Chapter 30: Using Peptide Aptamers to Study Proteins and Protein Networks—References
Biocca S. and Cattaneo A. 1995. Intracellular immunization: Antibody targeting to subcellular compartments. Trends Cell Biol. 5: 248–252.
Biocca S., Pierandrei-Amaldi P., and Cattaneo A. 1993. Intracellular expression of anti-p21ras single chain Fv fragments inhibits meiotic maturation of Xenopus oocytes. Biochem. Biophys. Res. Commun. 197: 422–427.
Biocca S., Pierandrei-Amaldi P., Campioni N., and Cattaneo A. 1994. Intracellular immunization with cytosolic recombinant antibodies. Biotechnology 12: 396–399.
Biocca S., Ruberti F., Tafani M., Pierandrei-Amaldi P., and Cattaneo A. 1995. Redox state of single chain Fv fragments targeted to the endoplasmic reticulum, cytosol and mitochondria. Biotechnology 13: 1110–1115.
Bird R.E., Hardman K.D., Jacobson J.W., Johnson S., Kaufman B.M., Lee S.M., Lee T., Pope S.H., Riordan G.S., and Whitlow M. 1988. Single-chain antigen-binding proteins. Science 242: 423–426.
Blum J.H., Dove S.L., Hochschild A., and Mekalanos J.J. 2000. Isolation of peptide aptamers that inhibit intracellular processes. Proc. Natl. Acad. Sci. 97: 2241–2246.
Broder Y.C., Katz S., and Aronheim A. 1998. The ras recruitment system, a novel approach to the study of protein-protein interactions. Curr. Biol. 8: 1121–1124.
Bunker C.A. and Kingston R.E. 1995. Identification of a cDNA for SSRP1, an HMG-box protein, by interaction with the c-Myc oncoprotein in a novel bacterial expression screen. Nucleic Acids Res. 23: 269–276.
Butz K., Denk C., Ullmann A., Scheffner M., and Hoppe-Seyler F. 2000. Induction of apoptosis in human papillomavirus positive cancer cells by peptide aptamers targeting the viral E6 oncoprotein. Proc. Natl. Acad. Sci. 97: 6693–6697.
Cadwell R.C. and Joyce G.F. 1995. Mutagenic PCR. In PCR primer: A laboratory manual (ed. C.W. Dieffenbach and G.S. Dveksler), pp. 583–590. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Caponigro G., Abedi M.R., Hurlburt A.P., Maxfield A., Judd W., and Kamb A. 1998. Transdominant genetic analysis of a growth control pathway. Proc. Natl. Acad. Sci. 95: 7508–7513.
Cech T.R. 1987. The chemistry of self-splicing RNA and RNA enzymes. Science 236: 1532–1539.
Chien C.-T., Bartel P.L., Sternglanz R., and Fields S. 1991. The two-hybrid system: A method to identify and clone genes for proteins that interact with a protein of interest. Proc. Natl. Acad. Sci. 88: 9578–9582.
Cohen B.A., Colas P., and Brent R. 1998. An artificial cell-cycle inhibitor isolated from a combinatorial library. Proc. Natl. Acad. Sci. 95: 14272–14277.
Colas P., Cohen B., Ko Ferrigno P., Silver P.A., and Brent R. 2000. Targeted modification and transportation of cellular proteins. Proc. Natl. Acad. Sci. 97: 13720–13725.
Colas P., Cohen B., Jessen T., Grishina I., McCoy J., and Brent R. 1996. Genetic selection of peptide aptamers that recognize and inhibit cyclin-dependent kinase 2. Nature 380: 548–550.
de Nooij J.C., Letendre M.A., and Hariharan I.K. 1996. A cyclin-dependent kinase inhibitor, Dacapo, is necessary for timely exit from the cell cycle during Drosophila embryogenesis. Cell 87: 1237–1247.
de Soultrait V.R., Lozach P.Y., Altmeyer R., Tarrago-Litvak L., Litvak S., and Andreola M.L. 2002. DNA aptamers derived from HIV-1 RNase H inhibitors are strong anti-integrase agents. J. Mol. Biol. 324: 195–203.
Du K., Herzig S., Kulkarni R.N., and Montminy M. 2003. TRB3: A tribbles homolog that inhibits Akt/PKB activation by insulin in liver. Science 300: 1574–1577.
Edgar B.A. and Lehner C.F. 1996. Developmental control of cell cycle regulators: A fly's perspective. Science 274: 1646–1652.
Ellington A.D. and Szostak J.W. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818–822.
Estojak J., Brent R., and Golemis E.A. 1995. Correlation of two-hybrid affinity data with in vitro measurements. Mol. Cell. Biol. 15: 5820–5829.
Evangelista C., Lockshon D., and Fields S. 1996. The yeast two-hybrid system: Prospects for protein linkage maps. Trends Cell Biol. 6: 196–199.
Fabbrizio E., Le Cam L., Polanowska J., Kaczorek M., Lamb N., Brent R., and Sardet C. 1999. Inhibition of mammalian cell proliferation by genetically selected peptide aptamers that functionally antagonize E2F activity. Oncogene 18: 4357–4363.
Fields S. and Song O. 1989. A novel genetic system to detect protein-protein interactions. Nature 340: 245–246.
Finley R.L., Jr., and Brent R. 1995. Interaction trap cloning with yeast. In DNA cloning 2: Expression systems: A practical approach (ed. B.D. Hames and D.M. Glover), pp. 169–203. Oxford University Press, Oxford, United Kingdom.
Finley R.L., Jr., Soans A.H., and Stanyon C.A. 2002. Peptide aptamers to study protein networks. In Protein-protein interactions: A molecular cloning manual (ed. E. Golemis), pp. 489–505. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., and Mello C.C. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806–811.
Fromont-Racine M., Mayes A.E., Brunet-Simon A., Rain J.C., Colley A., Dix I., Decourty L., Joly N., Ricard F., Beggs J.D., and Legrain P. 2000. Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins. Yeast 17: 95–110.
Geyer C.R., Colman-Lerner A., and Brent R. 1999. "Mutagenesis" by peptide aptamers identifies genetic network members and pathway connections. Proc. Natl. Acad. Sci. 96: 8567–8572.
Giot L., Bader J.S., Brouwer C., Chaudhuri A., Kuang B., Li Y., Hao Y.L., Ooi C.E., Godwin B., Vitols E., et al. 2003. A protein interaction map of Drosophila melanogaster. Science 302: 1727–1736.
Golemis E.A., Serebriiskii I., Finley R.L., Jr., Kolonin M.G., Gyuris J., and Brent R. 1998-2004. Interaction trap/two-hybrid system to identify interacting proteins. In Current protocols in molecular biology (ed. F.M. Ausubel et al.). Wiley, New York.
Griffin L.C., Tidmarsh G.F., Bock L.C., Toole J.J., and Leung L.L. 1993. In vivo anticoagulant properties of a novel nucleotide-based thrombin inhibitor and demonstration of regional anticoagulation in extracorporeal circuits. Blood 81: 3271–3276.
Gyuris J., Golemis E., Chertkov H., and Brent R. 1993. Cdi1, a human G1 and S phase protein phosphatase that associates with Cdk2. Cell 75: 791–803.
Hammond S.M., Bernstein E., Beach D., and Hannon G.J. 2000. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404: 293–296.
Herskowitz I. 1987. Functional inactivation of genes by dominant negative mutations. Nature 329: 219–222.
Holmgren A. 1985. Thioredoxin. Annu. Rev. Biochem. 54: 237–271.
Ito T., Tashiro K., Muta S., Ozawa R., Chiba T., Nishizawa M., Yamamoto K., Kuhara S., and Sakaki Y. 2000. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. 97: 1143–1147.
Izant J.G. and Weintraub H. 1984. Inhibition of thymidine kinase gene expression by anti-sense RNA: A molecular approach to genetic analysis. Cell 36: 1007–1015.
Jiang R. and Carlson M. 1996. Glucose regulates protein interactions within the yeast SNF1 protein kinase complex. Genes Dev. 10: 3105–3115.
Joung J.K., Ramm E.I., and Pabo C.O. 2000. A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc. Natl. Acad. Sci. 97: 7382–7387.
Karimova G., Pidoux J., Ullmann A., and Ladant D. 1998. A bacterial two-hybrid system based on a reconstituted signal transduction pathway. Proc. Natl. Acad. Sci. 95: 5752–5756.
Kolonin M.G. and Finley R.L., Jr. 1998. Targeting cyclin-dependent kinases in Drosophila with peptide aptamers. Proc. Natl. Acad. Sci. 95: 14266–14271.
Kolonin M.G. and Finley R.L., Jr. 2000. A role for cyclin J in the rapid nuclear division cycles of early Drosophila embryogenesis. Dev. Biol. 227: 661–672.
Kolonin M.G., Zhong J., and Finley R.L. 2000. Interaction mating methods in two-hybrid systems. Methods Enzymol. 328: 26–46.
Ladner R.C. 1995. Constrained peptides as binding entities. Trends Biotechnol. 13: 426–430.
Lane M.E., Sauer K., Wallace K., Jan Y.N., Lehner C.F., and Vaessin H. 1996. Dacapo, a cyclin-dependent kinase inhibitor, stops cell proliferation during Drosophila development. Cell 87: 1225–1235.
LaVallie E.R., DiBlasio E.A., Kovacic S., Grant K.L., Schendel P.F., and McCoy J.M. 1993. A thioredoxin gene fusion expression system that circumvents inclusion body formation in the E. coli cytoplasm. Biotechnology 11: 187–193.
Lee S.S., Kennedy S., Tolonen A.C., and Ruvkun G. 2003. DAF-16 target genes that control C. elegans life-span and metabolism. Science 300: 644–647.
Lener M., Horn I.R., Cardinale A., Messina S., Nielsen U.B., Rybak S.M., Hoogenboom H.R., Cattaneo A., and Biocca S. 2000. Diverting a protein from its cellular location by intracellular antibodies. The case of p21Ras. Eur. J. Biochem. 267: 1196–1205.
Li S., Armstrong C.M., Bertin N., Ge H., Milstein S., Boxem M., Vidalain P.O., Han J.D., Chesneau A., Hao T., et al. 2004. A map of the interactome network of the metazoan C. elegans. Science 303: 540–543.
Lin-Goerke J.L., Robbins D.J., and Burczak J.D. 1997. PCR-based random mutagenesis using manganese and reduced dNTP concentration. Biotechniques 23: 409–412.
Lu Z., Murray K.S., Van Cleave V., LaVallie E.R., Stahl M.L., and McCoy J.M. 1995. 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 13: 366–372.
Lum L., Yao S., Mozer B., Rovescalli A., Von Kessler D., Nirenberg M., and Beachy P.A. 2003. Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science 299: 2039–2045.
Ma H., Kunes S., Schatz P.J., and Botstein D. 1987. Plasmid construction by homologous recombination in yeast. Gene 58: 201–216.
McCraith S., Holtzman T., Moss B., and Fields S. 2000. Genome-wide analysis of vaccinia virus protein-protein interactions. Proc. Natl. Acad. Sci. 97: 4879–4884.
Murphy M.B., Fuller S.T., Richardson P.M., and Doyle S.A. 2003. An improved method for the in vitro evolution of aptamers and applications in protein detection and purification. Nucleic Acids Res. 31: e110.
Nagel-Wolfrum K., Buerger C., Wittig I., Butz K., Hoppe-Seyler F., and Groner B. 2004. The interaction of specific peptide aptamers with the DNA binding domain and the dimerization domain of the transcription factor Stat3 inhibits transactivation and induces apoptosis in tumor cells. Mol. Cancer Res. 2: 170–182.
Norman T.C., Smith D.L., Sorger P.K., Drees B.L., O'Rourke S.M., Hughes T.R., Roberts C.J., Friend S.H., Fields S., and Murray A.W. 1999. Genetic selection of peptide inhibitors of biological pathways. Science 285: 591–595.
Roberts R.W. and Szostak J.W. 1997. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc. Natl. Acad. Sci. 94: 12297–12302.
Schramke V. and Allshire R. 2003. Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 301: 1069–1074.
Scott J.K. and Smith G.P. 1990. Searching for peptide ligands with an epitope library. Science 249: 386–390.
Serebriiskii I., Khazak V., and Golemis E.A. 1999. A two-hybrid dual bait system to discriminate specificity of protein interactions. J. Biol. Chem. 274: 17080–17087.
Serebriiskii I.G., Mitina O., Pugacheva E.N., Benevolenskaya E., Kotova E., Toby G.G., Khazak V., Kaelin W.G., Chernoff J., and Golemis E.A. 2002. Detection of peptides, proteins, and drugs that selectively interact with protein targets. Genome Res. 12: 1785–1791.
Shi H., Hoffman B.E., and Lis J.T. 1999. RNA aptamers as effective protein antagonists in a multicellular organism. Proc. Natl. Acad. Sci. 96: 10033–10038.
Smith G.P. 1985. Filamentous fusion phage: Novel expression vectors that display cloned antigens on the virion surface. Science 228: 1315–1317.
Tse E. and Rabbitts T.H. 2000. Intracellular antibody-caspase-mediated cell killing: An approach for application in cancer therapy. Proc. Natl. Acad. Sci. 97: 12266–12271.
Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P., Qureshi-Emili A., Li Y., Godwin B., Conover D., Kalbfleisch T., Vijayadamodar G., Yang M., Johnston M., Fields S., and Rothberg J.M. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623–627.
Vidal M., Brachmann R.K., Fattaey A., Harlow E., and Boeke J.D. 1996. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc. Natl. Acad. Sci. 93: 10315–10320.
Volpe T.A., Kidner C., Hall I.M., Teng G., Grewal S.I., and Martienssen R.A. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297: 1833–1837.
Xu C.W. and Luo Z. 2002. Inactivation of Ras function by allele-specific peptide aptamers. Oncogene 21: 5753–5757.
Xu C.W., Mendelsohn A.R., and Brent R. 1997. Cells that register logical relationships among proteins. Proc. Natl. Acad. Sci. 94: 12473–12478.
Yang M., Wu Z., and Fields S. 1995. Protein-peptide interactions analyzed with the yeast two-hybrid system. Nucleic Acids Res. 23: 1152–1156.
Zhang Z., Zhu W., and Kodadek T. 2000. Selection and application of peptide-binding peptides. Nat. Biotechnol. 18: 71–74.
Zhao J.J. and Pick L. 1993. Generating loss-of-function phenotypes of the fushi tarazu gene with a targeted ribozyme in Drosophila. Nature 365: 448–451.
<<< Chapter 29 References
Chapter 31 References >>>
|
