Sci. 8, 1668-1674 (1999).
59. Iakoucheva, L.M., Brown, C.J., Lawton, J.D., Obradovic, Z. & Dunker, A.K. Intrinsic disorder in cell-signaling and cancer-associated proteins. J. Mol. Biol. 323, 573-584 (2002).
60. Frenkiel-Krispin D. et al. Plant transformation by Agrobacterium tumefaciens: Modulation of single-stranded DNA-VirE2 complex assembly by VirE1. J. Biol. Chem. 282, 3458-3464 (2007).
61. Tolia, N.H. & Joshua-Tor, L. Strategies for protein coexpresion in Escherichia coli. Nat. Methods 3, 55-64 (2006).
62. Romier, C. et al. Co-expression of protein complexes in prokaryotic and eukaryotic hosts: Experimental procedures, database tracking and case studies. Acta Crystallogr. 62, 1232-1242 (2006).
63. Bullock, A.N., Debreczeni, J.E., Edwards, A.M., Sundström,M. & Knapp, S. Crystal structure of the SOCS2-elongin C-elongin B complex defines a prototypical SOCS box ubiquitin ligase. Proc. Natl. Acad. Sci. USA 103, 7637-7642 (2006).
64. Vedadi, M. et al. Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination. Proc. Natl. Acad. Sci. USA 103, 15835-15840 (2006).
65. Niesen, F.H., Berglund, H. & Vedadi, M. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat. Protoc. 2, 2212-2221 (2007).
66. Elleby, B. et al. High-level production and optimization of monodispersity of a 11beta-hydroxysteroid dehydrogenase type 1. Biochim. Biophys. Acta 1700, 199-207 (2004).
67. Strauss, A. et al. Improved expression of kinases in Baculovirus-infected insect cells upon addition of specific kinase inhibitors to the culture helpful for structural studies. Protein Expr. Purif. 56, 167-176 (2007).
68. Smith, G.E., Summers, M.D. & Fraser, M.J. Production of human beta interferon in insect tells infected with a baculovirus expression vector. Mol. Cell. Biol. 3, 2156-2165 (1983).
69. Boettner, M., Prinz, B., Holz, C., Stahl, U. & Lang, C. High-throughput screening for expression of heterologous proteins in the yeast Pichia pastoris. J. Biotechnol. 99, 51-62 (2002).
70. Holz, C., Hesse, O., Bolotina, N., Stahl, U. & Lang, C. A micro-scale process for high-throughput expression of cDNAs in the yeast Saccharomyces cerevisiae. Protein Expr. Purif. 25, 372-378 (2002).
71. Aricescu, A.R., Lu, W. & Jones, E.Y. A time- and cost-efficient system for high-level protein production in mammalian cells. Acta Crystallogr. D62, 1243-1250 (2006).
72. Yokoyama, S. Protein expression systems far structural genomics and proteomics. Curr. Opin. Chem. Biol. 7, 39-43 (2003).
73. Kigawa, T. et al. Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J. Struct. Funct. Genomics 5, 63-68 (2004).
74. Matsuda, T. et al. Cell-free synthesis of zinc-binding proteins. J. Struct. Funct. Genomics 7, 93-100 (2006).
75. Endo, Y. & Sawasaki, T. Cell-free expression systems for eukaryotic protein production. Curr. Opin. Biotechnol. 17, 373-380 (2006).
76. Mikami, S., Masutani, M., Sonenberg, N., Yokoyama, S. & Imataka, H. An efficient mammalian cell-free translation system supplemented with translation factors. Protein Expr. Purif. 46, 348-357 (2006).
77. Yokoyama, S., Terwilliger, T.C., Kuramitsu, S., Moras, D. & Sussman, J.L. RIKEN aids international structural genomics efforts. Nature 445, 21 (2007).
78. Murayama, K. et al. Crystal structure of the rac activator, Asef, reveals its autoinhibitory mechanism. J. Biol. Chem. 282, 4238-4242 (2007).
79. Miyazono, K. et al. Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic Acids Res. 35, 1908-1918 (2007).
80. Nishihara, K., Kanemori, M., Yanagi, H. & Yura, T. Overexpression of trigger factor prevents aggregation of recombinant proteins in Escherichia coli. Appl. Environ. Microbiol. 66, 884-889 (2000).
81. Wynn, R.M., Song, J.L. & Chuang, D.T. GroEL/GroES promote dissociation/reassociation cycles of a heterodimeric intermediate during alpha(2)beta(2) protein assembly. Iterative annealing at the quaternary structure level. J. Biol. Chem. 275, 2786-2794 (2000).
82. Kaiser, C.M. et al. Real-time observation of trigger factor function on translating ribosomes. Nature 444, 455-460 (2006).
83. Willis, M.S. et al. Investigation of protein refolding using a fractional factorial screen: A study of reagent effects and interactions. Protein Sci. 14, 1818-1826 (2005).
84. Vincentelli, R. et al. High-throughput automated refolding screening of inclusion bodies. Protein Sci. 13, 2782-2792 (2004).
85. Kim, S. H. et al. Structural genomics of minimal organisms and protein fold space. J. Struct, Funct. Genomics 6, 63-70 (2005).
86. Lesley, S.A. & Wilson, I.A. Protein production and crystallization at the joint center for structural genomics. J. Struct. Funct. Genomics 6, 71-79 (2005).
87. Kreusch, A. & Lesley, S.A. High throughput cloning, expression and purification technologies. in Genomics, Proteomics, and Vaccines (ed., G. Grandi) 171-184 (Wiley Press, Chichester, UK, 204).
88. McMullan, D. et al. High-throughput protein production for X-ray Crystallography and use of size exclusion chromatography to validate or refute computational biological unit predictions. J. Struct. Funct. Genomics 6, 135-141 (2005).
89. Stols L., Millard, C.S., Dementieva, I. & Donnelly, M.I. Production of selenomethionine-labeled proteins in two-liter plastic bottles for structure determination. J. Struct. Funct. Genomics 5, 95-102 (2004).
90. Geerlof, A. et al. The impact of protein characterization in structural proteomics. Acta Crystallogr. D62, 1125-1136 (2006).