Experimental mapping of soluble protein domains using a hierarchical approach

Nucleic Acids Research

Volumn 39, Issue 18, 2011, Pages

  Pedelacq, Jean Denis ^a,b   Nguyen, Hau B ^c   Cabantous, Stephanie ^b,d,e   Mark, Brian L ^f   Listwan, Pawel ^c   Bell, Carolyn ^c   Friedland, Natasha ^c   Lockard, Meghan ^c   Faille, Alexandre ^a,b   Mourey, Lionel ^a,b   Terwilliger, Thomas C ^c   Waldo, Geoffrey S ^c  

^a INSTITUT DE PHARMACOLOGIE ET DE BIOLOGIE STRUCTURALE   (France)

^b UNIVERSITÉ DE TOULOUSE   (France)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d CANCER RESEARCH CENTER OF TOULOUSE   (France)

^e INSTITUT CLAUDIUS REGAUD   (France)

^f UNIVERSITY OF MANITOBA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACYLTRANSFERASE DEHYDROGENASE; AMINO ACID; DIHYDROFOLATE REDUCTASE; ENOYL REDUCTASE; OXIDOREDUCTASE; PHOSPHATIDYLINOSITOL 3 KINASE; POLYKETIDE SYNTHASE; PROTEIN P85; PROTEIN PPSC; UNCLASSIFIED DRUG;

ARTICLE; ASSAY; BIOTECHNOLOGY; CELL MEMBRANE; COST EFFECTIVENESS ANALYSIS; CRYSTAL STRUCTURE; DNA LIBRARY; DNA SEQUENCE; ENZYME SUBUNIT; EXPERIMENTAL STUDY; LIPOGENESIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN TARGETING; SPLIT GFP ASSAY; X RAY;

CLASS IA PHOSPHATIDYLINOSITOL 3-KINASE; CRYSTALLOGRAPHY, X-RAY; GENE LIBRARY; GREEN FLUORESCENT PROTEINS; MYCOBACTERIUM TUBERCULOSIS; POLYKETIDE SYNTHASES; POLYMERASE CHAIN REACTION; PROTEIN STRUCTURE, TERTIARY; SOLUBILITY; TETRAHYDROFOLATE DEHYDROGENASE;

MYCOBACTERIUM TUBERCULOSIS;

EID: 80054069005     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr548     Document Type: Article

References (38)

1. Pedelacq, J.D., Piltch, E., Liong, E.C., Berendzen, J., Kim, C.Y., Rho, B.S., Park, M.S., Terwilliger, T.C. and Waldo, G.S. (2002) Engineering soluble proteins for structural genomics. Nat. Biotechnol., 20, 927-932. (Pubitemid 35001131)
2. Pedelacq, J.D., Cabantous, S., Tran, T., Terwilliger, T.C. and Waldo, G.S. (2006) Engineering and characterization of a superfolder green fluorescent protein. Nat. Biotechnol., 24, 79-88. (Pubitemid 43083170)
3. Sippl, M.J. (2009) Fold space unlimited. Curr. Opin. Struct. Biol., 19, 312-320.
4. Prodromou, C., Savva, R. and Driscoll, P.C. (2007) DNA fragmentation-based combinatorial approaches to soluble protein expression Part I. Generating DNA fragment libraries. Drug Discov. Today, 12, 931-938. (Pubitemid 350052674)
5. Cornvik, T., Dahlroth, S.L., Magnusdottir, A., Herman, M.D., Knaust, R., Ekberg, M. and Nordlund, P. (2005) Colony filtration blot: a new screening method for soluble protein expression in Escherichia coli. Nat. Methods, 2, 507-509.
6. Reich, S., Puckey, L.H., Cheetham, C.L., Harris, R., Ali, A.A., Bhattacharyya, U., Maclagan, K., Powell, K.A., Prodromou, C., Pearl, L.H. et al. (2006) Combinatorial domain hunting: an effective approach for the identification of soluble protein domains adaptable to high-throughput applications. Protein Sci., 15, 2356-2365. (Pubitemid 44496390)
7. Waldo, G.S., Standish, B.M., Berendzen, J. and Terwilliger, T.C. (1999) Rapid protein-folding assay using green fluorescent protein. Nat. Biotechnol., 17, 691-695. (Pubitemid 29316148)
8. Kawasaki, M. and Inagaki, F. (2001) Random PCR-based screening for soluble domains using green fluorescent protein. Biochem. Biophys. Res. Commun., 280, 842-844. (Pubitemid 32924507)
9. Yumerefendi, H., Tarendeau, F., Mas, P.J. and Hart, D.J. (2010) ESPRIT: an automated, library-based method for mapping and soluble expression of protein domains from challenging targets. J. Struct. Biol., 172, 66-74.
10. Nadal, M., Mas, P.J., Blanco, A.G., Arnan, C., Sola, M., Hart, D.J. and Coll, M. (2010) Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain. Proc. Natl Acad. Sci. USA, 107, 16078-16083.
11. Dyson, M.R., Perera, R.L., Shadbolt, S.P., Biderman, L., Bromek, K., Murzina, N.V. and McCafferty, J. (2008) Identification of soluble protein fragments by gene fragmentation and genetic selection. Nucleic Acids Res., 36, e51.
12. Nakayama, M. and Ohara, O. (2003) A system using convertible vectors for screening soluble recombinant proteins produced in Escherichia coli from randomly fragmented cDNAs. Biochem. Biophys. Res. Commun., 312, 825-830. (Pubitemid 37468246)
13. Zacchi, P., Sblattero, D., Florian, F., Marzari, R. and Bradbury, A.R. (2003) Selecting open reading frames from DNA. Genome Res., 13, 980-990. (Pubitemid 36621757)
14. Cho, G., Keefe, A.D., Liu, R., Wilson, D.S. and Szostak, J.W. (2000) Constructing high complexity synthetic libraries of long ORFs using in vitro selection. J. Mol. Biol., 297, 309-319.
15. Seehaus, T., Breitling, F., Dubel, S., Klewinghaus, I. and Little, M. (1992) A vector for the removal of deletion mutants from antibody libraries. Gene, 114, 235-237.
16. Daugelat, S. and Jacobs, W.R. Jr (1999) The Mycobacterium tuberculosis recA intein can be used in an ORFTRAP to select for open reading frames. Protein Sci., 8, 644-653. (Pubitemid 29117979)
17. Lutz, S., Fast, W. and Benkovic, S.J. (2002) A universal, vector-based system for nucleic acid reading-frame selection. Protein Eng., 15, 1025-1030. (Pubitemid 36331374)
18. Gerth, M.L., Patrick, W.M. and Lutz, S. (2004) A second-generation system for unbiased reading frame selection. Protein Eng. Des. Sel., 17, 595-602. (Pubitemid 39576486)
19. Smith, V.F. and Matthews, C.R. (2001) Testing the role of chain connectivity on the stability and structure of dihydrofolate reductase from E. coli: fragment complementation and circular permutation reveal stable, alternatively folded forms. Protein Sci., 10, 116-128. (Pubitemid 32221170)
20. Cabantous, S., Terwilliger, T.C. and Waldo, G.S. (2005) Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein. Nat. Biotechnol., 23, 102-107. (Pubitemid 41724632)
21. Hoskins, R.A., Stapleton, M., George, R.A., Yu, C., Wan, K.H., Carlson, J.W. and Celniker, S.E. (2005) Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP). Nucleic Acids Res., 33, e185.
22. Cabantous, S. and Waldo, G.S. (2006) In vivo and in vitro protein solubility assays using split GFP. Nat. Methods, 3, 845-854. (Pubitemid 44445833)
23. Listwan, P., Terwilliger, T.C. and Waldo, G.S. (2009) Automated, high-throughput platform for protein solubility screening using a split-GFP system. J. Struct. Funct. Genomics, 10, 47-55.
24. Marley, J., Lu, M. and Bracken, C. (2001) A method for efficient isotopic labeling of recombinant proteins. J. Biomol. NMR, 20, 71-75. (Pubitemid 32519656)
25. Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J. and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR, 6, 277-293.
26. Wishart, D.S., Bigam, C.G., Yao, J., Abildgaard, F., Dyson, H.J., Oldfield, E., Markley, J.L. and Sykes, B.D. (1995) 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J. Biomol. NMR, 6, 135-140.
27. Tarendeau, F., Boudet, J., Guilligay, D., Mas, P.J., Bougault, C.M., Boulo, S., Baudin, F., Ruigrok, R.W., Daigle, N., Ellenberg, J. et al. (2007) Structure and nuclear import function of the C-terminal domain of influenza virus polymerase PB2 subunit. Nat. Struct. Mol. Biol., 14, 229-233. (Pubitemid 46355581)
28. Tarendeau, F., Crepin, T., Guilligay, D., Ruigrok, R.W., Cusack, S. and Hart, D.J. (2008) Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. PLoS Pathog., 4, e1000136.
29. Guilligay, D., Tarendeau, F., Resa-Infante, P., Coloma, R., Crepin, T., Sehr, P., Lewis, J., Ruigrok, R.W., Ortin, J., Hart, D.J. et al. (2008) The structural basis for cap binding by influenza virus polymerase subunit PB2. Nat. Struct. Mol. Biol., 15, 500-506. (Pubitemid 351653591)
30. Angelini, A., Tosi, T., Mas, P., Acajjaoui, S., Zanotti, G., Terradot, L. and Hart, D.J. (2009) Expression of Helicobacter pylori CagA domains by library-based construct screening. FEBS J., 276, 816-824.
31. Booker, G.W., Gout, I., Downing, A.K., Driscoll, P.C., Boyd, J., Waterfield, M.D. and Campbell, I.D. (1993) Solution structure and ligand-binding site of the SH3 domain of the p85 alpha subunit of phosphatidylinositol 3-kinase. Cell, 73, 813-822. (Pubitemid 23159018)
32. Musacchio, A., Cantley, L.C. and Harrison, S.C. (1996) Crystal structure of the breakpoint cluster region-homology domain from phosphoinositide 3-kinase p85 alpha subunit. Proc. Natl Acad. Sci. USA, 93, 14373-14378. (Pubitemid 26418973)
33. Nolte, R.T., Eck, M.J., Schlessinger, J., Shoelson, S.E. and Harrison, S.C. (1996) Crystal structure of the PI 3-kinase p85 amino-terminal SH2 domain and its phosphopeptide complexes. Nat. Struct. Biol., 3, 364-374.
34. Siegal, G., Davis, B., Kristensen, S.M., Sankar, A., Linacre, J., Stein, R.C., Panayotou, G., Waterfield, M.D. and Driscoll, P.C. (1998) Solution structure of the C-terminal SH2 domain of the p85 alpha regulatory subunit of phosphoinositide 3-kinase. J. Mol. Biol., 276, 461-478. (Pubitemid 28085333)
35. Derewenda, Z.S. (2010) Application of protein engineering to enhance crystallizability and improve crystal properties. Acta Crystallogr. D Biol. Crystallogr., 66, 604-615.
36. Camacho, L.R., Ensergueix, D., Perez, E., Gicquel, B. and Guilhot, C. (1999) Identification of a virulence gene cluster of Mycobacterium tuberculosis by signature-tagged transposon mutagenesis. Mol. Microbiol., 34, 257-267. (Pubitemid 29486244)
37. Cox, J.S., Chen, B., McNeil, M. and Jacobs, W.R. Jr (1999) Complex lipid determines tissue-specific replication of Mycobacterium tuberculosis in mice. Nature, 402, 79-83.
38. Oefner, P.J., Hunicke-Smith, S.P., Chiang, L., Dietrich, F., Mulligan, J. and Davis, R.W. (1996) Efficient random subcloning of DNA sheared in a recirculating point-sink flow system. Nucleic Acids Res., 24, 3879-3886. (Pubitemid 26385316)