FRET and mechanobiology

Integrative Biology

Volumn 1, Issue 10, 2009, Pages 565-573

  Wang, Yingxiao ^a   Wang, Ning ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; EQUIPMENT DESIGN; FLUORESCENCE MICROSCOPY; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMAN; INSTRUMENTATION; MECHANOTRANSDUCTION; METHODOLOGY; PHYSIOLOGY; REVIEW;

ANIMALS; EQUIPMENT DESIGN; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMANS; MECHANOTRANSDUCTION, CELLULAR; MICROSCOPY, FLUORESCENCE;

EID: 70849116975     PISSN: 17579694     EISSN: 17579708     Source Type: Journal    
DOI: 10.1039/b913093b     Document Type: Review

References (101)

1. H. W. Ai K. L. Hazelwood M. W. Davidson R. E. Campbell Fluorescent protein FRET pairs for ratiometric imaging of dual biosensors Nat. Methods 2008 5 401 403
2. H. W. Ai J. N. Henderson S. J. Remington R. E. Campbell Directed evolution of a monomeric, bright and photostable version of Clavularia cyan fluorescent protein: structural characterization and applications in fluorescence imaging Biochem. J. 2006 400 531 540
3. H. W. Ai N. C. Shaner Z. Cheng R. Y. Tsien R. E. Campbell Exploration of new chromophore structures leads to the identification of improved blue fluorescent proteins Biochemistry 2007 46 5904 5910
4. B. Ananthanarayanan Q. Ni J. Zhang Signal propagation from membrane messengers to nuclear effectors revealed by reporters of phosphoinositide dynamics and Akt activity Proc. Natl. Acad. Sci. U. S. A. 2005 102 15081 15086
5. G. S. Baird D. A. Zacharias R. Y. Tsien Biochemistry, mutagenesis, and oligomerization of DsRed, a red fluorescent protein from coral Proc. Natl. Acad. Sci. U. S. A. 2000 97 11984 11989
6. R. E. Campbell O. Tour A. E. Palmer P. A. Steinbach G. S. Baird et al. A monomeric red fluorescent protein Proc. Natl. Acad. Sci. U. S. A. 2002 99 7877 7882
7. M. Chachisvilis Y. L. Zhang J. A. Frangos G protein-coupled receptors sense fluid shear stress in endothelial cells Proc. Natl. Acad. Sci. U. S. A. 2006 103 15463 15468
8. M. Chalfie Y. Tu G. Euskirchen W. W. Ward D. C. Prasher Green fluorescent protein as a marker for gene expression Science 1994 263 802 805
9. R. M. Clegg, Fluorescence resonance energy transfer, in Fluorescence Imaging Spectroscopy and Microscopy, ed., X. F. Wang, and, B. Herman, John Wiley & Sons, Inc., New York, 1996, pp. 179-252
10. R. M. Clegg, Nuts and bolts of excitation energy migration and energy transfer, in Chlorophyll a Fluorescence: A Signature of Photosynthesis, ed., G. C. Papageorgiou, and, Govindjee, Springer, New York, 2005, pp. 83-105
11. B. P. Cormack R. H. Valdivia S. Falkow FACS-optimized mutants of the green fluorescent protein (GFP) Gene 1996 173 33 38
12. L. M. DiPilato X. Cheng J. Zhang Fluorescent indicators of cAMP and Epac activation reveal differential dynamics of cAMP signaling within discrete subcellular compartments Proc. Natl. Acad. Sci. U. S. A. 2004 101 16513 16518
13. T. Ehrig D. J. O'Kane F. G. Prendergast Green-fluorescent protein mutants with altered fluorescence excitation spectra FEBS Lett. 1995 367 163 166
14. A. J. Engler S. Sen H. L. Sweeney D. E. Discher Matrix elasticity directs stem cell lineage specification Cell 2006 126 677 689
15. G. Fu C. Wang G. Y. Wang Y. Z. Chen C. He Z. Z. Xu Detection of constitutive homomeric associations of the integrins Mac-1 subunits by fluorescence resonance energy transfer in living cells Biochem. Biophys. Res. Commun. 2006 351 847 852
16. G. Fu H. Y. Yang C. Wang F. Zhang Z. D. You et al. Detection of constitutive heterodimerization of the integrin Mac-1 subunits by fluorescence resonance energy transfer in living cells Biochem. Biophys. Res. Commun. 2006 346 986 991
17. A. Fujioka K. Terai R. E. Itoh K. Aoki T. Nakamura et al. Dynamics of the Ras/ERK MAPK cascade as monitored by fluorescent probes J. Biol. Chem. 2006 281 8917 8926
18. A. Ganguli L. Persson I. R. Palmer I. Evans L. Yang et al. Distinct NF-kappaB regulation by shear stress through Ras-dependent IkappaBalpha oscillations: real-time analysis of flow-mediated activation in live cells Circ. Res. 2005 96 626 634
19. S. Gasman Y. Kalaidzidis M. Zerial RhoD regulates endosome dynamics through Diaphanous-related Formin and Src tyrosine kinase Nat. Cell Biol. 2003 5 195 204
20. B. N. Giepmans S. R. Adams M. H. Ellisman R. Y. Tsien The fluorescent toolbox for assessing protein location and function Science 2006 312 217 224
21. O. Griesbeck G. S. Baird R. E. Campbell D. A. Zacharias R. Y. Tsien Reducing the environmental sensitivity of yellow fluorescent protein. Mechanism and applications J. Biol. Chem. 2001 276 29188 29194
22. R. Heim D. C. Prasher R. Y. Tsien Wavelength mutations and posttranslational autoxidation of green fluorescent protein Proc. Natl. Acad. Sci. U. S. A. 1994 91 12501 12504
23. R. Heim R. Y. Tsien Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer Curr. Biol. 1996 6 178 182
24. L. Hemsath M. R. Ahmadian Fluorescence approaches for monitoring interactions of Rho GTPases with nucleotides, regulators, and effectors Methods 2005 37 173 182
25. L. Hodgson O. Pertz K. M. Hahn Design and optimization of genetically encoded fluorescent biosensors: GTPase biosensors Methods Cell Biol. 2008 85 63 81
26. S. Hu J. Chen B. Fabry Y. Numaguchi A. Gouldstone et al. Intracellular stress tomography reveals stress focusing and structural anisotropy in cytoskeleton of living cells Am. J. Physiol.: Cell Physiol. 2003 285 C1082 C1090
27. S. Inouye F. I. Tsuji Aequorea green fluorescent protein. Expression of the gene and fluorescence characteristics of the recombinant protein FEBS Lett. 1994 341 277 280
28. R. E. Itoh K. Kurokawa Y. Ohba H. Yoshizaki N. Mochizuki M. Matsuda Activation of rac and cdc42 video imaged by fluorescent resonance energy transfer-based single-molecule probes in the membrane of living cells Mol. Cell. Biol. 2002 22 6582 6591
29. C. Janetopoulos T. Jin P. Devreotes Receptor-mediated activation of heterotrimeric G-proteins in living cells Science 2001 291 2408 2411
30. K. B. Kaplan J. R. Swedlow H. E. Varmus D. O. Morgan Association of p60c-src with endosomal membranes in mammalian fibroblasts J. Cell Biol. 1992 118 321 333
31. S. Karasawa T. Araki M. Yamamoto-Hino A. Miyawaki A green-emitting fluorescent protein from Galaxeidae coral and its monomeric version for use in fluorescent labeling J. Biol. Chem. 2003 278 34167 34171
32. A. Katsumi A. W. Orr E. Tzima M. A. Schwartz Integrins in mechanotransduction J. Biol. Chem. 2003 279 12001 12004
33. M. Kim C. V. Carman T. A. Springer Bidirectional transmembrane signaling by cytoplasmic domain separation in integrins Science 2003 301 1720 1725
34. T. J. Kim J. Seong M. Ouyang J. Sun S. Lu et al. Substrate rigidity regulates Ca2+ oscillation via RhoA pathway in stem cells J. Cell. Physiol. 2009 218 285 293
35. V. S. Kraynov C. Chamberlain G. M. Bokoch M. A. Schwartz S. Slabaugh K. M. Hahn Localized Rac activation dynamics visualized in living cells Science 2000 290 333 337
36. M. T. Kunkel Q. Ni R. Y. Tsien J. Zhang A. C. Newton Spatio-temporal dynamics of protein kinase B/Akt signaling revealed by a genetically encoded fluorescent reporter J. Biol. Chem. 2004 280 5581 5587
37. M. Lorenz H. Yamaguchi Y. Wang R. H. Singer J. Condeelis Imaging sites of N-wasp activity in lamellipodia and invadopodia of carcinoma cells Curr. Biol. 2004 14 697 703
38. K. Q. Luo V. C. Yu Y. Pu D. C. Chang Application of the fluorescence resonance energy transfer method for studying the dynamics of caspase-3 activation during UV-induced apoptosis in living HeLa cells Biochem. Biophys. Res. Commun. 2001 283 1054 1060
39. N. P. Mahajan D. C. Harrison-Shostak J. Michaux B. Herman Novel mutant green fluorescent protein protease substrates reveal the activation of specific caspases during apoptosis Chem. Biol. 1999 6 401 409
40. N. P. Mahajan K. Linder G. Berry G. W. Gordon R. Heim B. Herman Bcl-2 and Bax interactions in mitochondria probed with green fluorescent protein and fluorescence resonance energy transfer Nat. Biotechnol. 1998 16 547 552
41. M. V. Matz A. F. Fradkov Y. A. Labas A. P. Savitsky A. G. Zaraisky et al. Fluorescent proteins from nonbioluminescent Anthozoa species Nat. Biotechnol. 1999 17 969 973
42. M. A. Mena T. P. Treynor S. L. Mayo P. S. Daugherty Blue fluorescent proteins with enhanced brightness and photostability from a structurally targeted library Nat. Biotechnol. 2006 24 1569 1571
43. E. M. Merzlyak J. Goedhart D. Shcherbo M. E. Bulina A. S. Shcheglov et al. Bright monomeric red fluorescent protein with an extended fluorescence lifetime Nat. Methods 2007 4 555 557
44. H. Miao Y. L. Hu Y. T. Shiu S. Yuan Y. Zhao et al. Effects of flow patterns on the localization and expression of VE-cadherin at vascular endothelial cell junctions: in vivo and in vitro investigations J. Vasc. Res. 2005 42 77 89
45. R. D. Mitra C. M. Silva D. C. Youvan Fluorescence resonance energy transfer between blue-emitting and red-shifted excitation derivatives of the green fluorescent protein Gene 1996 173 13 17
46. A. Miyawaki O. Griesbeck R. Heim R. Y. Tsien Dynamic and quantitative Ca2+ measurements using improved cameleons Proc. Natl. Acad. Sci. U. S. A. 1999 96 2135 2140
47. A. Miyawaki J. Llopis R. Heim J. M. McCaffery J. A. Adams et al. Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin Nature 1997 388 882 887
48. A. Miyawaki R. Y. Tsien Monitoring protein conformations and interactions by fluorescence resonance energy transfer between mutants of green fluorescent protein Methods Enzymol. 2000 327 472 500
49. N. Mochizuki S. Yamashita K. Kurokawa Y. Ohba T. Nagai et al. Spatio-temporal images of growth-factor-induced activation of Ras and Rap1 Nature 2001 411 1065 1068
50. S. Na O. Collin F. Chowdhury B. Tay M. Ouyang et al. Rapid signal transduction in living cells is a unique feature of mechanotransduction Proc. Natl. Acad. Sci. U. S. A. 2008 105 6626 6631
51. S. Na N. Wang Application of fluorescence resonance energy transfer and magnetic twisting cytometry to quantify mechanochemical signaling activities in a living cell Sci. Signal 2008 1 pl1
52. T. Nagai K. Ibata E. S. Park M. Kubota K. Mikoshiba A. Miyawaki A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications Nat. Biotechnol. 2002 20 87 90
53. T. Nagai A. Sawano E. S. Park A. Miyawaki Circularly permuted green fluorescent proteins engineered to sense Ca2+ Proc. Natl. Acad. Sci. U. S. A. 2001 98 3197 3202
54. T. Nagai S. Yamada T. Tominaga M. Ichikawa A. Miyawaki Expanded dynamic range of fluorescent indicators for Ca(2+) by circularly permuted yellow fluorescent proteins Proc. Natl. Acad. Sci. U. S. A. 2004 101 10554 10559
55. J. Nakai M. Ohkura K. Imoto A high signal-to-noise Ca(2+) probe composed of a single green fluorescent protein Nat. Biotechnol. 2001 19 137 141
56. P. Nalbant L. Hodgson V. Kraynov A. Toutchkine K. M. Hahn Activation of endogenous Cdc42 visualized in living cells Science 2004 305 1615 1619
57. A. W. Nguyen P. S. Daugherty Evolutionary optimization of fluorescent proteins for intracellular FRET Nat. Biotechnol. 2005 23 355 360
58. S. Noria D. B. Cowan A. I. Gotlieb B. L. Langille Transient and steady-state effects of shear stress on endothelial cell adherens junctions Circ. Res. 1999 85 504 514
59. M. Ormö A. B. Cubitt K. Kallio L. A. Gross R. Y. Tsien S. J. Remington Crystal structure of the Aequorea victoria green fluorescent protein Science 1996 273 1392 1395
60. A. W. Orr B. P. Helmke B. R. Blackman M. A. Schwartz Mechanisms of mechanotransduction Dev. Cell 2006 10 11 20
61. M. Ouyang J. Sun S. Chien Y. Wang Determination of hierarchical relationship of Src and Rac at subcellular locations with FRET biosensors Proc. Natl. Acad. Sci. U. S. A. 2008 105 14353 14358
62. G. J. Palm A. Zdanov G. A. Gaitanaris R. Stauber G. N. Pavlakis A. Wlodawer The structural basis for spectral variations in green fluorescent protein Nat. Struct. Biol. 1997 4 361 365
63. J. D. Pédelacq S. Cabantous T. Tran T. C. Terwilliger G. S. Waldo Engineering and characterization of a superfolder green fluorescent protein Nat. Biotechnol. 2006 24 79 88
64. O. Pertz K. M. Hahn Designing biosensors for Rho family proteins - deciphering the dynamics of Rho family GTPase activation in living cells J. Cell Sci. 2004 117 1313 1318
65. O. Pertz L. Hodgson R. L. Klemke K. M. Hahn Spatiotemporal dynamics of RhoA activity in migrating cells Nature 2006 440 1069 1072
66. A. Piljic C. Schultz Simultaneous recording of multiple cellular events by FRET ACS Chem. Biol. 2008 3 156 160
67. D. W. Piston G. J. Kremers Fluorescent protein FRET: the good, the bad and the ugly Trends Biochem. Sci. 2007 32 407 414
68. D. C. Prasher V. K. Eckenrode W. W. Ward F. G. Prendergast M. J. Cormier Primary structure of the Aequorea victoria green-fluorescent protein Gene 1992 111 229 233
69. M. A. Rizzo G. H. Springer B. Granada D. W. Piston An improved cyan fluorescent protein variant useful for FRET Nat. Biotechnol. 2004 22 445 449
70. V. A. Romoser P. M. Hinkle A. Persechini Detection in living cells of Ca2+-dependent changes in the fluorescence emission of an indicator composed of two green fluorescent protein variants linked by a calmodulin-binding sequence. A new class of fluorescent indicators J. Biol. Chem. 1997 272 13270 13274
71. M. Sato T. Ozawa K. Inukai T. Asano Y. Umezawa Fluorescent indicators for imaging protein phosphorylation in single living cells Nat. Biotechnol. 2002 20 287 294
72. A. Seth T. Otomo H. L. Yin M. K. Rosen Rational design of genetically encoded fluorescence resonance energy transfer-based sensors of cellular Cdc42 signaling Biochemistry 2003 42 3997 4008
73. N. C. Shaner R. E. Campbell P. A. Steinbach B. N. Giepmans A. E. Palmer R. Y. Tsien Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein Nat. Biotechnol. 2004 22 1567 1572
74. N. C. Shaner M. Z. Lin M. R. McKeown P. A. Steinbach K. L. Hazelwood et al. Improving the photostability of bright monomeric orange and red fluorescent proteins Nat. Methods 2008 5 545 551
75. N. C. Shaner P. A. Steinbach R. Y. Tsien A guide to choosing fluorescent proteins Nat. Methods 2005 2 905 909
76. D. Shcherbo E. M. Merzlyak T. V. Chepurnykh A. F. Fradkov G. V. Ermakova et al. Bright far-red fluorescent protein for whole-body imaging Nat. Methods 2007 4 741 746
77. O. Shimomura F. H. Johnson Y. Saiga Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, Aequorea J. Cell. Comp. Physiol. 1962 59 223 239
78. X. Shu A. Royant M. Z. Lin T. A. Aguilera V. Lev-Ram et al. Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome Science 2009 324 804 807
79. A. Y. Ting K. H. Kain R. L. Klemke R. Y. Tsien Genetically encoded fluorescent reporters of protein tyrosine kinase activities in living cells Proc. Natl. Acad. Sci. U. S. A. 2001 98 15003 15008
80. 2+ imaging by a new calmodulin-GFP fusion molecule Nat. Struct. Biol. 2001 8 1069 1073
81. R. Y. Tsien Fluorescent probes of cell signaling Annu. Rev. Neurosci. 1989 12 227 253
82. R. Y. Tsien The green fluorescent protein Annu. Rev. Biochem. 1998 67 509 544
83. R. Y. Tsien Building and breeding molecules to spy on cells and tumors FEBS Lett. 2005 579 927 932
84. E. Tzima M. A. Del Pozo W. B. Kiosses S. A. Mohamed S. Li et al. Activation of Rac1 by shear stress in endothelial cells mediates both cytoskeletal reorganization and effects on gene expression EMBO J. 2002 21 6791 6800
85. E. Tzima W. B. Kiosses M. A. del Pozo M. A. Schwartz Localized cdc42 activation detected using a novel assay mediates microtubule organizing center positioning in endothelial cells in response to fluid shear stress J. Biol. Chem. 2003 278 31020 31023
86. J. D. Violin J. Zhang R. Y. Tsien A. C. Newton A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C J. Cell Biol. 2003 161 899 909
87. V. Vogel M. Sheetz Local force and geometry sensing regulate cell functions Nat. Rev. Mol. Cell Biol. 2006 7 265 275
88. L. Wang W. C. Jackson P. A. Steinbach R. Y. Tsien Evolution of new nonantibody proteins via iterative somatic hypermutation Proc. Natl. Acad. Sci. U. S. A. 2004 101 16745 16749
89. N. Wang J. D. Tytell D. E. Ingber Mechanotransduction at a distance: mechanically coupling the extracellular matrix with the nucleus Nat. Rev. Mol. Cell Biol. 2009 10 75 82
90. Y. Wang E. L. Botvinick Y. Zhao M. W. Berns S. Usami et al. Visualizing the mechanical activation of Src Nature 2005 434 1040 1045
91. M. R. Webb Development of fluorescent biosensors for probing the function of motor proteins Mol. BioSyst. 2007 3 249 256
92. F. Yang L. G. Moss G. N. Phillips Jr The molecular structure of green fluorescent protein Nat. Biotechnol. 1996 14 1246 1251
93. H. Yoshizaki Y. Ohba K. Kurokawa R. E. Itoh T. Nakamura et al. Activity of Rho-family GTPases during cell division as visualized with FRET-based probes J. Cell Biol. 2003 162 223 232
94. M. Zaccolo F. De Giorgi C. Y. Cho L. Feng T. Knapp et al. A genetically encoded, fluorescent indicator for cyclic AMP in living cells Nat. Cell Biol. 2000 2 25 29
95. M. Zaccolo T. Pozzan Discrete microdomains with high concentration of cAMP in stimulated rat neonatal cardiac myocytes Science 2002 295 1711 1715
96. D. A. Zacharias J. D. Violin A. C. Newton R. Y. Tsien Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells Science 2002 296 913 916
97. R. Zaidel-Bar Z. Kam B. Geiger Polarized downregulation of the paxillin-p130CAS-Rac1 pathway induced by shear flow J. Cell Sci. 2005 118 3997 4007
98. O. Zapata-Hommer O. Griesbeck Efficiently folding and circularly permuted variants of the Sapphire mutant of GFP BMC Biotechnol. 2003 3 5
99. J. Zhang R. E. Campbell A. Y. Ting R. Y. Tsien Creating new fluorescent probes for cell biology Nat. Rev. Mol. Cell Biol. 2002 3 906 918
100. J. Zhang C. J. Hupfeld S. S. Taylor J. M. Olefsky R. Y. Tsien Insulin disrupts beta-adrenergic signalling to protein kinase A in adipocytes Nature 2005 437 569 573
101. J. Zhang Y. Ma S. S. Taylor R. Y. Tsien Genetically encoded reporters of protein kinase A activity reveal impact of substrate tethering Proc. Natl. Acad. Sci. U. S. A. 2001 98 14997 15002