Small-scale, semi-automated purification of eukaryotic proteins for structure determination
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Knaust RK, Nordlund P (2001) Screening for soluble expression of recombinant proteins in a 96-well format. Anal Biochem 297:79–85
Stevens RC (2000) Design of high-throughput methods of protein production for structural biology. Structure 8:R177–185
Kawasaki M, Inagaki F (2001) Random PCR-based screening for soluble domains using green fluorescent protein. Biochem Biophys Res Commun 280:842–844
King DA, Hall BE, Iwamoto MA, Win KZ, Chang JF, Ellenberger T (2006) Domain structure and protein interactions of the silent information regulator Sir3 revealed by screening a nested deletion library of protein fragments. J Biol Chem 281:20107–20119
Reich S, Puckey LH, Cheetham CL, Harris R, Ali AA, Bhattacharyya U, Maclagan K, Powell KA, Prodromou C, Pearl LH, Driscoll PC, Savva R (2006) Combinatorial domain hunting: an effective approach for the identification of soluble protein domains adaptable to high-throughput applications. Protein Sci 15:2356–2365
Kato A, Maki K, Ebina T, Kuwajima K, Soda K, Kuroda Y (2007) Mutational analysis of protein solubility enhancement using short peptide tags. Biopolymers 85:12–18
Zhou P, Lugovskoy AA, Wagner G (2001) A solubility-enhancement tag (SET) for NMR studies of poorly behaving proteins. J Biomol NMR 20:11–14
Garrard SM, Longenecker KL, Lewis ME, Sheffield PJ, Derewenda ZS (2001) Expression, purification, and crystallization of the RGS-like domain from the Rho nucleotide exchange factor, PDZ-RhoGEF, using the surface entropy reduction approach. Protein Expr Purif 21:412–416
Derewenda ZS, Vekilov PG (2006) Entropy and surface engineering in protein crystallization. Acta Crystallogr D Biol Crystallogr 62:116–124
Rayment I (1997) Reductive alkylation of lysine residues to alter crystallization properties of proteins. Methods Enzymol 276:171–179
Galvao-Botton LM, Katsuyama AM, Guzzo CR, Almeida FC, Farah CS, Valente AP (2003) High-throughput screening of structural proteomics targets using NMR. FEBS Lett 552:207–213
Scheich C, Leitner D, Sievert V, Leidert M, Schlegel B, Simon B, Letunic I, Bussow K, Diehl A (2004) Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis. BMC Struct Biol 4:4
Chayen NE, Saridakis E (2002) Protein crystallization for genomics: towards high-throughput optimization techniques. Acta Crystallogr D Biol Crystallogr 58:921–927
Kimber MS, Vallee F, Houston S, Necakov A, Skarina T, Evdokimova E, Beasley S, Christendat D, Savchenko A, Arrowsmith CH, Vedadi M, Gerstein M, Edwards AM (2003) Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens. Proteins 51:562–568
Yee AA, Savchenko A, Ignachenko A, Lukin J, Xu X, Skarina T, Evdokimova E, Liu CS, Semesi A, Guido V, Edwards AM, Arrowsmith CH (2005) NMR and X-ray crystallography, complementary tools in structural proteomics of small proteins. J Am Chem Soc 127:16512–16517
Smialowski P, Martin-Galiano AJ, Cox J, Frishman D (2007) Predicting experimental properties of proteins from sequence by machine learning techniques. Curr Protein Pept Sci 8:121–133
Goh CS, Lan N, Douglas SM, Wu B, Echols N, Smith A, Milburn D, Montelione GT, Zhao H, Gerstein M (2004) Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis. J Mol Biol 336:115–130
Watson JD, Todd AE, Bray J, Laskowski RA, Edwards A, Joachimiak A, Orengo CA, Thornton JM (2003) Target selection and determination of function in structural genomics. IUBMB Life 55:249–255
Brodsky O, Cronin CN (2006) Economical parallel protein expression screening and scale-up in Escherichia coli. J Struct Funct Genomics 7:101–108
Canaves JM, Page R, Wilson IA, Stevens RC (2004) Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics. J Mol Biol 344:977–991
Nguyen H, Martinez B, Oganesyan N, Kim R (2004) An automated small-scale protein expression and purification screening provides beneficial information for protein production. J Struct Funct Genomics 5:23–27
Page R, Moy K, Sims EC, Velasquez J, McManus B, Grittini C, Clayton TL, Stevens RC (2004) Scalable high-throughput micro-expression device for recombinant proteins. Biotechniques 37:364, 366, 368 passim
Peti W, Page R, Moy K, O’Neil-Johnson M, Wilson IA, Stevens RC, Wuthrich K (2005) Towards miniaturization of a structural genomics pipeline using micro-expression and microcoil NMR. J Struct Funct Genomics 6:259–267
Smialowski P, Schmidt T, Cox J, Kirschner A, Frishman D (2006) Will my protein crystallize? A sequence-based predictor. Proteins 62:343–355
Sugar FJ, Jenney FE Jr, Poole FL 2nd, Brereton PS, Izumi M, Shah C, Adams MW (2005) Comparison of small- and large-scale expression of selected Pyrococcus furiosus genes as an aid to high-throughput protein production. J Struct Funct Genomics 6:149–158
Vincentelli R, Bignon C, Gruez A, Canaan S, Sulzenbacher G, Tegoni M, Campanacci V, Cambillau C (2003) Medium-scale structural genomics: strategies for protein expression and crystallization. Acc Chem Res 36:165–172
Tyler RC, Sreenath HK, Singh S, Aceti DJ, Bingman CA, Markley JL, Fox BG (2005) Auto-induction medium for the production of [U-15N]- and [U-13C, U-15N]-labeled proteins for NMR screening and structure determination. Protein Expr Purif 40:268–278
Sreenath HK, Bingman CA, Buchan BW, Seder KD, Burns BT, Geetha HV, Jeon WB, Vojtik FC, Aceti DJ, Frederick RO, Phillips GN Jr, Fox BG (2005) Protocols for production of selenomethionine-labeled proteins in 2-l polyethylene terephthalate bottles using auto-induction medium. Protein Expr Purif 40:256–267
Jeon WB, Aceti DJ, Bingman CA, Vojtik FC, Olson AC, Ellefson JM, McCombs JE, Sreenath HK, Blommel PG, Seder KD, Burns BT, Geetha HV, Harms AC, Sabat G, Sussman MR, Fox BG, Phillips GN Jr (2005) High-throughput purification and quality assurance of Arabidopsis thaliana proteins for eukaryotic structural genomics. J Struct Funct Genomics 6:143–147
Tyler RC, Aceti DJ, Bingman CA, Cornilescu CC, Fox BG, Frederick RO, Jeon WB, Lee MS, Newman CS, Peterson FC, Phillips GN Jr, Shahan MN, Singh S, Song J, Sreenath HK, Tyler EM, Ulrich EL, Vinarov DA, Vojtik FC, Volkman BF, Wrobel RL, Zhao Q, Markley JL (2005) Comparison of cell-based and cell-free protocols for producing target proteins from the Arabidopsis thaliana genome for structural studies. Proteins 59:633–643
Blommel PG, Martin PA, Wrobel RL, Steffen E, Fox BG (2006) High efficiency single step production of expression plasmids from cDNA clones using the flexi vector cloning system. Protein Expr Purif 47:562–570
Blommel PG, Becker KJ, Duvnjak P, Fox BG (2007) Enhanced bacterial protein expression during auto-induction obtained by alteration of lac repressor dosage and medium composition. Biotechnol Prog 23:585–598
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp 15.44–15.48
Klein RD, Wells RD (1982) Effects of neighboring DNA homopolymers on the biochemical and physical properties of the Escherichia coli lactose promoter. I. Cloning and characterization studies. J Biol Chem 257:12954–12961
Patterson GH, Knobel SM, Sharif WD, Kain SR, Piston DW (1997) Use of the green fluorescent protein and its mutants in quantitative fluorescence microscopy. Biophys J 73:2782–2790
Yang TT, Cheng L, Kain SR (1996) Optimized codon usage and chromophore mutations provide enhanced sensitivity with the green fluorescent protein. Nucleic Acids Res 24:4592–4593
Crameri A, Whitehorn EA, Tate E, Stemmer WP (1996) Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat Biotechnol 14:315–319
Prodromou C, Pearl LH (1992) Recursive PCR: a novel technique for total gene synthesis. Protein Eng 5:827–829
Casimiro DR, Toy-Palmer A, Blake RC 2nd, Dyson HJ (1995) Gene synthesis, high-level expression, and mutagenesis of Thiobacillus ferrooxidans rusticyanin: his 85 is a ligand to the blue copper center. Biochemistry 34:6640–6648
Casimiro DR, Wright PE, Dyson HJ (1997) PCR-based gene synthesis and protein NMR spectroscopy. Structure 5:1407–1412
Sambrook J, Fritsch EF, Maniatis T (2001) Molecular cloning, a laboratory manual. Cold Spring Harbor, Cold Spring Harbor Laboratory Press, New York
Wood WB (1966) Host specificity of DNA produced by Escherichia coli: bacterial mutations affecting the restriction and modification of DNA. J Mol Biol 16:118–133
Arber W (1964) Host specificity of DNA produced by Escherichia coli. 3. Effects on transduction mediated by lambda Dg. Virology 23:173–182
Studier FW (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41:207–234
Blommel PG, Fox BG (2007) A combined approach to improving large-scale production of tobacco etch virus protease. Protein Expr Purif 55(1):53–68
The CCP4 suite: programs for protein crystallography (1994) Acta Crystallogr D Biol Crystallogr 50:760–763
Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132
Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53:240–255
Leahy DJ, Hendrickson WA, Aukhil I, Erickson HP (1992) Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein. Science 258:987–991
Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, J. Collado-Vides, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453–1474
Welch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J, Stroud D, Mayhew GF, Rose DJ, Zhou S, Schwartz DC, Perna NT, Mobley HL, Donnenberg MS, Blattner FR (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 99:17020–17024