Structural genomics of human proteins - Target selection and generation of public catalog of expression clones

Microbial Cell Factories

Volumn 4, Issue , 2005, Pages

  Büssow, Konrad ^a,b   Scheich, Christoph ^a,b   Sievert, Volker ^a,b   Harttig, Ulrich ^a,d,e   Schultz, Jörg ^c,h   Simon, Bernd ^c   Bork, Peer ^c   Lehrach, Hans ^a,b   Heineman, Udo ^a,f,g  

^a Protein Structure Factory   (Germany)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^d German Genome Resource Center RZPD   (Germany)

^e DIFE ^*  (Germany)

^f MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^g FREIE UNIVERSITÄT BERLIN   (Germany)

^h UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; ESCHERICHIA COLI PROTEIN;

ARTICLE; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; DNA STRUCTURE; ESCHERICHIA COLI; GENETIC SELECTION; HOST CELL; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; PROTEIN TARGETING; PUBLICATION; SEQUENCE ANALYSIS; STRUCTURAL GENOMICS; UNINDEXED SEQUENCE;

ESCHERICHIA COLI;

EID: 26844532090     PISSN: 14752859     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-4-21     Document Type: Article

References (60)

1. Heinemann U, Büssow K, Mueller U, Umbach P: Facilities and methods for the high-throughput crystal structure analysis of human proteins. Accounts of Chemical Research 2003, 36(3):157-163.
2. Protein Structure Factory [http://www.proteinstrukturfabrik.de]
3. Zhang C, Kim SH: Overview of structural genomics: from structure to function. Current Opinion in Chemical Biology 2003, 7(1):28-32.
4. Todd AE, Marsden RL, Thornton JM, Orengo CA: Progress of structural genomics initiatives: an analysis of solved target structures. Journal of Molecular Biology 2005, 348(5):1235-1260.
5. Gilbert M, Albala Joanna S: Accelerating code to function: Sizing up the protein production line. Current Opinion in Chemical Biology 2002, 6(1):102-105.
6. Yokoyama S: Protein expression systems for structural genomics and proteomics. Current Opinion in Chemical Biology 2003, 7(1):39-43.
7. Kigawa T, Yabuki T, Yoshida Y, Tsutsui M, Ito Y, Shibata T, Yokoyama S: Cell-free production and stable-isotope labeling of milligram quantities of proteins. FEBS Letters 1999, 442(1):15-19.
8. Tyler RC, Aceti DJ, Bingman CA, Cornilescu CC, Fox BG, Frederick RO, Jeon WB, Lee MS, Newman CS, Peterson FC et al: Comparison of cell-based and cell-free protocols for producing target proteins from the Arabidopsis thaliana genome for structural studies. Proteins 2005.
9. 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 Expression & Purification 2002, 25(3):372-378.
10. Boettner M, Prinz B, Holz C, Stahl U, Lang C: High-throughput screening for expression of heterologous proteins in the yeast Pichia pastoris. Journal of Biotechnology 2002, 99(1):51-62.
11. Holz C, Prinz B, Bolotina N, Sievert V, Büssow K, Simon B, Stahl U, Lang C: Establishing the yeast Saccharomyces cerevisiae as a system for expression of human proteins on a proteome-scale. Journal of Structural and Functional Genomics 2003, 4(2/3):97-108.
12. Studier FW, Rosenberg AH, Dunn JJ, Dubendorff JW: Use of T7 RNA polymerase to direct expression of cloned genes. Methods in Enzymology 1990, 185:60-89.
13. Hochuli E, Dobeli H, Schacher A: New metal chelate adsorbent selective for proteins and peptides containing neighboring histidine residues. Journal of Chromatography 1987, 411:177-184.
14. Schmidt TG, Skerra A: The random peptide library-assisted engineering of a C-terminal affinity peptide, useful for the detection and purification of a functional Ig Fv fragment. Protein Engineering 1993, 6(1):109-122.
15. Schmidt TGM, Koepke J, Frank R, Skerra A: Molecular interaction between the Strep-tag affinity peptide and its cognate target, streptavidin. Journal of0 Molecular Biology 1996, 255(5):753-766.
16. Mueller U, Büssow K, Diehl A, Bartl FJ, Niesen FH, Nyarsik L, Heinemann U: Rapid purification and crystal structure analysis of a small protein carrying two terminal affinity tags. Journal of Structural and Functional Genomics 2004, 4:217-225.
17. Kane JF: Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Current Opinion in Biotechnology 1995, 6(5):494-500.
18. Brinkmann U, Mattes RE, Buckel P: High-level expression of recombinant genes in Escherichia coli is dependent on the availability of the DNAY gene product. Gene 1989, 85(1):109-114.
19. Novy R, Drott D, Yaeger K, Mierendorf R: Overcoming the codon bias of E.coli for enhanced protein expression. inNovations 2001, 12:1-3.
20. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL: Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. Journal of Molecular Biology 2001, 305(3):567-580.
21. TMHMM [http://www.cbs.dtu.dk/services/TMHMM/]
22. Dyson HJ, Wright PE: Coupling of folding and binding for unstructured proteins. Current Opinion in Structural Biology 2002, 12(1):54-60.
23. Wootton J, Federhen S: Analysis of compositionally biased regions in sequence databases. Methods in Enzymology 1996, 266:554-571.
24. Wootton JC, Federhen S: Statistics of local complexity in amino acid sequences and sequence databases. Computers & Chemistry 1993, 17:149-163.
25. Wootton J: Non-globular domains in protein sequences: automated segmentation using complexity measures. Computers & Chemistry 1994, 18(3):269-285.
26. COILS [http://www.russell.embl.de/cgi-bin/coils-svr.pl]
27. Lupas A, Van Dyke M, Stock J: Predicting coiled coils from protein sequences. Science 1991, 252(5010):1162-1164.
28. Lupas A: Prediction and analysis of coiled-coil structures. Methods in Enzymology 1996, 266:513-525.
29. Eisenhaber F, Bork P: Wanted: Subcellular localization of proteins based on sequence. Trends in Cell Biology 1998, 8(4):169-170.
30. Meta_Annotator [http://mendel.imp.univie.ac.at/aat/CellLoc_MetaA]
31. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S et al: The protein data bank. Acta Crystallographica Section D 2002, 58(Pt 6 Pt 1):899-907.
32. Altschul SF, Madden TL, Schaeffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 1997, 25(17):3389-3402.
33. Lennon G, Auffray C, Polymeropoulos M, Soares MB: The I.M.A.G.E. consortium: an integrated molecular analysis of genomes and their expression. Genomics 1996, 33:151-152.
34. dbEST [http://www.ncbi.nlm.nih.gov/dbEST]
35. Bannasch D, Mehrle A, Glatting KH, Pepperkok R, Poustka A, Wiemann S: LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system. Nucleic Acids Research 2004, 32(Special Issue SI):D505-D508.
36. Wiemann S, Weil B, Wellenreuther R, Gassenhuber J, Glassl S, Ansorge W, Bocher M, Blocker H, Bauersachs S, Blum H et al: Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Genome Research 2001, 11(3):422-435.
37. Büssow K, Nordhoff E, Lübbert C, Lehrach H, Walter G: A human cDNA library for high-throughput protein expression screening. Genomics 2000, 65(1):1-8.
38. Büssow K, Cahill D, Nietfeld W, Bancroft D, Scherzinger E, Lehrach H, Walter G: A method for global protein expression and antibody screening on high-density filters of an arrayed cDNA library. Nucleic Acids Research 1998, 26(21):5007-5008.
39. Büssow K, Quedenau C, Sievert V, Tischer J, Scheich C, Seitz H, Hieke B, Niese FH, Gütz F, Harttig U et al: A catalogue of human cDNA expression clones and its application to structural genomics. Genome Biology 2004, 5:R71.
40. The hEx1 Database [http://www.proteinstrukturfabrik.de/hex1]
41. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al: The Ensembl genome database project. Nucleic Acids Research 2002, 30(1):38-41.
42. Aslanidis C, de Jong PJ: Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Research 1990, 18(20):6069-6074.
43. Scheich C, Sievert V, Büssow K: An automated method for high-throughput protein purification applied to a comparison of His-tag and GST-tag affinity chromatography. BMC Biotechnology 2003, 3:12.
44. German Resource Centre (RZPD) [http://www.rzpd.de]
45. Scheich C, Leitner D, Sievert V, Leidert M, Schlegel B, Simon B, Letunic I, Büssow K, Diehl A: Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis. BMC Structural Biology 2004, 4:4.
46. Brockmann C, Leitner D, Labudde D, Diehl A, Sievert V, Büssow K, Kühne R, Oschkinat H: The solution structure of the SODD BAG domain reveals additional electrostatic interactions in the HSP70 complexes of SODD subfamily BAG domains. FEBS Letters 2004, 558(1-3):101-106.
47. Soukenik M, Diehl A, Leidert M, Sievert V, Büssow K, Leitner D, Labudde D, Ball LJ, Lechner A, Nagler DK et al: The SEP domain of p47 acts as a reversible competitive inhibitor of cathepsin L. FEBS Letters 2004, 576(3):358-362.
48. McCall EJ, Danielsson A, Hardern IM, Dartsch C, Hicks R, Wahlberg JM, Abbott WM:0 Improvements to the throughput of recombinant protein expression in the baculovirus/insect cell system. Protein Expr Purif 2005, 42(1):29-36.
49. Eshaghi S, Hedren M, Nasser MI, Hammarberg T, Thornell A, Nordlund P: An efficient strategy for high-throughput expression screening of recombinant integral membrane proteins. Protein Sci 2005, 14(3):676-683.
50. Li C, Evans RM: Ligation independent cloning irrespective of restriction site compatibility. Nucleic Acids Research 1997, 25(20):4165-4166.
51. ORFprimer [http://www.proteinstrukturfabrik.de/ORFprimer]
52. Inoue H, Nojima H, Okayama H: High efficiency transformation of Escherichia coli with plasmids. Gene 1990, 96(1):23-28.
53. Kyte J, Doolittle RF: A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology 1982, 157(1):105-132.
54. Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends in Genetics 2000, 16(6):276-277.
55. Manjasetty BA, Quedenau C, Sievert V, Büssow K, Niesen F, Delbrück H, Heinemann U: X-ray structure of human gankyrin, the product of a gene linked to hepatocellular carcinome. Proteins: Structure, Function and Genetics 2004, 55(1):214-217.
56. Manjasetty BA, Niesen FH, Delbruck H, Gotz F, Sievert V, Bussow K, Behlke J, Heinemann U: X-ray structure of fumarylacetoacetate hydrolase family member homo sapiens FLJ36880. Biological Chemistry 2004, 385(10):935-942.
57. Manjasetty BA, Delbrück H, Pham D-T, Mueller U, Fieber-Erdmann M, Scheich C, Sievert V, Büssow K, Niesen F, Weihofen W et al: Crystal structure of Homo sapiens protein hp14.5. Proteins: Structure, Function and Bioinformatics 2004, 54:797-800.
58. Turnbull AP, Kümmel D, Prinz B, Holz C, Schultchen J, Lang C, Niesen FH, Hofmann KP, Delbrück H, Behlke J et al: Structure of palmitoylated BET3: insights into TRAPP complex assembly and membrane localization. EMBO Journal 2005, 24(5):875-884.
59. Kümmel D, Müller JJ, Roske Y, Misselwitz R, Büssow K, Heinemann U: Structure of the TRAPP subunit TPC6 suggests a model for a TRAPP subcomplex. EMBO Reports 2005, in press.
60. Werner E, Ziegler M, Lerner F, Schweiger M, Heinemann U: Crystal structure of human nicotinamide mononucleotide adenylyltransferase in complex with NMN. FEBS Letters 2002, 516(1-3):239-244.