Abstract
Cellular biochemical machineries, what we call pathways, consist of dynamically assembling and disassembling macromolecular complexes. Although our models for the organization of biochemical machines are derived largely from in vitro experiments, do they reflect their organization in intact, living cells? We have developed a general experimental strategy that addresses this question by allowing the quantitative probing of molecular interactions in intact, living cells. The experimental strategy is based on Protein fragment Complementation Assays (PCA), a method whereby protein interactions are coupled to refolding of enzymes from cognate fragments where reconstitution of enzyme activity acts as the detector of a protein interaction. A biochemical machine or pathway is defined by grouping interacting proteins into those that are perturbed in the same way by common factors (hormones, metabolites, enzyme inhibitors, etc.). In this chapter we review some of the essential principles of PCA and provide details and protocols for applications of PCA, particularly in mammalian cells, based on three PCA reporters, dihydrofolate reductase, green fluorescent protein, and β-lactamase.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Drees BL (1999) Progress and variations in two-hybrid and three-hybrid technologies. Curr Opin Chem Biol 3:64–70
Evangelista C, Lockshon D, Fields S (1996) The yeast two-hybrid system: prospects for protein linkage maps. Trends Cell Biol 6:196–199
Fields S, Song O (1989) A novel genetic system to detect protein-protein interactions. Nature 340:245–246
Vidal M, Legrain P (1999) Yeast forward and reverse ‘n’-hybrid systems. Nucleic Acids Res 27:919–929
Walhout AJ, Sordella R, Lu X et al (2000) Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287:116–122
Uetz P, Giot L, Cagney G et al (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623–627
Michnick SW, Remy I, Campbell-Valois FX et al (2000) Detection of protein-protein interactions by protein fragment complementation strategies. Methods Enzymol 328:208–230
Paulmurugan R, Umezawa Y, Gambhir SS (2002) Noninvasive imaging of protein-protein interactions in living subjects by using reporter protein complementation and reconstitution strategies. Proc Natl Acad Sci U S A 99:15608–15613
Hu CD, Kerppola TK (2003) Simultaneous visualization of multiple protein interactions in living cells using multicolor fluorescence complementation analysis. Nat Biotechnol 21:539–545
Paulmurugan R, Gambhir SS (2003) Monitoring protein-protein interactions using split synthetic renilla luciferase protein-fragment-assisted complementation. Anal Chem 75:1584–1589
Luker KE, Smith MC, Luker GD et al (2004) Kinetics of regulated protein-protein interactions revealed with firefly luciferase complementation imaging in cells and living animals. Proc Natl Acad Sci U S A 101:12288–12293
Magliery TJ, Wilson CG, Pan W et al (2005) Detecting protein-protein interactions with a green fluorescent protein fragment reassembly trap: scope and mechanism. J Am Chem Soc 127:146–157
Remy I, Michnick SW (2006) A highly sensitive protein-protein interaction assay based on Gaussia luciferase. Nat Methods 3:977–979
Wehr MC, Laage R, Bolz U et al (2006) Monitoring regulated protein-protein interactions using split TEV. Nat Methods 3:985–993
Michnick SW, Ear PH, Manderson EN et al (2007) Universal strategies in research and drug discovery based on protein-fragment complementation assays. Nat Rev Drug Discov 6:569–582
Remy I, Michnick SW (2007) Application of protein-fragment complementation assays in cell biology. Biotechniques 42:137, 139, 141 passim
Stefan E, Aquin S, Berger N et al (2007) Quantification of dynamic protein complexes using Renilla luciferase fragment complementation applied to protein kinase A activities in vivo. Proc Natl Acad Sci U S A 104:16916–16921
Michnick SW, Ear PH, Landry C et al (2010) A toolkit of protein-fragment complementation assays for studying and dissecting large-scale and dynamic protein-protein interactions in living cells. Methods Enzymol 470:335–368
Michnick SW, Ear PH, Landry C et al (2011) Protein-fragment complementation assays for large-scale analysis, functional dissection and dynamic studies of protein-protein interactions in living cells. Methods Mol Biol 756:395–425
Anfinsen CB, Haber E, Sela M et al (1961) The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc Natl Acad Sci U S A 47:1309–1314
Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223–230
Gutte B, Merrifield RB (1971) The synthesis of ribonuclease A. J Biol Chem 246:1922–1941
Richards FM (1958) On the Enzymic Activity of Subtilisin-Modified Ribonuclease. Proc Natl Acad Sci U S A 44:162–166
Taniuchi H, Anfinsen CB (1971) Simultaneous formation of two alternative enzymology active structures by complementation of two overlapping fragments of staphylococcal nuclease. J Biol Chem 246:2291–2301
Pelletier JN, Campbell-Valois FX, Michnick SW (1998) Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments. Proc Natl Acad Sci U S A 95:12141–12146
Pelletier JN, Michnick SW (1997) A protein complementation assay for detection of protein-protein interactions in vivo. Protein Eng 10:89
Johnsson N, Varshavsky A (1994) Split ubiquitin as a sensor of protein interactions in vivo. Proc Natl Acad Sci U S A 91:10340–10344
Rossi F, Charlton CA, Blau HM (1997) Monitoring protein-protein interactions in intact eukaryotic cells by beta-galactosidase complementation. Proc Natl Acad Sci U S A 94:8405–8410
Remy I, Michnick SW (1999) Clonal selection and in vivo quantitation of protein interactions with protein-fragment complementation assays. Proc Natl Acad Sci U S A 96:5394–5399
Remy I, Wilson IA, Michnick SW (1999) Erythropoietin receptor activation by a ligand-induced conformation change. Science 283:990–993
Remy I, Michnick SW (2001) Visualization of biochemical networks in living cells. Proc Natl Acad Sci U S A 98:7678–7683
Remy I, Campbell-Valois FX, Michnick SW (2007) Detection of protein-protein interactions using a simple survival protein-fragment complementation assay based on the enzyme dihydrofolate reductase. Nat Protoc 2:2120–2125
Tarassov K, Messier V, Landry CR et al (2008) An in vivo map of the yeast protein interactome. Science 320:1465–1470
Galarneau A, Primeau M, Trudeau LE et al (2002) Beta-lactamase protein fragment complementation assays as in vivo and in vitro sensors of protein protein interactions. Nat Biotechnol 20:619–622
Remy I, Ghaddar G, Michnick SW (2007) Using the beta-lactamase protein-fragment complementation assay to probe dynamic protein-protein interactions. Nat Protoc 2:2302–2306
Israel DI, Kaufman RJ (1993) Dexamethasone negatively regulates the activity of a chimeric dihydrofolate reductase/glucocorticoid receptor protein. Proc Natl Acad Sci U S A 90:4290–4294
Kaufman RJ, Bertino JR, Schimke RT (1978) Quantitation of dihydrofolate reductase in individual parental and methotrexate-resistant murine cells. Use of a fluorescence activated cell sorter. J Biol Chem 253:5852–5860
Kaufman RJ (1990) Selection and coamplification of heterologous genes in mammalian cells. Methods Enzymol 185:537–566
Zlokarnik G, Negulescu PA, Knapp TE et al (1998) Quantitation of transcription and clonal selection of single living cells with beta-lactamase as reporter. Science 279:84–88
Zlokarnik G (2000) Fusions to beta-lactamase as a reporter for gene expression in live mammalian cells. Methods Enzymol 326:221–244
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Remy, I., Michnick, S.W. (2015). Mapping Biochemical Networks with Protein Fragment Complementation Assays. In: Meyerkord, C., Fu, H. (eds) Protein-Protein Interactions. Methods in Molecular Biology, vol 1278. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2425-7_31
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2425-7_31
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2424-0
Online ISBN: 978-1-4939-2425-7
eBook Packages: Springer Protocols