Fretting about FRET: Correlation between κ and R

Biophysical Journal

Volumn 92, Issue 12, 2007, Pages 4168-4178

  VanBeek, Darren B ^a   Zwier, Matthew C ^a   Shorb, Justin M ^a   Krueger, Brent P ^a  

^a HOPE COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DYE; EGG PROTEIN; EOSIN; LYSOZYME; MALEIMIDE; PROTEIN; SUCCINIMIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONJUGATION; CORRELATION COEFFICIENT; EGG; ENERGY TRANSFER; FLUORESCENCE RESONANCE ENERGY TRANSFER; LINKAGE ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR PROBE; PARAMETER; PROTEIN BINDING; SIMULATION;

EID: 34250335726     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.092650     Document Type: Article

References (84)

1. Clegg, R. M. 1996. Fluorescence resonance energy transfer. In Fluorescence Imaging and Microscopy. Chemical Analysis, Vol. 137. X. F. Wang, and B. Herman, editors. Wiley Interscience, New York.
2. Andrews, D. L., and A. A. Demidov. 1999. Resonance Energy Transfer. John Wiley & Sons, New York.
3. Stryer, L., and R. P. Haugland. 1967. Energy transfer: a spectroscopic ruler. Proc. Natl. Acad. Sci. USA. 58:719-726.
4. Stryer, L. 1978. Fluorescence energy transfer as a spectroscopic ruler. Annu. Rev. Biochem. 47:819-846.
5. Dale, R. E., and J. Eisinger. 1974. Intramolecular distances determined by energy transfer. Dependence on orientational freedom of donor and acceptor. Biopolymers. 13:1573-1605.
6. Pullerits, T., and A. Freiberg. 1991. Picosecond fluorescence of simple photosynthetic membranes: evidence of spectral inhomogeneity and directed energy transfer. Chem. Phys. 149:409-418.
7. Hochstrasser, R. A., S. M. Chen, and D. P. Millar. 1992. Distance distribution in a dye-linked oligonucleotide determined by time-resolved fluorescence energy transfer. Biophys. Chem. 45:133-141.
8. Akimoto, S., S. Takaichi, T. Ogata, Y. Nishimura, I. Yamazaki, and M. Mimuro. 1996. Excitation energy transfer in carotenoid-chlorophyll protein complexes probed by femtosecond fluorescence decays. Chem. Phys. Lett. 260:147-152.
9. Yang, M., and D. P. Millar. 1997. Fluorescence resonance energy transfer as a probe of DNA structure and function. Methods Enzymol. 278:417-444.
10. Jia, Y., D. S. Talaga, W. L. Lau, H. S. M. Lu, W. F. DeGrado, and R. M. Hochstrasser. 1999. Folding dynamics of single GCN-4 peptides by fluorescence resonant energy transfer confocal microscopy. Chem. Phys. 247:69-83.
11. Reddy, L. G., L. R. Jones, and D. D. Thomas. 1999. Depolymerization of phospholamban in the presence of calcium pump: a fluorescence energy transfer study. Biochemistry. 38:3954-3962.
12. Klostermeier, D., and D. P. Millar. 2002. Time-resolved fluorescence resonance energy transfer: a versatile tool for the analysis of nucleic acids. Biopolymers. 67:159-179.
13. Wang, D., and E. Geva. 2005. Protein structure and dynamics from single-molecule fluorescence resonance energy transfer. J. Phys. Chem. B. 109:1626-1634.
14. Bradforth, S. E., R. Jimenez, F. van Mourik, R. van Grondelle, and G. R. Fleming. 1995. Excitation transfer in the core light-harvesting complex (lh-1) of Rhodobacter sphaeroides: an ultrafast fluorescence depolarization and annihilation study. J. Phys. Chem. 99:16179-16191.
15. Zhuang, X., L. E. Bartley, H. P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu. 2000. A single-molecule study of RNA catalysis and folding. Science. 288:2048-2051.
16. Stryer, L. 1968. Fluorescence spectroscopy of proteins. Science. 162:526-533.
17. Wallrabe, H., and A. Periasamy. 2005. Imaging protein molecules using FRET and FLIM microscopy. Curr. Opin. Biotechnol. 16:19-27.
18. Schuler, B., E. A. Lipman, P. J. Steinbach, M. Kumke, and W. A. Eaton. 2005. Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence. Proc. Natl. Acad. Sci. USA. 102:2754-2759.
19. Johnson, C. K., B. D. Slaughter, J. R. Unruh, and E. S. Price. 2006. Fluorescence probes of protein dynamics and conformations in freely diffusing molecules: single-molecule resonance energy transfer and time-resolved fluorescence methods. In Reviews in Fluorescence, Vol. 3. C. D. Geddes and J. R. Lakowicz, editors. Springer, New York.
20. Englert, A., and M. Leclerc. 1978. Intramolecular energy transfer in molecules with a large number of conformations. Proc. Natl. Acad. Sci. USA. 75:1050-1051.
21. Leclerc, M., S. Prémilat, and A. Englert. 1978. Nonradiative energy transfer in oligopeptide chains generated by a Monte Carlo method including long-range interactions. Biopolymers. 17:2459-2473.
22. Dale, R. E., and J. Eisinger. 1976. Intramolecular energy transfer and molecular conformation. Proc. Natl. Acad. Sci. USA. 73:271-273.
23. Jean, J. M., and B. P. Krueger. 2006. Structural fluctuations and excitation transfer between adenine and 2-aminopurine in single-stranded deoxytrinucleotides. J. Phys. Chem. B. 110:2899-2909.
24. Srinivas, G., and B. Bagchi. 2001. Effect of orientational motion of mobile chromophores on the dynamics of Förster energy transfer in polymers. J. Phys. Chem. B. 105:9370-9374.
25. Förster, T. 1965. Delocalized excitation and excitation transfer. In Modern Quantum Chemistry, Vol. III. O. Sinanoglu, editor. Academic Press, New York.
26. Förster, T. 1946. Energy migration and fluorescence. Naturwiss. 33:166-175.
27. Förster, T. 1948. Intermolecular energy transference and fluorescence. Ann. Phys. 2:55-75.
28. Van Der Meer, B. W., G. I. Coker, and S. Y. S. Chen. 1994. Resonance Energy Transfer: Theory and Data. VCH Publishers, New York.
29. Steinberg, I. Z., and E. Katchalski. 1968. Theoretical analysis of the role of diffusion in chemical reactions, fluorescence quenching, and nonradiative energy transfer. J. Chem. Phys. 48:2404-2410.
30. Haugland, R. P., J. Yguerabide, and L. Stryer. 1969. Dependence of the kinetics of singlet-singlet energy transfer on spectral overlap. Proc. Natl. Acad. Sci. USA. 63:23-30.
31. Dale, R. E., and J. Eisinger. 1975. Polarized excitation energy transfer. In Biochemical Fluorescence: Concepts, Vol. 1. R. F. Chen and H. Edelhoch, editors. Marcel Dekker, New York.
32. Dale, R. E. 1978. Fluorescence depolarization and orientation factors for excitation energy transfer between isolated donor and acceptor fluorophore pairs at fixed intermolecular separations. Acta Phys. A54:743-756.
33. Beardsley, K., and C. R. Cantor. 1970. Studies of transfer RNA tertiary structure by singlet-singlet energy transfer. Proc. Natl. Acad. Sci. USA. 65:39-46.
34. Eisinger, J., and R. E. Dale. 1974. Interpretation of intramolecular energy transfer experiments. J. Mol. Biol. 84:643-647.
35. Blumberg, W. E., R. E. Dale, J. Eisinger, and D. M. Zuckerman. 1974. Energy transfer in TRNAPHE (yeast). The solution structure of transfer RNA. Biopolymers. 13:1607-1620.
36. Dale, R. E., J. Eisinger, and W. E. Blumberg. 1979. The orientational freedom of molecular probes: the orientation factor in intramolecular energy transfer. Biophys. J. 26:161-194.
37. Haas, E., E. Katchalski-Katzir, and I. Z. Steinberg. 1978. Brownian motion of the ends of oligopeptide chains in solution as estimated by energy transfer between the chain ends. Biopolymers. 17:11-31.
38. Van Der Meer, B. W., M. A. Raymer, S. L. Wagoner, R. L. Hackney, J. M. Beechem, and E. Gratton. 1993. Designing matrix models for fluorescence energy transfer between moving donors and acceptors. Biophys. J. 64:1243-1263.
39. Wu, P., and L. Brand. 1992. Orientation factor in steady-state and time-resolved resonance energy transfer measurements. Biochemistry. 31:7939-7947.
40. Rothwell, P. J., S. Berger, O. Kensch, S. Felekyan, M. Antonik, B. M. Wohrl, R. Restle, R. S. Goody, and C. A. M. Seidel. 2003. Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase: primer/template complexes. Proc. Natl. Acad. Sci. USA. 100:1655-1660.
41. Amir, D., D. P. Levy, Y. Levin, and E. Haas. 1986. Selective fluorescent labeling of amino groups of bovine pancreatic trypsin inhibitor by reductive alkylation. Biopolymers. 25:1645-1658.
42. Ortiz, W., B. P. Krueger, V. D. Kleiman, J. L. Krause, and A. E. Roitberg. 2005. Energy transfer in the nanostar: the role of Coulombic coupling and dynamics. J. Phys. Chem. B. 109:11512-11519.
43. Srinivas, G., and B. Bagchi. 2000. Distribution of reaction times in diffusion controlled reactions in polymers. Chem. Phys. Lett. 328:420-424.
44. Srinivas, G., A. Yethiraj, and B. Bagchi. 2001. Nonexponentiality of time dependent survival probability and the fractional viscosity dependence of the rate in diffusion controlled reactions in a polymer chain nonexponentiality of time-dependent survival probability and the fractional viscosity dependence of the rate in diffusion controlled reactions in a polymer chain. J. Chem. Phys. 114:9170-9178.
45. Srinivas, G., A. Yethiraj, and B. Bagchi. 2001. FRET by FET and dynamics of polymer folding. J. Phys. Chem. B. 105:2475-2478.
46. Stultz, C. M., A. D. Levin, and E. R. Edelman. 2002. Phosphorylation- induced conformational changes in a mitogen-activated protein kinase substrate. J. Biol. Chem. 277:47653-47661.
47. Beierlein, F. R., O. G. Othersen, H. Lanig, S. Schneider, and T. Clark. 2006. Simulating FRET from tryptophan: is the rotamer model correct? J. Am. Chem. Soc. 128:5142-5152.
48. Gustiananda, M., J. R. Liggins, P. L. Cummins, and J. E. Gready. 2004. Conformation of prion protein repeat peptides probed by FRET measurements and molecular dynamics simulations. Biophys. J. 86:2467-2483.
49. Jordanides, X. J., M. J. Lang, X. Song, and G. R. Fleming. 1999. Solvation dynamics in protein environments studied by photon echo spectroscopy. J. Phys. Chem. B. 103:7995-8005.
50. Kepka, A. G., and L. I. Grossweiner. 1973. Photodynamic inactivation of lysozyme by eosin. Photochem. Photobiol. 18:49-61.
51. Baugher, J. F., L. I. Grossweiner, and C. Lewis. 1974. Intramolecular energy-transfer in lysozyme-eosin complex. J. Chem. Soc. Faraday II. 70:1389-1398.
52. Chang, M. C., A. J. Cross, and G. R. Fleming. 1983. Internal dynamics and overall motion of lysozyme studied by fluorescence depolarization of the eosin lysozyme complex. J. Biomol. Struct. Dyn. 1:299-318.
53. Cross, A. J., and G. R. Fleming. 1986. Influence of inhibitor binding on the internal motions of lysozyme. Biophys. J. 50:507-512.
54. Adams, S. R., R. E. Campbell, L. A. Gross, B. R. Martin, G. K. Walkup, Y. Yao, J. Llopis, and R. Y. Tsien. 2002. New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications. J. Am. Chem. Soc. 124:6063-6076.
55. Wang, J., R. M. Wolf, J. W. Caldwell, P. A. Kollman, and D. A. Case. 2004. Development and testing of a general AMBER force field. J. Comput. Chem. 25:1157-1174.
56. Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
57. Case, D. A., T. A. Darden, T. E. Cheatam, III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, K. M. Merz, B. Wang, D. A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, J. Hornak, G. Cui, P. Beroza, C. Schafmeister, J. W. Caldwell, W. S. Ross, and P. A. Kollman. 2004. AMBER 8. University of California, San Francisco, San Francisco, CA.
58. Bytheway, I., and M. W. Wong. 1998. The prediction of vibrational frequencies of inorganic molecules using density functional theory. Chem. Phys. Lett. 282:219-226.
59. Frisch, M. J., G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. J. A. Montgomery, R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P. M.W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, M. Head-Gordon, E. S. Replogle, and J. A. Pople. 1998. Gaussian 98. Gaussian, Wallingford, CT.
60. Bayly, C. I., P. Cieplak, W. D. Cornell, and P. A. Kollman. 1993. A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: the RESP model. J. Phys. Chem. 97:10269-10280.
61. Cieplak, P., W. D. Cornell, C. Bayly, and P. A. Kollman. 1995. Application of the multimolecule and multiconformational RESP methodology to biopolymers: charge derivation for DNA, RNA, and proteins. J. Comput. Chem. 16:1357-1377.
62. Dong, J., T. J. Boggon, N. E. Chayen, J. Raftery, R.-C. Bi, and J. R. Helliwell. 1999. Bound-solvent structures for microgravity-, ground control-, gel- and microbatch-grown hen egg-white lysozyme crystals at 1.8 Å resolution. Acta Crystallogr. D55:745-752.
63. Machida, M., N. Ushijima, M. I. Machida, and Y. Kanaoka. 1975. N-(7-dimethylamino-4-methyl-coumarinyl)maleimide (DACM): novel fluorescent thiol reagents. Chem. Pharm. Bull. (Tokyo). 23:1385-1386.
64. Machida, M., N. Ushijima, M. I. Machida, and Y. Kanaoka. 1977. A novel fluorescent thiol reagent: Syntheses and electronic spectra of n-(7-dimethylamino-4-methyl-3-coumarinyl)-maleimide (DACM-3) and the related compounds. Chem. Pharm. Bull. (Tokyo). 25:1285-1288.
65. Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: an N logN method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
66. York, D. M., T. A. Darden, and L. G. Pedersen. 1993. The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J. Chem. Phys. 99:8345-8348.
67. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of Cartesian equations of motion of a system with constraints - molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
68. Haas, E., E. Katchalski-Katzir, and I. Z. Steinberg. 1978. Effect of the orientation of donor and acceptor on the probability of energy transfer involving electronic transitions of mixed polarization. Biochemistry. 17:5064-5070.
69. Ruggiero, A. J., D. C. Todd, and G. R. Fleming. 1990. Subpicosecond fluorescence anisotropy studies of tryptophan in water. J. Am. Chem. Soc. 112:1003-1014.
70. Hansen, J. E., S. J. Rosenthal, and G. R. Fleming. 1992. Subpico-second fluorescence depolarization studies of tryptophan and tryptophanyl residues of proteins. J. Phys. Chem. 96:3034-3040.
71. Lakowicz, J. R. 1999. Principles of Fluorescence Spectroscopy. Kluwer Academic/Plenum Publishers, Dordrecht, The Netherlands.
72. Valeur, B., and G. Weber. 1977. Resolution of the fluorescence excitation spectrum of indole into the 1la and 1lb excitation bands. Photochem. Photobiol. 25:441-444.
73. Cross, A. J., and G. R. Fleming. 1984. Analysis of time-resolved fluorescence anisotropy decays. Biophys. J. 46:45-56.
74. Horng, M. L., J. A. Gardecki, A. Papazyan, and M. Maroncelli. 1995. Subpicosecond measurements of polar solvation dynamics: Coumarin 153 revisited. J. Phys. Chem. 99:17311-17337.
75. Lewis, J. E., and M. Maroncelli. 1998. On the (uninteresting) dependence of the absorption and emission transition moments of coumarin 153 on solvent. Chem. Phys. Lett. 282:197-203.
76. Fleming, G. R., A. W. E. Knight, J. M. Morris, R. J. S. Morrison, and G. W. Robinson. 1977. Picosecond fluorescence studies of xanthene dyes. J. Am. Chem. Soc. 99:4306-4311.
77. Walker, R. C., I. P. Mercer, I. R. Gould, and D. R. Klug. 2006. A comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuations. J. Comput. Chem. 28:478-490.
78. Zwier, M. C., J. M. Shorb, and B. P. Krueger. 2007. Hybrid molecular dynamics-quantum mechanics simulations of solute spectral properties in the condensed phase: evaluation of simulation parameters. J. Comput. Chem. In press.
79. Reference deleted in proof.
80. Chang, J. C. 1977. Monopole effects on electronic excitation interactions between large molecules. I. Application to energy transfer in chlorophylls. J. Chem. Phys. 67:3901-3909.
81. Krueger, B. P., G. D. Scholes, and G. R. Fleming. 1998. Calculation of couplings and energy-transfer pathways between the pigments of lh2 by the ab initio transition density cube method. J. Phys. Chem. B. 102:5378-5386, 9603.
82. Scholes, G. D., I. R. Gould, R. J. Cogdell, and G. R. Fleming. 1999. Ab initio molecular orbital calculations of electronic coupling in the lh2 bacterial light-harvesting complex of Rps. acidophila. J. Phys. Chem. B. 103:2543-2553.
83. Wong, K. F., B. Bagchi, and P. J. Rossky. 2004. Distance and orientation dependence of excitation transfer rates in conjugated systems: beyond the Förster theory. J. Phys. Chem. A. 108:5752-5763.
84. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD - visual molecular dynamics. J. Mol. Graph. 14:33-38.