Systems for the detection and analysis of protein–protein interactions

The analysis of protein–protein interactions is important for developing a better understanding of the functional annotations of proteins that are involved in various biochemical reactions in vivo. The discovery that a protein with an unknown function binds to a protein with a known function could provide a significant clue to the cellular pathway concerning the unknown protein. Therefore, information on protein–protein interactions obtained by the comprehensive analysis of all gene products is available for the construction of interactive networks consisting of individual protein–protein interactions, which, in turn, permit elaborate biological phenomena to be understood. Systems for detecting protein–protein interactions in vitro and in vivo have been developed, and have been modified to compensate for limitations. Using these novel approaches, comprehensive and reliable information on protein–protein interactions can be determined. Systems that permit this to be achieved are described in this review.

[1]  K. Terpe.  Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems , 2002, Applied Microbiology and Biotechnology.

[2]  J. M. McDonnell,et al.  Surface plasmon resonance: towards an understanding of the mechanisms of biological molecular recognition. , 2001, Current opinion in chemical biology.

[3]  A. Galarneau,et al.  β-Lactamase protein fragment complementation assays as in vivo and in vitro sensors of protein–protein interactions , 2002, Nature Biotechnology.

[4]  B. André,et al.  K+ channel interactions detected by a genetic system optimized for systematic studies of membrane protein interactions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Chu di Guana,et al.  Vectors that facilitate the expression and purification of foreign peptides in Escherichia coli by fusion to maltose-binding protein. , 1988 .

[6]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[7]  Horst Wallrabe,et al.  Characterization of one- and two-photon excitation fluorescence resonance energy transfer microscopy. , 2003, Methods.

[8]  R. Karlsson,et al.  SPR for molecular interaction analysis: a review of emerging application areas , 2004, Journal of molecular recognition : JMR.

[9]  S. Elledge,et al.  Isolation of an AP-1 repressor by a novel method for detecting protein-protein interactions , 1997, Molecular and cellular biology.

[10]  H. Blau,et al.  Monitoring protein-protein interactions in intact eukaryotic cells by beta-galactosidase complementation. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[11]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[12]  M. Vidal,et al.  Protein interaction mapping in C. elegans using proteins involved in vulval development. , 2000, Science.

[13]  M. Ueda,et al.  Genetic immobilization of proteins on the yeast cell surface. , 2000, Biotechnology advances.

[14]  A. Bauer,et al.  Analyzing protein complexes in Drosophila with tandem affinity purification–mass spectrometry , 2005, Developmental dynamics : an official publication of the American Association of Anatomists.

[15]  S. Michnick,et al.  Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[16]  S. Fields,et al.  A tethered catalysis, two-hybrid system to identify protein-protein interactions requiring post-translational modifications , 2004, Nature Biotechnology.

[17]  G K Lewis,et al.  Isolation of monoclonal antibodies specific for human c-myc proto-oncogene product , 1985, Molecular and cellular biology.

[18]  R. Farràs,et al.  Detection of in vivo protein interactions between Snf1-related kinase subunits with intron-tagged epitope-labelling in plants cells. , 2001, Nucleic acids research.

[19]  H. Lehrach,et al.  A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome , 2005, Cell.

[20]  D. Ladant,et al.  A bacterial two-hybrid system based on a reconstituted signal transduction pathway. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[21]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[22]  A. Yergey,et al.  Mass spectrometry after capture and small-volume elution of analyte from a surface plasmon resonance biosensor. , 2002, Analytical Chemistry.

[23]  H Inouye,et al.  Vectors that facilitate the expression and purification of foreign peptides in Escherichia coli by fusion to maltose-binding protein. , 1988, Gene.

[24]  R. Nelson,et al.  Surface plasmon resonance mass spectrometry: recent progress and outlooks. , 2003, Trends in biotechnology.

[25]  A. Varshavsky,et al.  Split ubiquitin as a sensor of protein interactions in vivo. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[26]  B. Séraphin,et al.  A generic protein purification method for protein complex characterization and proteome exploration , 1999, Nature Biotechnology.

[27]  Stanley Fields,et al.  A protein linkage map of Escherichia coli bacteriophage T7 , 1996, Nature Genetics.

[28]  Gaudenz Danuser,et al.  FRET or no FRET: a quantitative comparison. , 2003, Biophysical journal.

[29]  A. Shevchenko,et al.  Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry , 1996, Nature.

[30]  S S Gambhir,et al.  Monitoring protein-protein interactions using split synthetic renilla luciferase protein-fragment-assisted complementation. , 2003, Analytical chemistry.

[31]  Matthew A Cooper,et al.  Advances in membrane receptor screening and analysis , 2004, Journal of molecular recognition : JMR.

[32]  S. Michnick,et al.  Clonal selection and in vivo quantitation of protein interactions with protein-fragment complementation assays. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[33]  M C Davies,et al.  Characterization of the surfaces generated by liposome binding to the modified dextran matrix of a surface plasmon resonance sensor chip. , 2000, Analytical biochemistry.

[34]  M. Dimitrova,et al.  A new LexA-based genetic system for monitoring and analyzing protein heterodimerization in Escherichia coli , 1998, Molecular and General Genetics MGG.

[35]  K. Kuroda,et al.  Detection of protein–protein interactions by a combination of a novel cytoplasmic membrane targeting system of recombinant proteins and fluorescence resonance energy transfer , 2006, Applied Microbiology and Biotechnology.

[36]  Y. Umezawa,et al.  Protein splicing-based reconstitution of split green fluorescent protein for monitoring protein-protein interactions in bacteria: improved sensitivity and reduced screening time. , 2001, Analytical chemistry.

[37]  J. Lidholm,et al.  BIACORE analysis of histidine-tagged proteins using a chelating NTA sensor chip. , 1997, Analytical biochemistry.

[38]  K. Mikoshiba,et al.  Combination of biomolecular interaction analysis and mass spectrometric amino acid sequencing. , 2000, Analytical chemistry.

[39]  J. Piehler.  New methodologies for measuring protein interactions in vivo and in vitro. , 2005, Current opinion in structural biology.

[40]  L. Stryer.  Fluorescence energy transfer as a spectroscopic ruler. , 1978, Annual review of biochemistry.

[41]  D. Smith,et al.  Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase. , 1988, Gene.

[42]  P. Legrain,et al.  A genomic approach of the hepatitis C virus generates a protein interaction map. , 2000, Gene.

[43]  D. O'Shannessy,et al.  Immobilization chemistries suitable for use in the BIAcore surface plasmon resonance detector. , 1992, Analytical biochemistry.

[44]  S. Weissman,et al.  A contingent replication assay for the detection of protein-protein interactions in animal cells. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[45]  A. Podtelejnikov,et al.  Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Igor Stagljar,et al.  Application of the split-ubiquitin membrane yeast two-hybrid system to investigate membrane protein interactions. , 2004, Methods.

[47]  A. Aronheim,et al.  The Ras recruitment system, a novel approach to the study of protein–protein interactions , 1998, Current Biology.

[48]  Horst Wallrabe,et al.  Imaging protein molecules using FRET and FLIM microscopy. , 2005, Current opinion in biotechnology.

[49]  T. Köcher,et al.  An efficient protein complex purification method for functional proteomics in higher eukaryotes , 2003, Nature Biotechnology.

[50]  J. Keith Joung,et al.  Activation of prokaryotic transcription through arbitrary protein–protein contacts , 1997, Nature.

[51]  H. Stunnenberg,et al.  Rapid and efficient purification of native histidine-tagged protein expressed by recombinant vaccinia virus. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[53]  T. Jovin,et al.  FRET imaging , 2003, Nature Biotechnology.

[54]  Horst Wallrabe,et al.  Confocal FRET microscopy to measure clustering of ligand-receptor complexes in endocytic membranes. , 2003, Biophysical journal.

[55]  S. Kessler.  Use of protein A-bearing staphylococci for the immunoprecipitation and isolation of antigens from cells. , 1981, Methods in enzymology.

[56]  M. Ueda,et al.  Yeast cell-surface display—applications of molecular display , 2004, Applied Microbiology and Biotechnology.

[57]  S. Fields,et al.  Genome-wide analysis of vaccinia virus protein-protein interactions. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[58]  B. Séraphin,et al.  The DEXD/H‐box RNA helicase RHII/Gu is a co‐factor for c‐Jun‐activated transcription , 2002, The EMBO journal.

[59]  D. Ladant,et al.  Interaction Network among Escherichia coli Membrane Proteins Involved in Cell Division as Revealed by Bacterial Two-Hybrid Analysis , 2005, Journal of bacteriology.

[60]  Giulio Superti-Furga,et al.  A physical and functional map of the human TNF-α/NF-κB signal transduction pathway , 2004, Nature Cell Biology.

[61]  J. Wojcik,et al.  The protein–protein interaction map of Helicobacter pylori , 2001, Nature.

[62]  William Stafford Noble,et al.  Large-scale identification of yeast integral membrane protein interactions. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[63]  R. Heim,et al.  Using GFP in FRET-based applications. , 1999, Trends in cell biology.

[64]  H. Dohlman,et al.  Use of G-protein fusions to monitor integral membrane protein–protein interactions in yeast , 2000, Nature Biotechnology.

[65]  I. Stagljar,et al.  A genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[66]  E. Hochuli,et al.  New metal chelate adsorbent selective for proteins and peptides containing neighbouring histidine residues. , 1987, Journal of chromatography.

[67]  Bo Johnsson,et al.  A novel hydrogel matrix on gold surfaces in surface plasmon resonance sensors for fast and efficient covalent immobilization of ligands , 1990 .

[68]  M. Ueda.  Future direction of molecular display by yeast-cell surface engineering , 2004 .

[69]  M. Vidal,et al.  Combined Functional Genomic Maps of the C. elegans DNA Damage Response , 2002, Science.

[70]  M. Kornacker,et al.  Gene activation by the AraC protein can be inhibited by DNA looping between AraC and a LexA repressor that interacts with AraC: possible applications as a two‐hybrid system , 1998, Molecular microbiology.

[71]  A. Aronheim,et al.  A novel approach for the identification of protein-protein interaction with integral membrane proteins. , 2001, Nucleic acids research.

[72]  M. Hofnung,et al.  Sequences of the malE gene and of its product, the maltose-binding protein of Escherichia coli K12. , 1984, The Journal of biological chemistry.

[73]  R. Karlsson,et al.  Kinetic analysis of monoclonal antibody-antigen interactions with a new biosensor based analytical system. , 1991, Journal of immunological methods.

[74]  H. Dohlman,et al.  Erratum: Use of G-protein fusions to monitor integral membrane protein-protein interactions in yeast (Nature Biotechnology (October 2000) (1075)) , 2000 .

[75]  Y. Hayashizaki,et al.  Protein-protein interaction panel using mouse full-length cDNAs. , 2001, Genome research.

[76]  H. Fritz,et al.  Membrane insertion of the bacterial signal transduction protein ToxR and requirements of transcription activation studied by modular replacement of different protein substructures. , 1995, The EMBO journal.

[77]  Ammasi Periasamy,et al.  Fluorescence resonance energy transfer (FRET) microscopy imaging of live cell protein localizations , 2003, The Journal of cell biology.

[78]  M. Cooper.  Label-free screening of bio-molecular interactions , 2003, Analytical and bioanalytical chemistry.

[79]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[80]  W. Lennarz,et al.  Subunits of the Translocon Interact with Components of the Oligosaccharyl Transferase Complex* , 2005, Journal of Biological Chemistry.

[81]  James R. Knight,et al.  A Protein Interaction Map of Drosophila melanogaster , 2003, Science.

[82]  Kathryn S. Prickett,et al.  A Short Polypeptide Marker Sequence Useful for Recombinant Protein Identification and Purification , 1988, Bio/Technology.

[83]  S. Loefas,et al.  Flow-mediated on-surface reconstitution of G-protein coupled receptors for applications in surface plasmon resonance biosensors. , 2002, Analytical biochemistry.