Spectroscopic techniques for monitoring protein interactions in living cells

Current Opinion in Structural Biology

Volumn 24, Issue 1, 2014, Pages 54-62

  Piehler, Jacob ^a  

^a UNIVERSITY OF OSNABRÜCK   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CELL MEMBRANE PROTEIN; G PROTEIN COUPLED RECEPTOR; NANOPARTICLE; PROTEIN;

ANALYTIC METHOD; BIOLUMINESCENCE RESONANCE ENERGY TRANSFER; CELL COMPARTMENTALIZATION; EQUILIBRIUM CONSTANT; FLUORESCENCE CORRELATION SPECTROSCOPY; FLUORESCENCE CROSS CORRELATION SPECTROSCOPY; FLUORESCENCE RESONANCE ENERGY TRANSFER; IMAGE CORRELATION SPECTROSCOPY; IMAGE CROSS CORRELATION SPECTROSCOPY; MOLECULAR DYNAMICS; NANOENGINEERING; NANOTECHNOLOGY; NONHUMAN; PARTICLE IMAGE CROSS CORRELATION SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; REVIEW; SOLID; SPECTROSCOPY; SURFACE PROPERTY; CELLS; CELLULAR DISTRIBUTION; COMPLEX FORMATION; CORRELATION ANALYSIS; FLUORESCENCE IMAGING; FLUORESCENCE MICROSCOPY; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; LIVING CELL; PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; ANIMAL; CHEMICAL STRUCTURE; HUMAN; METABOLISM; PROCEDURES; SPECTROFLUOROMETRY;

ANIMALS; HUMANS; MICROSCOPY, FLUORESCENCE; MODELS, MOLECULAR; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; PROTEINS; SPECTROMETRY, FLUORESCENCE;

EID: 84890835535     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2013.11.008     Document Type: Review

References (59)

1. Ngounou Wetie A.G., Sokolowska I., Woods A.G., Roy U., Loo J.A., Darie C.C. Investigation of stable and transient protein-protein interactions: past, present, and future. Proteomics 2013, 13:538-557.
2. Lam M.H., Stagljar I. Strategies for membrane interaction proteomics: no mass spectrometry required. Proteomics 2012, 12:1519-1526.
3. Lowder M.A., Appelbaum J.S., Hobert E.M., Schepartz A. Visualizing protein partnerships in living cells and organisms. Curr Opin Chem Biol 2011, 15:781-788.
4. Luker K.E., Smith M.C., Luker G.D., Gammon S.T., Piwnica-Worms H., Piwnica-Worms D. Kinetics of regulated protein-protein interactions revealed with firefly luciferase complementation imaging in cells and living animals. Proc Natl Acad Sci U S A 2004, 101:12288-12293.
5. Padilla-Parra S., Tramier M. Fret microscopy in the living cell: different approaches, strengths and weaknesses. Bioessays 2012, 34:369-376.
6. Phillip Y., Kiss V., Schreiber G. Protein-binding dynamics imaged in a living cell. Proc Natl Acad Sci U S A 2012, 109:1461-1466.
7. Stahl Y., Grabowski S., Bleckmann A., Kuhnemuth R., Weidtkamp-Peters S., Pinto K.G., Kirschner G.K., Schmid J.B., Wink R.H., Hulsewede A., Felekyan S., et al. Moderation of arabidopsis root stemness by clavata1 and arabidopsis crinkly4 receptor kinase complexes. Curr Biol 2013, 23:362-371.
8. Day R.N., Davidson M.W. Fluorescent proteins for fret microscopy: monitoring protein interactions in living cells. Bioessays 2012, 34:341-350.
9. Maurel D., Comps-Agrar L., Brock C., Rives M.L., Bourrier E., Ayoub M.A., Bazin H., Tinel N., Durroux T., Prezeau L., Trinquet E., et al. Cell-surface protein-protein interaction analysis with time-resolved fret and snap-tag technologies: application to gpcr oligomerization. Nat Methods 2008, 5:561-567.
10. Albizu L., Cottet M., Kralikova M., Stoev S., Seyer R., Brabet I., Roux T., Bazin H., Bourrier E., Lamarque L., Breton C., et al. Time-resolved fret between gpcr ligands reveals oligomers in native tissues. Nat Chem Biol 2010, 6:587-594.
11. Chen N.T., Cheng S.H., Liu C.P., Souris J.S., Chen C.T., Mou C.Y., Lo L.W. Recent advances in nanoparticle-based forster resonance energy transfer for biosensing, molecular imaging and drug release profiling. Int J Mol Sci 2012, 13:16598-16623.
12. Michelman-Ribeiro A., Mazza D., Rosales T., Stasevich T.J., Boukari H., Rishi V., Vinson C., Knutson J.R., McNally J.G. Direct measurement of association and dissociation rates of DNA binding in live cells by fluorescence correlation spectroscopy. Biophys J 2009, 97:337-346.
13. Bacia K., Kim S.A., Schwille P. Fluorescence cross-correlation spectroscopy in living cells. Nat Methods 2006, 3:83-89.
14. Fitzpatrick J.A., Lillemeier B.F. Fluorescence correlation spectroscopy: linking molecular dynamics to biological function in vitro and in situ. Curr Opin Struct Biol 2011, 21:650-660.
15. Sadamoto H., Saito K., Muto H., Kinjo M., Ito E. Direct observation of dimerization between different creb1 isoforms in a living cell. PLoS ONE 2011, 6:e20285.
16. Tiwari M., Mikuni S., Muto H., Kinjo M. Determination of dissociation constant of the nfkappab p50/p65 heterodimer using fluorescence cross-correlation spectroscopy in the living cell. Biochem Biophys Res Commun 2013, 436:430-435.
17. Chen J., Irudayaraj J. Fluorescence lifetime cross correlation spectroscopy resolves egfr and antagonist interaction in live cells. Anal Chem 2010, 82:6415-6421.
18. Weidemann T., Worch R., Kurgonaite K., Hintersteiner M., Bokel C., Schwille P. Single cell analysis of ligand binding and complex formation of interleukin-4 receptor subunits. Biophys J 2011, 101:2360-2369.
19. Shi X., Foo Y.H., Sudhaharan T., Chong S.W., Korzh V., Ahmed S., Wohland T. Determination of dissociation constants in living zebrafish embryos with single wavelength fluorescence cross-correlation spectroscopy. Biophys J 2009, 97:678-686.
20. Padilla-Parra S., Auduge N., Coppey-Moisan M., Tramier M. Dual-color fluorescence lifetime correlation spectroscopy to quantify protein-protein interactions in live cell. Microsc Res Tech 2011, 74:788-793.
21. Foo Y.H., Naredi-Rainer N., Lamb D.C., Ahmed S., Wohland T. Factors affecting the quantification of biomolecular interactions by fluorescence cross-correlation spectroscopy. Biophys J 2012, 102:1174-1183.
22. Petersen N.O., Hoddelius P.L., Wiseman P.W., Seger O., Magnusson K.E. Quantitation of membrane receptor distributions by image correlation spectroscopy: concept and application. Biophys J 1993, 65:1135-1146.
23. Digman M.A., Brown C.M., Sengupta P., Wiseman P.W., Horwitz A.R., Gratton E. Measuring fast dynamics in solutions and cells with a laser scanning microscope. Biophys J 2005, 89:1317-1327.
24. Digman M.A., Gratton E. Scanning image correlation spectroscopy. Bioessays 2012, 34:377-385.
25. Rappaz B., Wiseman P.W. Image correlation spectroscopy for measurements of particle densities and colocalization. Curr Protoc Cell Biol 2013, 27:15-21. Chapter 4(Unit 4).
26. Digman M.A., Wiseman P.W., Horwitz A.R., Gratton E. Detecting protein complexes in living cells from laser scanning confocal image sequences by the cross correlation raster image spectroscopy method. Biophys J 2009, 96:707-716.
27. Digman M.A., Wiseman P.W., Choi C., Horwitz A.R., Gratton E. Stoichiometry of molecular complexes at adhesions in living cells. Proc Natl Acad Sci U S A 2009, 106:2170-2175.
28. Comeau J.W., Kolin D.L., Wiseman P.W. Accurate measurements of protein interactions in cells via improved spatial image cross-correlation spectroscopy. Mol Biosyst 2008, 4:672-685.
29. Toplak T., Pandzic E., Chen L., Vicente-Manzanares M., Horwitz A.R., Wiseman P.W. Sticcs reveals matrix-dependent adhesion slipping and gripping in migrating cells. Biophys J 2012, 103:1672-1682.
30. Vetri V., Ossato G., Militello V., Digman M.A., Leone M., Gratton E. Fluctuation methods to study protein aggregation in live cells: concanavalin a oligomers formation. Biophys J 2011, 100:774-783.
31. Ossato G., Digman M.A., Aiken C., Lukacsovich T., Marsh J.L., Gratton E. A two-step path to inclusion formation of huntingtin peptides revealed by number and brightness analysis. Biophys J 2010, 98:3078-3085.
32. Schmidt T., Schutz G.J., Baumgartner W., Gruber H.J., Schindler H. Imaging of single molecule diffusion. Proc Natl Acad Sci U S A 1996, 93:2926-2929.
33. Yildiz A., Forkey J.N., McKinney S.A., Ha T., Goldman Y.E., Selvin P.R. Myosin v walks hand-over-hand: single fluorophore imaging with 1.5-nm localization. Science 2003, 300:2061-2065.
34. Siebrasse J.P., Kaminski T., Kubitscheck U. Nuclear export of single native mrna molecules observed by light sheet fluorescence microscopy. Proc Natl Acad Sci U S A 2012, 109:9426-9431.
35. 2+ signaling: single-molecule tracking study 2. J Cell Biol 2007, 177:731-742.
36. Trabesinger W., Schutz G.J., Gruber H.J., Schindler H., Schmidt T. Detection of individual oligonucleotide pairing by single-molecule microscopy. Anal Chem 1999, 71:279-283.
37. Trabesinger W., Hecht B., Wild U.P., Schutz G.J., Schindler H., Schmidt T. Statistical analysis of single-molecule colocalization assays. Anal Chem 2001, 73:1100-1105.
38. Dunne P.D., Fernandes R.A., McColl J., Yoon J.W., James J.R., Davis S.J., Klenerman D. Dysco: quantitating associations of membrane proteins using two-color single-molecule tracking. Biophys J 2009, 97:L5-L7.
39. Kasai R.S., Suzuki K.G., Prossnitz E.R., Koyama-Honda I., Nakada C., Fujiwara T.K., Kusumi A. Full characterization of gpcr monomer-dimer dynamic equilibrium by single molecule imaging. J Cell Biol 2011, 192:463-480.
40. Suzuki K.G., Kasai R.S., Hirosawa K.M., Nemoto Y.L., Ishibashi M., Miwa Y., Fujiwara T.K., Kusumi A. Transient gpi-anchored protein homodimers are units for raft organization and function. Nat Chem Biol 2012, 8:774-783.
41. Low-Nam S.T., Lidke K.A., Cutler P.J., Roovers R.C., van Bergen en Henegouwen P.M., Wilson B.S., Lidke D.S. Erbb1 dimerization is promoted by domain co-confinement and stabilized by ligand binding. Nat Struct Mol Biol 2011, 18:1244-1249.
42. You C., Wilmes S., Richter C.P., Beutel O., Lisse D., Piehler J. Electrostatically controlled quantum dot monofunctionalization for interrogating the dynamics of protein complexes in living cells. ACS Chem Biol 2013, 8:320-326.
43. Moertelmaier M., Brameshuber M., Linimeier M., Schutz G.J., Stockinger H. Thinning out clusters while conserving stoichiometry of labeling. Appl Phys Lett 2005, 87.
44. Ruprecht V., Brameshuber M., Schutz G.J. Two-color single molecule tracking combined with photobleaching for the detection of rare molecular interactions in fluid biomembranes. Soft Matter 2010, 6:568-581.
45. Lord S.J., Lee H.L., Moerner W.E. Single-molecule spectroscopy and imaging of biomolecules in living cells. Anal Chem 2010, 82:2192-2203.
46. Semrau S., Holtzer L., Gonzalez-Gaitan M., Schmidt T. Quantification of biological interactions with particle image cross-correlation spectroscopy (piccs). Biophys J 2011, 100:1810-1818.
47. Betzig E., Patterson G.H., Sougrat R., Lindwasser O.W., Olenych S., Bonifacino J.S., Davidson M.W., Lippincott-Schwartz J., Hess H.F. Imaging intracellular fluorescent proteins at nanometer resolution. Science 2006, 313:1642-1645.
48. Sengupta P., Jovanovic-Talisman T., Skoko D., Renz M., Veatch S.L., Lippincott-Schwartz J. Probing protein heterogeneity in the plasma membrane using palm and pair correlation analysis. Nat Methods 2011, 8:969-975.
49. Schwarzenbacher M., Kaltenbrunner M., Brameshuber M., Hesch C., Paster W., Weghuber J., Heise B., Sonnleitner A., Stockinger H., Schutz G.J. Micropatterning for quantitative analysis of protein-protein interactions in living cells. Nat Methods 2008, 5:1053-1060.
50. Sunzenauer S., Zojer V., Brameshuber M., Trols A., Weghuber J., Stockinger H., Schutz G.J. Determination of binding curves via protein micropatterning in vitro and in living cells. Cytometry A 2013, 83:847-854.
51. Arrabito G., Reisewitz S., Dehmelt L., Bastiaens P.I., Pignataro B., Schroeder H., Niemeyer C.M. Biochips for cell biology by combined dip-pen nanolithography and DNA-directed protein immobilization. Small (Weinheim an der Bergstrasse, Germany) 2013, 10.1002/smll.201300941.
52. Gandor S., Reisewitz S., Venkatachalapathy M., Arrabito G., Reibner M., Schroder H., Ruf K., Niemeyer C.M., Bastiaens P.I., Dehmelt L. A protein-interaction array inside a living cell. Angew Chem Int Ed 2013, 52:4790-4794.
53. Lisse D., Wilkens V., You C., Busch K., Piehler J. Selective targeting of fluorescent nanoparticles to proteins inside live cells. Angew Chem Int Ed Engl 2011, 50:9352-9355.
54. Etoc F., Lisse D., Bellaiche Y., Piehler J., Coppey M., Dahan M. Subcellular control of rac-gtpase signalling by magnetogenetic manipulation inside living cells. Nat Nanotechnol 2013, 8:193-198.
55. Huang Z.L., Zhu H., Long F., Ma H., Qin L., Liu Y., Ding J., Zhang Z., Luo Q., Zeng S. Localization-based super-resolution microscopy with an scmos camera. Opt Express 2011, 19:19156-19168.
56. Planchon T.A., Gao L., Milkie D.E., Davidson M.W., Galbraith J.A., Galbraith C.G., Betzig E. Rapid three-dimensional isotropic imaging of living cells using bessel beam plane illumination. Nat Methods 2011, 8:417-423.
57. Chmyrov A., Keller J., Grotjohann T., Ratz M., d'Este E., Jakobs S., Eggeling C., Hell S.W. Nanoscopy with more than 100,000 'doughnuts'. Nat Methods 2013, 10:737-740.
58. Lukinavicius G., Umezawa K., Olivier N., Honigmann A., Yang G., Plass T., Mueller V., Reymond L., Correa I.R., Luo Z.G., Schultz C., et al. A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nat Chem 2013, 5:132-139.
59. You C., Wilmes S., Beutel O., Lochte S., Podoplelowa Y., Roder F., Richter C., Seine T., Schaible D., Uze G., Clarke S., et al. Self-controlled monofunctionalization of quantum dots for multiplexed protein tracking in live cells. Angew Chem Int Ed Engl 2010, 49:4108-4112.