Functional genomics with protein-protein interactions

Biotechnology Annual Review

Volumn 5, Issue , 2000, Pages 45-86

  Rudert, Fritz ^a   Ge, Liming ^a   Ilag, Leodevico L ^a  

^a Xerion Pharmaceuticals GmbH   (Germany)

Author keywords

Antibodies; Bio informatics; Databases; FRET; Genomics; High throughput screening; MALDI; Mass spectrometry; Multiprotein complexes; Nanoelectrospray; Peptides; Phage display; Protein linkage map; Protein sequencing; Protein protein interaction; Proteomics; SELDI

Indexed keywords

DNA; PEPTIDE; LIGAND; PROTEIN;

BACTERIUM; BIOTECHNOLOGY; CELL ORGANELLE; DNA SEQUENCE; EUKARYOTE; FUNCTIONAL GENOMICS; GENE FUNCTION; GENE SEQUENCE; HIGH THROUGHPUT SCREENING; HOST CELL; NONHUMAN; PHAGE DISPLAY; PLASMID; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; REVIEW; RIBOSOME; RNA TRANSLATION; SIGNAL TRANSDUCTION; TWO HYBRID SYSTEM; BACTERIOPHAGE; EUKARYOTIC CELL; FORECASTING; GENETIC PROCEDURES; GENETICS; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; MOLECULAR BIOLOGY;

BACTERIOPHAGES; EUKARYOTIC CELLS; FORECASTING; GENETIC TECHNIQUES; LIGANDS; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PROTEINS; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 0033648988     PISSN: 13872656     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1387-2656(00)05032-8     Document Type: Article

References (209)

1. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM. Whole-genome random sequencing and assembly of Haemophilus influenza Rd. Science 1995;269:496-512.
2. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y. The complete genome sequence of Escherichia coli K-12. Science 1997;277:1453-1474.
3. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG. Life with 6000 genes. Science 1996;274:546-563, 567.
4. Wodicka L, Dong H, Mittmann M, Ho MH, Lockhart DJ. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nature Biotechnol 1997;15:1359-1367.
5. Fairhead C, Llorente B, Denis F, Soler M, Dujon B. New vectors for combinatorial deletions in yeast chromosomes and for gap-repair cloning using "split-marker" recombination. Yeast 1996;12:1439-1457.
6. Jansen G, Hazendonk E, Thijssen KL, Plasterk RH. Reverse genetics by chemical mutagenesis in Caenorhabditis elegans. Nature Genet 1997;17:119-121.
7. Hudson JRJ, Dawson EP, Rushing KL, Jackson CH, Lockshon D, Conover D, Lanciault C, Harris JR, Simmons SJ, Rothstein R, Fields S. The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form. Genome Res 1997;7:1169-1173.
8. Bartel PL, Roecklein JA, SenGupta D, Fields S. A protein linkage map of Escherichia coli bacteriophage T7. Nature Genet 1996;12:72-77.
9. Neubauer G, Gottschalk A, Fabrizio P, Seraphin B, Luhrmann R, Mann M. Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc Natl Acad Sci USA 1997;94:385-390.
10. Lamond AI, Mann M. Cell biology and the genome projects - a concerted strategy for characterizing multiprotein complexes by using mass spectrometry. Trends Cell Biol 1997;7:139-142.
11. Zutshi R, Brickner M, Chmielewski J. Inhibiting the assembly of protein-protein interfaces. Curr Opin Chem Biol 1998;2:62-66.
12. Smith GP. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 1985;228:1315-1317.
13. Scott JK, Smith GP. Searching for peptide ligands with an epitope library. Science 1990;249:386-390.
14. Lowman HB, Bass SH, Simpson N, Wells JA. Selecting high-affinity binding proteins by monovalent phage display. Biochemistry 1991;30:10832-10838.
15. Marks JD, Hoogenboom HR, Bonnert TP, McCafferty J, Griffiths AD, Winter G. By-passing immunization. Human antibodies from V-gene libraries displayed on phage. J Molec Biol 1991;222:581-597.
16. Clackson T, Hoogenboom HR, Griffiths AD, Winter G. Making antibody fragments using phage display libraries. Nature 1991;352:624-628.
17. Felici F, Luzzago A, Monacci P, Nicosia A, Sollazzo M, and Traboni C. In: El-Gewely M R (ed) Biotechnology Annual Review 1. Amsterdam: Elsevier Science B.V., 1995;149-183.
18. Model P, Russel M. In: Calendar E (ed) The bacteriophages 2. New York: Plenum, 1988;375-456.
19. Schier R, Bye J, Apell G, McCall A, Adams GP, Malmqvist M, Weiner LM, Marks JD. Isolation of high-affinity monomeric human anti-c-erbB-2 single chain Fv using affinity-driven selection. J Molec Biol 1996;255:28-43.
20. Hoogenboom HR, Griffiths AD, Johnson KS, Chiswell DJ, Hudson P, Winter G. Multisubunit proteins on the surface of filamentous phage: methodologies for displaying antibody (Fab) heavy and light chains. Nucl Acid Res 1991;19:4133-4137.
21. McCafferty J, Griffiths AD, Winter G, Chiswell DJ. Phage antibodies: filamentous phage displaying antibody variable domains. Nature 1990;348:552-554.
22. Sheets MD, Amersdorfer P, Finnern R, Sargent P, Lindqvist E, Schier R, Hemingsen G, Wong C, Gerhart JC, Marks JD. Efficient construction of a large nonimmune phage antibody library: the production of high-affinity human single-chain antibodies to protein antigens. Proc Natl Acad Sci USA 1998;95:6157-6162.
23. Lang IM, Chuang TL, Barbas CF, Schleef RR. Purification of storage granule protein-23. A novel protein identified by phage display technology and interaction with type I plasminogen activator inhibitor. J Biol Chem 1996;271:30126-30135.
24. Crameri R, Suter M. Display of biologically active proteins on the surface of filamentous phages: a cDNA cloning system for selection of functional gene products linked to the genetic information responsible for their production. Gene 1993;137:69-75.
25. Crameri R, Jaussi R, Menz G, Blaser K. Display of expression products of cDNA libraries on phage surfaces. A versatile screening system for selective isolation of genes by specific gene-product/ligand interaction. Eur J Biochem 1994;226:53-58.
26. Crameri R, Blaser K. Cloning Aspergillus fumigatus allergens by the pJuFo filamentous phage display system. Int Arch Allergy Immunol 1996;110:41-45.
27. Hottiger M, Gramatikoff K, Georgiev O, Chaponnier C, Schaffner W, Hubscher U. The large subunit of HIV-1 reverse transcriptase interacts with beta-actin. Nucleic Acid Res 1995;23:736-741.
28. Light J, Maki R, Assa-Munt N. Expression cloning of cDNA by phage display selection. Nucleic Acid Res 1996;24:4367-4368.
29. Hennecke M, Kola A, Baensch M, Wrede A, Klos A, Bautsch W, Kohl J. A selection system to study C5a-C5a-receptor interactions: phage display of a novel C5a anaphylatoxin, Fos-C5aAla27. Gene 1997;184:263-272.
30. Jespers LS, De Keyser A, Stanssens PE. LambdaZLG6: a phage lambda vector for high-efficiency cloning and surface expression of cDNA libraries on filamentous phage. Gene 1996;173:179-181.
31. Davis CA, Benzer S. Generation of cDNA expression libraries enriched for in-frame sequences. Proc Natl Acad Sci USA 1997;94:2128-2132.
32. Dunn IS. Assembly of functional bacteriophage lambda virions incorporating C- terminal peptide or protein fusions with the major tail protein. J Molec Biol 1995;248:497-506.
33. Bothmann H, Pluckthun A. Selection for a periplasmic factor improving phage display and functional periplasmic expression. Nat Biotechnol 1998;16:376-380.
34. Peters EA, Schatz PJ, Johnson SS, Dower WJ. Membrane insertion defects caused by positive charges in the early mature region of protein pill of filamentous phage fd can be corrected by pr1A suppressors. J Bacteriol 1994;176:4296-4305.
35. Cortese R, Monaci P, Luzzago A, Santini C, Bartoli F, Cortese I, Fortugno P, Galfre G, Nicosia A, Felici F. Selection of biologically active peptides by phage display of random peptide libraries. Curr Opin Biotechnol 1996;7:616-621.
36. Cortese R, Felici F, Galfre G, Luzzago A, Monaci P, Nicosia A. Epitope discovery using peptide libraries displayed on phage. Trends Biotechnol 1994;12:262-267.
37. Livnah O, Stura EA, Johnson DL, Middleton SA, Mulcahy LS, Wrighton NC, Dower WJ, Jolliffe LK, Wilson IA. Functional mimicry of a protein hormone by a peptide agonist: the EPO receptor complex at 2.8 A. Science 1996;273:464-471.
38. Wrighton NC, Farrell FX, Chang R, Kashyap AK, Barbone FP, Mulcahy LS, Johnson DL, Barrett RW, Jolliffe LK, Dower WJ. Small peptides as potent mimetics of the protein hormone erythropoietin. Science 1996;273:458-464.
39. Cwirla SE, Balasubramanian P, Duffin DJ, Wagstrom CR, Gates CM, Singer SC, Davis AM, Tansik RL, Mattheakis LC, Boytos CM, Schatz PJ, Baccanari DP, Wrighton NC, Barrett RW, Dower WJ. Peptide agonist of the thrombopoietin receptor as potent as the natural cytokine. Science 1997;276:1696-1699.
40. Jacobsson K, Frykberg L. Phage display shot-gun cloning of ligand-binding domains of prokaryotic receptors approaches 100% correct clones. Biotechniques 1996;20:1070-1071.
41. Jacobsson K, Frykberg L. Cloning of ligand-binding domains of bacterial receptors by phage display. Biotechniques 1995;18:878-885.
42. Jacobsson K, Jonsson H, Lindmark H, Guss B, Lindberg M, Frykberg L. Shot-gun phage display mapping of two streptococcal cell-surface proteins. Microbiol Res 1997;152:121-128.
43. Jacobsson K, Frykberg L. Gene VIII-based, phage-display vectors for selection against complex mixtures of ligands. Biotechniques 1998;24:294-301.
44. Sparks AB, Hoffman NG, McConnell SJ, Fowlkes DM, Kay BK. Cloning of ligand targets: systematic isolation of SH3 domain-containing proteins. Nat Biotechnol 1996;14:741-744.
45. Pirozzi G, McConnell SJ, Uveges AJ, Carter JM, Sparks AB, Kay BK, Fowlkes DM. Identification of novel human WW domain-containing proteins by cloning of ligand targets. J Biol Chem 1997;272:14611-14616.
46. Sparks AB, Rider JE, Hoffman NG, Fowlkes DM, Quillam LA, Kay BK. Distinct ligand preferences of Src homology 3 domains from Src, Yes, Ab1, Cortactin, p53bp2, PLCgamma, Crk, and Grb2. Proc Natl Acad Sci USA 1996;93:1540-1544.
47. Sparks AB, Adey NB, Quilliam LA, Thorn JM, Kay BK. Screening phage-displayed random peptide libraries for SH3 ligands. Methods Enzymol 1995;255:498-509.
48. Sparks AB, Quilliam LA, Thorn JM, Der CJ, Kay BK. Identification and characterization of Src SH3 ligands from phage- displayed random peptide libraries. J Biol Chem 1994;269:23853-23856.
49. Pierce HH, Adey N, Kay BK. Identification of cyclized calmodulin antagonists from a phage display random peptide library. Mol Divers 1996;1:259-265.
50. Nord K, Gunneriusson E, Ringdahl J, Stahl S, Uhlen M, Nygren PA. Binding proteins selected from combinatorial libraries of an alpha-helical bacterial receptor domain. Nature Biotechnol 1997;15:772-777.
51. Smith GP, Patel SU, Windass JD, Thornton JM, Winter G, Griffiths AD. Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage. J Molec Biol 1998;277:317-332.
52. Dunn IS. Phage display of proteins. Curr Opin Biotechnol 1996;7:547-553.
53. Mikawa YG, Maruyama IN, Brenner S. Surface display of proteins on bacteriophage lambda heads. J Molec Biol 1996;262:21-30.
54. Kuwabara I, Maruyama H, Mikawa YG, Zuberi RI, Liu FT, Maruyama IN. Efficient epitope mapping by bacteriophage lambda surface display. Nature Biotechnol 1997;15:74-78.
55. Dunn IS. In vitro alpha-complementation of beta-galactosidase on a bacteriophage surface. Eur J Biochem 1996;242:720-726.
56. Rosenberg A, Griffin K, Studier W, McCormick M, Berg J, Novy R, Mierendorf R. T7Select phage display system: a poweful new protein display system based on bacteriophage T7. Innovations 1996;6:1-6.
57. Condron BG, Atkins JF, Gesteland RF. Frameshifting in gene 10 of bacteriophage T7. J Bacteriol 1991;173:6998-7003.
58. Lu Z, Murray KS, Van Cleave V, LaVallie ER, Stahl ML, McCoy JM. Expression of thioredoxin random peptide libraries on the Escherichia coli cell surface as functional fusions to flagellin: a system designed for exploring protein-protein interactions. Biotechnology 1995;13:366-372.
59. Lu Z, Tripp BC, McCoy JM. Displaying libraries of conformationally constrained peptides on the surface of Escherichia coli as flagellin fusions. Methods Molec Biol 1998;87:265-280.
60. Hofnung M. Expression of foreign polypeptides at the Escherichia coli cell surface. Methods Cell Biol 1991;34:77-105.
61. Klauser T, Pohlner J, Meyer TF. Extracellular transport of cholera toxin B subunit using Neisseria IgA protease beta-domain: conformation-dependent outer membrane translocation. EMBO J 1990;9:1991-1999.
62. Fuchs P, Breitling F, Dubel S, Seehaus T, Little M. Targeting recombinant antibodies to the surface of Escherichia coli: fusion to a peptidoglycan associated lipoprotein. Biotechnology 1991;9:1369-1372.
63. Georgiou G, Stathopoulos C, Daugherty PS, Nayak AR, Iverson BL, Curtiss R. Display of heterologous proteins on the surface of microorganisms: from the screening of combinatorial libraries to live recombinant vaccines. Nature Biotechnol 1997;15:29-34.
64. Stahl S, Uhlen M. Bacterial surface display: trends and progress. Trends Biotechnol 1997;15:185-192.
65. LaVallie ER, DiBlasio EA, Kovacic S, Grant KL, Schendel PF, McCoy JM. A thioredoxin gene fusion expression system that circumvents inclusion body formation in the E. coli cytoplasm. Biotechnology 1993;11:187-192.
66. Pohlner J, Halter R, Beyreuther K, Meyer TF Gene structure and extracellular secretion of Neisseria gonorrhoeae IgA protease. Nature 1987;325:458-462.
67. Flaut AG, Gilbert JV, Artenstein MS, Capra JD: Neisseria gonorrhoeae and neisseria meningitidis: extracellular enzyme cleaves human immunoglobulin A. Science 1975;190:1103-1105.
68. Kilian M, Mestecky J, Schrohenloher RE. Pathogenic species of the genus Haemophilus and Streptococcus pneumoniae produce immunoglobulin Al protease. Infect Immun 1979;26:143-149.
69. Strauss A, Pohlner J, Klauser T, Meyer TF. C-terminal glycine-histidine tagging of the outer membrane protein Iga beta of Neisseria gonorrhoeae. FEMS Microbiol Lett 1995;127:249-254.
70. Klauser T, Pohlner J, Meyer TF. Selective extracellular release of cholera toxin B subunit by Escherichia coli: dissection of Neisseria Iga beta-mediated outer membrane transport. EMBO J 1992;11:2327-2335.
71. Fuchs P, Weichel W, Dubel S, Breitling F, Little M. Separation of E. coli expressing functional cell-wall bound antibody fragments by FACS. Immunotechnology. 1996;2:97-102.
72. Francisco JA, Campbell R, Iverson BL, Georgiou G. Production and fluorescence-activated cell sorting of Escherichia coli expressing a functional antibody fragment on the external surface. Proc Natl Acad Sci USA 1993;90:10444-10448.
73. Gunneriusson E, Samuelson P, Uhlen M, Nygren PA, Stahl S. Surface display of a functional single-chain Fv antibody on staphylococci. J Bacteriol 1996;178:1341-1346.
74. Duenas M, Borrebaeck CA. Clonal selection and amplification of phage displayed antibodies by linking antigen recognition and phage replication. Biotechnology 1994;12:999-1002.
75. Gramatikoff K, Georgiev O, Schaffner W: Direct interaction rescue, a novel filamentous phage technique to study protein-protein interactions. Nucleic Acid Res 1994;22:5761-5762.
76. Gramatikoff K, Schaffner W, Georgiev O. The leucine zipper of c-Jun binds to ribosomal protein L18a: a role in Jun protein regulation? Biol Chem Hoppe-Seyler 1995;376:321-325.
77. Chevray PM, Nathans D. Protein interaction cloning in yeast: identification of mammalian proteins that react with the leucine zipper of Jun. Proc Natl Acad Sci USA 1992;89:5789-5793.
78. Krebber C, Spada S, Desplancq D, Plückthun A. Coselection of cognate antibody-antigen pairs by selectively infective phages. FEBS Lett 1995;377:227-231.
79. Krebber C, Spada S, Desplancq D, Krebber A, Ge L, Plückthun A. Selectively infective phage (SIP): a mechanistic dissection of a novel in vivo selection for protein-ligand interactions. J Mol Biol 1997;268:607-618.
80. Hennecke F, Krebber C, Plückthun A. Nonrepetitive single-chain Fv linkers selected by the selectively infective phage (SIP) technology. Protein (Eng) 1998;11:405-410.
81. Pedrazzi G, Schwesinger F, Honegger A, Krebber C, Pluckthun A. Affinity and folding properties both influence the selection of antibodies with the selectively infective phage (SIP) methodology. FEBS Lett 1997;415:289-293.
82. Spada S, Krebber C, Plückthun A. Selectively infective phages (SIP). Biol Chem 1997;378:445-456.
83. Rudert F, Woltering C, Frisch C, Rottenberger C, Hag LL. A phage-based system to select multiple protein-protein interactions simultaneously from combinatorial libraries. FEBS Lett 1998;440:135-140.
84. Hag LL, Rottenberger C, Liepinsh E, Wellnhofer G, Rudert F, Otting G, Ilag LL. Selection of a peptide ligand to the p75 neurotrophin receptor death domain and determination of its binding sites by NMR. Biochem Biophys Res Commun 1999;255:104-109.
85. Enea V, Zinder ND. Interference resistant mutants of phage f1. Virology 1982;122:222-226.
86. Waterhouse P, Griffiths AD, Johnson KS, Winter G. Combinatorial infection and in vivo recombination: a strategy for making large phage antibody repertoires. Nucleic Acid Res 1993;21:2265-2266.
87. Malmborg A-C Söderlind E, Frost L, Borrebaeck CAK. Selective phage infection mediated by epitope expression on F pilus. J Mol Biol 1997;273:544-551.
88. Cull MG, Miller JF, Schatz PJ. Screening for receptor ligands using large libraries of peptides linked to the C terminus of the lac repressor. Proc Natl Acad Sci USA 1992;89:1865-1869.
89. Schatz PJ. Use of peptide libraries to map the substrate specificity of a peptide- modifying enzyme: a 13 residue consensus peptide specifies biotinylation in Escherichia coli. Biotechnology 1993;11:1138-1143.
90. Gates CM, Stemmer WP, Kaptein R, Schatz PJ. Affinity selective isolation of ligands from peptide libraries through display on a lac repressor "headpiece dimer". J Molec Biol 1996;255:373-386.
91. Schatz PJ, Cull MG, Martin EL, Gates CM. Screening of peptide libraries linked to lac repressor. Methods Enzymol 1996;267:171-191.
92. Kraus JP, Rosenberg LE. Purification of low-abundance messenger RNAs from rat liver by polysome immunoadsorption. Proc Natl Acad Sci USA 1982;79:4015-4019.
93. Schlechter I. Biologically and chemically pure mRNA coding for a mouse immunoglobulin L-chain prepared with the aid of antibodies and immobilized oligothymidine. Proc Natl Acad Sci USA 1973;70:2256-2260.
94. Payvar F, Schimke RT. Improvements in immunoprecipitation of specific messenger RNA. Isolation of highly purified conalbumin mRNA in high yield. Eur J Biochem 1979;101:271-282.
95. Mattheakis LC, Bhatt RR, Dower WJ. An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc Natl Acad Sci USA 1994;91:9022-9026.
96. Hanes J, Plückthun A. In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl Acad Sci USA 1997;94:4937-4942.
97. He M,Taussig MJ. Antibody-ribosome-mRNA (ARM) complexes as efficient selection particles for in vitro display and evolution of antibody combining sites. Nucleic Acid Res 1997;25:5132-5134.
98. Cadwell RC, Joyce GF: Mutagenic PCR. PCR Methods Appl 1994;3:S136-S140
99. Stemmer WP. Rapid evolution of a protein in vitro by DNA shuffling. Nature 1994;370:389-391.
100. Stemmer WP. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci USA 1994;91:10747-10751.
101. Fields S, Song O. A novel genetic system to detect protein-protein interactions. Nature 1989;340:245-246.
102. Li JJ, Herskowitz I. Isolation of ORC6, a component of the yeast origin recognition complex by a one-hybrid system. Science 1993;262:1870-1874.
103. Wang MM, Reed RR. Molecular cloning of the olfactory neuronal transcription factor Olf-1 by genetic selection in yeast. Nature 1993;364:121-126.
104. SenGupta DJ, Zhang B, Kraemer B, Pochart P, Fields S, Wickens M. A three-hybrid system to detect RNA-protein interactions in vivo. Proc Natl Acad Sci USA 1996;93:8496-8501.
105. Vidai M, Brachmann RK, Fattaey A, Harlow E, Boeke JD. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc Natl Acad Sci USA 1996;93:10315-10320.
106. Shih HM, Goldman PS, DeMaggio AJ, Hollenberg SM, Goodman RH, Hoekstra MF: A positive genetic selection for disrupting protein-protein interactions: identification of CREB mutations that prevent association with the coactivator CBP. Proc Natl Acad Sci USA 1996;93:13896-13901.
107. Osborne MA, Dalton S, Kochan JP. The yeast tribrid system-genetic detection of transphosphorylated ITAM-SH2-interactions. Biotechnology 1995;13:1474-1478.
108. Tirode F, Malaguti C, Romero F, Attar R, Camonis J, Egly JM. A conditionally expressed third partner stabilizes or prevents the formation of a transcriptional activator in a three-hybrid system. J Biol Chem 1997;272:22995-22999.
109. Zhang J, Lautar S. A yeast three-hybrid method to clone ternary protein complex components. Anal Biochem 1996;242:68-72.
110. Licitra EJ, Liu JO. A three-hybrid system for detecting small ligand-protein receptor interactions. Proc Natl Acad Sci USA 1996;93:12817-12821.
111. Inouye C, Dhillon N, Durfee T, Zambryski PC, Thorner J. Mutational analysis of STE5 in the yeast Saccharomyces cerevisiae: application of a differential interaction trap assay for examining protein-protein interactions. Genetics 1997;147:479-492.
112. Fearon ER, Finkel T, Gillison ML, Kennedy SP, Casella JF, Tomaselli GF, Morrow JS, Van Dang C. Karyoplasmic interaction selection strategy: a general strategy to detect protein-protein interactions in mammalian cells. Proc Natl Acad Sci USA 1992;89:7958-7962.
113. Vasavada HA, Ganguly S, Germino FJ, Wang ZX, Weissman SM. A contingent replication assay for the detection of protein-protein interactions in animal cells. Proc Natl Acad Sci USA 1991;88:10686-10690.
114. Bunker CA, Kingston RE. Identification of a cDNA for SSRP1, an HMG-box protein, by interaction with the c-Myc oncoprotein in a novel bacterial expression screen. Nucleic Acid Res 1995;23:269-276.
115. Munder T, Ninkovic M, and Rudakoff B. In: El-Gewely MR (ed) Biotechnology Annual Review 3. Amsterdam: Elsevier Science BV. 1997;31-58.
116. Brachmann RK, Boeke JD: Tag games in yeast: the two-hybrid system and beyond. Curr Opin Biotechnol 1997;8:561-568.
117. Frederickson RM: Macromolecular matchmaking: advances in two-hybrid and related technologies. Curr Opin Biotechnol 1998;9:90-96.
118. Bertaux F, Sharp AH, Ross CA, Lehrach H, Bates GP, Wanker E. HAP1-huntingtin interactions do not contribute to the molecular pathology in Huntingtons disease transgenic mice. FEBS Lett 1998;426:229-232.
119. Stark LA, Hay RT. Human immunodeficiency virus type 1 (HIV-1) viral protein R (Vpr) interacts with Lys-tRNA synthetase: implications for priming of HIV-1 reverse transcription. J Virol 1998;72:3037-3044.
120. Kennedy NJ, Budd RC. Phosphorylation of FADD/MORT1 and Fas by kinases that associate with the membrane-proximal cytoplasmic domain of Fas. J Immunol 1998;160:4881-4888.
121. Mamoun CB, Sullivan DJJ, Banerjee R, Goldberg DE. Identification and characterization of an unusual double serine/threonine protein phosphatase 2C in the malaria parasite Plasmodium falciparum. J Biol Chem 1998;273:11241-11247.
122. Byrne JA, Nourse CR, Basset P, Gunning P: Identification of homo- and heteromeric interactions between members of the breast carcinoma-associated D52 protein family using the yeast two-hybrid system. Oncogene 1998;16:873-881.
123. Cuconati A, Xiang W, Lahser F, Pfister T, Wimmer E. A protein linkage map of the P2 nonstructural proteins of poliovirus. J Virol 1998;72:1297-1307.
124. Fromont-Racine M, Rain JC, Legrain P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet 1997;16:277-282.
125. Finley RLJ, Brent R. Interaction mating reveals binary and ternary connections between Drosophila cell cycle regulators. Proc Natl Acad Sci USA 1994;91:12980-12984.
126. Lecrenier N, Foury F, Goffeau A. Two-hybrid systematic screening of the yeast proteome. Bioessays 1998;20:1-5.
127. Cho RJ, Fromont-Racine M, Wodicka L, Feierbach B, Stearns T, Legrain P, Lockhart DJ, Davis RW Parallel analysis of genetic selections using whole genome oligonucleotide arrays. Proc Natl Acad Sci USA 1998;95:3752-3757.
128. Petermann R, Mossier BM, Aryee DN, Kovar H. A recombination based method to rapidly assess specificity of two-hybrid clones in yeast. Nucleic Acid Res 1998;26:2252-2253.
129. Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC. Green fluorescent protein as a marker for gene expression. Science 1994;263:802-805.
130. Inouye S, Tsuji FI. Aequorea green fluorescent protein. Expression of the gene and fluorescence characteristics of the recombinant protein. FEBS Lett 1994;341:277-280.
131. Ren P, Lim CS, Johnsen R, Albert PS, Pilgrim D, Riddle DL. Control of C. elegans larval development by neuronal expression of a TGF-beta homolog. Science 1996;274:1389-1391.
132. Heim R, Cubitt AB, Tsien RY Improved green fluorescence. Nature 1995;373:663-664.
133. Johnsson N, Varshavsky A. Split ubiquitin as a sensor of protein interactions in vivo. Proc Natl Acad Sci USA 1994;91:10340-10344.
134. Stagljar I, Korostensky C, Johnsson N, teHeesen HS. A genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo. Proc Natl Acad Sci USA 1998;95:5187-5192.
135. Aronheim A, Zandi E, Hennemann H, Elledge SJ, Karin M. Isolation of an AP-1 repressor by a novel method for detecting protein-protein interactions. Molec Cell Biol 1997;17:3094-3102.
136. Karimova G, Pidoux J, Ullmann A, Ladant D. A bacterial two-hybrid system based on a reconstituted signal transduction pathway. Proc Natl Acad Sci USA 1998;95:5752-5756.
137. Li X, McDermott B, Yuan B, Goff SP. Homomeric interactions between transmembrane proteins of Moloney murine leukemia virus. J Virol 1996;70:1266-1270.
138. Munder T, Furst P. The Saccharomyces cerevisiae CDC25 gene product binds specifically to catalytically inactive ras proteins in vivo. Molec Cell Biol 1992;12:2091-2099.
139. Mahajan NP, Linder K, Berry G, Gordon GW, Heim R, Herman B. Bcl-2 and Bax interactions in mitochondria probed with green fluorescent protein and fluorescence resonance energy transfer. Nat Biotechnol 1998;16:547-552.
140. Boder ET, Wittrup KD. Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol 1997;15:553-557.
141. Kieke MC, Cho BK, Boder ET, Kranz DM, Wittrup KD. Isolation of anti-T cell receptor scFv mutants by yeast surface display. Protein (Eng) 1997;10:1303-1310.
142. Aruffo A, Seed B. Molecular cloning of a CD28 cDNA by a high-efficiency COS cell expression system. Proc Natl Acad Sci USA 1987;84:8573-8577.
143. Rice GC, Goeddel DV, Cachianes G, Woronicz J, Chen EY Williams SR, Leung DW Random PCR mutagenesis screening of secreted proteins by direct expression in mammalian cells. Proc Natl Acad Sci USA 1992;89:5467-5471.
144. Ernst W, Grabherr R, Wegner D, Borth N, Grassauer A, Katinger H. Baculovirus surface display: construction and screening of a eukaryotic epitope library. Nucleic Acid Res 1998;26:1718-1723.
145. Granziero L, Nelboeck P, Bedoucha M, Lanzavecchia A, Reid HH. Baculovirus cDNA libraries for expression cloning of genes encoding cell-surface antigens. J Immunol Methods 1997;203:131-139.
146. Buratti E, Tisminetzky SG, Scodeller ES, Baralle FE. Conformational display of two neutralizing epitopes of HIV-1 gp41 on the Flock House virus capsid protein. J Immunol Methods 1996;197:7-18.
147. Michael SI, Hong JS, Curiel DT, Engler JA: Addition of a short peptide ligand to the adenovirus fiber protein. Gene Ther 1995;2:660-668.
148. Grabherr R, Ernst W, Doblhoff-Dier O, Sara M, Katinger H. Expression of foreign proteins on the surface of Autographa californica nuclear polyhedrosis virus. Biotechniques 1997;22:730-735.
149. Eckhart L, Raffelsberger W, Ferko B, Klima A, Purtscher M, Katinger H, Ruker F. Immunogenic presentation of a conserved gp41 epitope of human immunodeficiency virus type 1 on recombinant surface antigen of hepatitis B virus. J Gen Virol 1996;77:2001-2008.
150. Johnson JE, Schnell MJ, Buonocore L, Rose JK. Specific targeting to CD4+ cells of recombinant vesicular stomatitis viruses encoding human immunodeficiency virus envelope proteins. J Virol 1997;71:5060-5068.
151. Mebatsion T, Conzelmann KK. Specific infection of CD4+ target cells by recombinant rabies virus pseudotypes carrying the HIV-I envelope spike protein. Proc Natl Acad Sci USA 1996;93:11366-11370.
152. Henzel WJ, Billed TM, Stults JT, Wong SC, Grimley Q, Watanabe C. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci USA 1993;90:5011-5015.
153. Mann M, Hojrup P, Roepstorff P. Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol Mass Spectrom 1993;22:338-345.
154. Pappin D, Hojrup P, Bleasby A: Rapid identification of proteins by peptide mass fingerprinting. Curr Biol 1993;3:327-332.
155. James P, Quadroni M, Carafoli E, Gonnet G. Protein identification by mass profile fingerprinting. Biochem Biophys Res Commun 1993;195:58-64.
156. Yates JR, Speicher S, Griffin PR, Hunkapiller T. Peptide mass maps: a highly informative approach to protein identification. Anal Biochem 1993;214:397-408.
157. Shevchenko A, Wilm M, Mann M. Peptide sequencing by mass spectrometry for homology searches and cloning of genes. J Protein Chem 1997;16:481-490.
158. Wilm M, Shevchenko A, Houthaeve T, Breit S, Schweigerer L, Fotsis T, Mann M. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 1996;379:466-469.
159. Deissler H, Wilm M, Gene B, Schmitz B, Ternes T, Naumann F, Mann M, Doerfler W: Rapid protein sequencing by tandem mass spectrometry and cDNA cloning of p20-CGGBP. A novel protein that binds to the unstable triplet repeat 5′-d(CGG)n-3′ in the human FMR1 gene. J Biol Chem 1997;272:16761-16768.
160. Lingner J, Hughes TR, Shevchenko A, Mann M, Lundblad V, Cech TR. Reverse transcriptase motifs in the catalytic subunit of telomerase. Science 1997;276:561-567.
161. Horiuchi H, Lippe R, McBride HM, Rubino M, Woodman P, Stenmark H, Rybin V, Wilm M, Ashman K, Mann M, Zerial M. A novel Rab5 GDP/GTP exchange factor complexed to Rabap-tin-5 links nucleotide exchange to effector recruitment and function. Cell 1997;90:1149-1159.
162. Mercurio F, Zhu H, Murray BW, Shevchenko A, Bennett BL, Li J, Young DB, Barbosa M, Mann M, Manning A, Rao A. IKK-1 and IKK-2: cytokine-activated IkappaB kinases essential for NF- kappaB activation. Science 1997;278:860-866.
163. Szuidak G. Mass spectrometry for biotechnology: San Diego, Academic Press, 1996.
164. Yates JR. Mass spectrometry and the age of the proteome. J Mass Spectrom 1998;33:1-19.
165. Emmet MR, Caprioli RM. Micro-electrospray mass spectrometry: ultra-high sensitivity analysis of peptides and proteins. J Am Soc Mass Spectrom. 1994;5:605-613.
166. Shevchenko A, Wilm M, Vorm O, Mann M. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 1996;68:850-858.
167. Ducret A, Van Oostveen I, Eng JK, Yates JR, Aebersold R. High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry. Protein Sci 1998;7:706-719.
168. McCormack AL, Schieltz DM, Goode B, Yang S, Barnes G, Drubin D, Yates JR. Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level. Anal Chem 1997;69:767-776.
169. Yates JR, McCormack AL, Link AJ, Schieltz D, Eng J, Hays L. Future prospects for the analysis of complex biological systems using micro-column liquid chromatography-electrospray tandem mass spectrometry. Analyst 1996;121:65R-76R.
170. Shevchenko A, Wilm M, Vorm O, Jensen ON, Podtelejnikov AV, Neubauer G, Mortensen P, Mann M. A strategy for identifying gel-separated proteins in sequence databases by MS alone. Biochem Soc Trans 1996;24:893-896.
171. Houthaeve T, Gausepohl H, Ashman K, Nillson T, Mann M. Automated protein preparation techniques using a digest robot. J Protein Chem 1997;16:343-348.
172. Hillenkamp F, Karas M, Beavis RC, Chait BT. Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal Chem 1991;63:1193A-1203A.
173. Shevchenko A, Jensen ON, Podtelejnikov AV, Sagliocco F, Wilm M, Vorm O, Mortensen P, Boucherie H, Mann M. Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proc Natl Acad Sci USA 1996;93:14440-14445.
174. Dongre AR, Eng JK, Yates JR. Emerging tandem-mass-spectrometry techniques for the rapid identification of proteins. Trends Biotechnol 1997;15:418-425.
175. Mann M, Wilm M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem 1994;66:4390-4399.
176. Wilm M, Mann M. Analytical properties of the nanoelectrospray ion source. Anal Chem 1996;68:1-8.
177. Link AJ, Hays LG, Carmack EB, Yates JR. Identifying the major proteome components of Haemophilus influenza type-strain NCTC 8143. Electrophoresis 1997;18:1314-1334.
178. Mann M. A shortcut to interesting human genes: peptide sequence tags, expressed- sequence tags and computers. Trends Biochem Sci 1996;21:494-495.
179. Mortz E, O'Connor PB, Roepstorff P, Kelleher NL, Wood TD, McLafferty FW, Mann M. Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases. Proc Natl Acad Sci USA 1996;93:8264-8267.
180. Patterson SD, Thomas D, Bradshaw RA. Application of combined mass spectrometry and partial amino acid sequence to the identification of gel-separated proteins. Electrophoresis 1996;17:877-891.
181. Eng JK, McCormack AL, Yates JRI. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 1994;5:976-989.
182. Grawunder U, Wilm M, Wu X, Kulesza P, Wilson TE, Mann M, Lieber MR. Activity of DNA ligase IV stimulated by complex formation with XRCC4 protein in mammalian cells. Nature 1997;388:492-495.
183. Varga-Weisz PD, Wilm M, Bonte E, Dumas K, Mann M, Becker PB. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 1997;388:598-602.
184. Liu HY, Badarinarayana V, Audino DC, Rappsilber J, Mann M, Denis CL. The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively. EMBO J 1998;17:1096-1106.
185. Calvio C, Neubauer G, Mann M, Lamond AI. Identification of hnRNP P2 as TLS/FUS using electrospray mass spectrometry. RNA 1995;1:724-733.
186. Mitchell P, Petfalski E, Shevchenko A, Mann M, Tollervey D. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3′→5′ exoribonucleases. Cell 1997;91:457-466.
187. Simos G, Segref A, Fasiolo F, Hellmuth K, Shevchenko A, Mann M, Hurt EC. The yeast protein Arc1p binds to tRNA and functions as a cofactor for the methionyl- and glutamyl-tRNA synthetases. EMBO J 1996;15:5437-5448.
188. Muzio M, Chinnaiyan AM, Kischkel FC, O'Rourke K, Shevchenko A, Ni J, Scaffidi C, Bretz JD, Zhang M, Gentz R, Mann M, Krammer PH, Peter ME, Dixit VM. FLICE, a novel FADD-homologous ICE/CED-3-like protease, is recruited to the CD95 (Fas/APO-1) death-inducing signaling complex. Cell 1996;85:817-827.
189. Medema JP, Scaffidi C, Kischkel FC, Shevchenko A, Mann M, Krammer PH, Peter ME. FLICE is activated by association with the CD95 death-inducing signaling complex (DISC). EMBO J 1997;16:2794-2804.
190. Witke W, Podtelejnikov AV, Di Nardo A, Sutherland JD, Gurniak CB, Dotti C, Mann M. In mouse brain profilin I and profilin II associate with regulators of the endocytic pathway and actin assembly. EMBO J 1998;17:967-976.
191. Winter D, Podtelejnikov AV, Mann M, Li R. The complex containing actin-related proteins Arp2 and Arp3 is required for the motility and integrity of yeast actin patches. Curr Biol 1997;7:519-529.
192. Grandi P, Dang T, Pane N, Shevchenko A, Mann M, Forbes D, Hurt E. Nup93, a vertebrate homologue of yeast Nic96p, forms a complex with a novel 205-kDa protein and is required for correct nuclear pore assembly. Molec Biol Cell 1997;8:2017-2038.
193. Zachariae W, Shevchenko A, Andrews PD, Ciosk R, Galova M, Stark MJ, Mann M, Nasmyth K. Mass spectrometric analysis of the anaphase-promoting complex from yeast: identification of a subunit related to cullins. Science 1998;279:1216-1219.
194. Yu H, Peters JM, King RW, Page AM, Hieter P, Kirschner MW: Identification of a cullin homology region in a subunit of the anaphase-promoting complex. Science 1998;279:1219-1222.
195. James P, Halladay J, Craig EA. Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 1996;144:1425-1436.
196. Yavuzer U, Coding CR. pWITCH: a versatile two-hybrid assay vector for the production of epitope/activation domain-tagged proteins both in vitro and in yeast. Gene 1995;165:93-96.
197. Ward AC, Castelli LA, Lucantoni AC, White JF, Azad AA, Macreadie IG: Expression and analysis of the NS2 protein of influenza A virus. Arch Virol 1995;140:2067-2073.
198. Lowman HB. Bacteriophage display and discovery of peptide leads for drug development. Annu Rev Biophys Biomol Struct 1997;26:401-424.
199. Harlow E, Whyte P, Franza BRJ, Schley C. Association of adenovirus early region 1A proteins with cellular polypeptides. Molec Cell Biol 1986;6:1579-1589.
200. Leatherwood J, Lopez-Girona A, Russell P. Interaction of Cdc2 and Cdc18 with a fission yeast ORC2-like protein. Nature 1996;379:360-363.
201. Mitchell DA, Marshall TK, Deschenes RJ. Vectors for the inducible overexpression of glutathione S-transferase fusion proteins in yeast. Yeast 1993;9:715-722.
202. Cohen BD, Lowy DR, Schiller JT. The conserved C-terminal domain of the bovine papilloma-virus E5 oncoprotein can associate with an alpha-adaptin-like molecule: a possible link between growth factor receptors and viral transformation. Molec Cell Biol 1993;13:6462-6468.
203. Lackmann M, Bucci T, Mann RJ, Kravets LA, Viney E, Smith F, Moritz RL, Carter W, Simpson RJ, Nicola NA, Mackwell K, Nice EC, Wilks AF, Boyd AW. Purification of a ligand for the EPH-like receptor HEK using a biosensor-based affinity detection approach. Proc Natl Acad Sci USA 1996;93:2523-2527.
204. Bartley TD, Hunt RW, Welcher AA, Boyle WJ, Parker VP, Lindberg RA, Lu HS, Colombero AM, Elliott RL, Guthrie BA. B61 is a ligand for the ECK receptor protein-tyrosine kinase. Nature 1994;368:558-560.
205. Sakano S, Serizawa R, Inada T, Iwama A, Itoh A, Kato C, Shimizu Y, Shinkai F, Shimizu R, Kondo S, Ohno M, Suda T. Characterization of a ligand for receptor protein-tyrosine kinase HTK expressed in immature hematopoietic cells. Oncogene 1996;13:813-822.
206. Krone JR, Nelson RW, Dogruel D, Williams P, Granzow R. BIA/MS: interfacing biomolecular interaction analysis with mass spectrometry. Anal Biochem 1997;244:124-132.
207. Nelson RW, Krone JR, Jansson O. Surface plasmon resonance biomolecular interaction analysis mass spectrometry. 1. Chip-based analysis. Anal Chem 1997;69:4363-4368.
208. Nelson RW, Krone JR, Jansson O. Surface plasmon resonance biomolecular interaction analysis mass spectrometry. 2. Fiber optic-based analysis. Anal Chem 1997;69:4369-4374.
209. Kuwata H, Yip TT, Yip CL, Tomita M, Hutchens TW. Bactericidal domain of lactoferrin: detection, quantitation, and characterization of lactoferricin in serum by SELDI affinity mass spectrometry. Biochem Biophys Res Commun 1998;245:764-773.