Studies of photo-induced protein reactions by spectrally silent reaction dynamics detection methods: Applications to the photoreaction of the LOV2 domain of phototropin from Arabidopsis thaliana
Tài liệu tham khảo
Nelson, 2000
van Holde, 1998
2004
Torre, 2007
Neusius, 2009
Terazima, 2004, Quantities, terminology and symbols in photothermal and related spectroscopies, Pure Appl. Chem., 76, 1083, 10.1351/pac200476061083
Landau, 1959
Eichler, 1986
Takeshita, 2000, Temperature dependent volume change of initial step of the photoreaction of Photoactive Yellow Protein studied by the transient grating, J. Am. Chem. Soc., 122, 8524, 10.1021/ja000426d
Khan, 2006, Time-resolved thermodynamics: heat capacity change of transient species during photo-reaction of PYP, J. Am. Chem. Soc., 128, 1002, 10.1021/ja055584p
Khan, 2006, Conformational changes of PYP monitored by diffusion coefficient: effect of N-terminal α-helices, Biophys. J., 90, 3686, 10.1529/biophysj.105.078196
Eitoku, 2006, Time-resolved detection of conformational changes in Oat Phytochrome A: time-dependent diffusion, Biophys. J., 91, 3797, 10.1529/biophysj.106.092882
Nakasone, 2007, Transient dimerization and conformational change of a BLUF protein: YcgF, J. Am. Chem. Soc., 129, 7028, 10.1021/ja065682q
Nishioku, 2002, Energetics and volume changes of the intermediates in the photolysis of octopus rhodopsin at a physiological temperature, Biophys. J., 83, 1136, 10.1016/S0006-3495(02)75237-5
Nishioku, 2001, A spectrally silent transformation in the photolysis of octopus rhodopsin: a protein conformational change without any accompanying change of the chromophore's absorption, Biophys. J., 80, 2922, 10.1016/S0006-3495(01)76257-1
Inoue, 2004, Time-resolved detection of the sensory rhodopsin: II. Transducer interaction, Biophys. J., 87, 2587, 10.1529/biophysj.104.043521
Inoue, 2007, Laser-induced transient grating analysis of dynamics of interaction between sensory rhodopsin II D75N and the HtrII transducer, Biophys. J., 92, 2028, 10.1529/biophysj.106.097493
Hazra, 2006, Tetramer formation kinetics in the signaling state of AppA monitored by the time-resolved diffusion, Biophys. J., 91, 654, 10.1529/biophysj.106.083915
Tanaka, 2009, Oligomeric state-dependent conformational change of a BLUF protein TePixD (Tll0078), J. Mol. Biol., 386, 1290, 10.1016/j.jmb.2009.01.026
Eitoku, 2005, Conformational dynamics of Phototropin 2 LOV2 domain with the linker upon photoexcitation, J. Am. Chem. Soc., 127, 13238, 10.1021/ja052523i
Nakasone, 2006, Kinetic measurement of transient dimerization and dissociation reactions of Arabidopsis phototropin 1 LOV2 domain, Biophys. J., 91, 645, 10.1529/biophysj.106.084772
Nakasone, 2007, Dynamics of conformational changes of Arabidopsis phototropin 1 LOV2 with the linker domain, J. Mol. Biol., 367, 432, 10.1016/j.jmb.2006.12.074
Eitoku, 2007, Photochemical intermediates of Arabidopsis phototropin 2 LOV domains associated with conformational changes, J. Mol. Biol., 371, 1290, 10.1016/j.jmb.2007.06.035
Nakasone, 2008, Stability of dimer and domain–domain interaction of Arabidopsis phototropin 1 LOV2, J. Mol. Biol., 383, 904, 10.1016/j.jmb.2008.08.074
Sakakura, 2001, Dynamics of structure and energy of horse carboxymyoglobin after photodissociation of the carbon monoxide, J. Am. Chem. Soc., 123, 4286, 10.1021/ja9944655
Sakakura, 2001, The structural dynamics and ligand releasing process after the photodissociation of sperm whale carboxymyoglobin, J. Phys. Chem. B, 105, 10424, 10.1021/jp0116252
Nada, 2003, A novel method for study of protein folding kinetics by monitoring diffusion coefficient in time domain, Biophys. J., 85, 1876, 10.1016/S0006-3495(03)74615-3
Nishida, 2004, Kinetics of intermolecular interaction during protein folding of reduced cytochrome c, Biophys. J., 87, 2663, 10.1529/biophysj.104.042531
Hirota, 2006, Conformational changes during apoplastocyanin folding observed by Photocleavable modification and transient grating, J. Am. Chem. Soc., 128, 7551, 10.1021/ja058788e
Terazima, 2002, Molecular volume and enthalpy changes associated with irreversible photo-reactions, J. Photochem. Photobiol. C, 3, 81, 10.1016/S1389-5567(02)00021-7
Terazima, 2004, Time-resolved thermodynamic properties of intermediate species during photochemical reactions, Bull. Chem. Soc. Jpn, 77, 23, 10.1246/bcsj.77.23
2010
Cussler, 1997
Baden, 2007, Thermodynamical properties of reaction intermediates during apoplastocyanin folding in time-domain, J. Chem. Phys., 127, 175103, 10.1063/1.2780860
Terazima, 1993, Translational diffusion of a transient radical studied by the transient grating method; pyrazinyl radical in 2-propanol, J. Chem. Phys., 98, 6257, 10.1063/1.464819
Terazima, 2000, Translational diffusion of organic radicals in solution, Acc. Chem. Res., 33, 687, 10.1021/ar000003g
Choi, 2002, Denaturation of a protein monitored by diffusion coefficients: myoglobin, J. Phys. Chem. B, 106, 6587, 10.1021/jp0256802
Choi, 1998, Correlation dimension as a measure of surface roughness of protein molecules, J. Chem. Phys., 109, 7001, 10.1063/1.477336
Huala, 1997, Arabidopsis NPH1: a protein kinase with a putative redox-sensing domain, Science, 278, 2120, 10.1126/science.278.5346.2120
Briggs, 1999, Blue-light photo-receptors in higher plants, Annu. Rev. Cell Dev. Biol., 15, 33, 10.1146/annurev.cellbio.15.1.33
Christie, 1998, Arabidopsis NPH1: a flavoprotein with the properties of a photo-receptor for phototropism, Science, 282, 1698, 10.1126/science.282.5394.1698
Jarriol, 2001, Phototropin-related NPL1 controls chloroplast relocation induces by blue light, Nature, 410, 952, 10.1038/35073622
Kinoshita, 2001, Phot1 and phot2 mediate blue light regulation of stomatal opening, Nature, 414, 656, 10.1038/414656a
Kimura, 2006, Phototropin and light-signaling in phototropism, Curr. Opin. Plant Biol., 9, 503, 10.1016/j.pbi.2006.07.003
Christie, 2007, Phototropin blue-light receptors, Annu. Rev. Plant Biol., 58, 21, 10.1146/annurev.arplant.58.032806.103951
Demarsy, 2009, Higher plants use LOV to perceive blue light, Curr. Opin. Plant Biol., 12, 69, 10.1016/j.pbi.2008.09.002
Swartz, 2001, The photocycle of a flavin-binding domain of the blue light photoreceptor phototropin, J. Biol. Chem., 276, 33500, 10.1074/jbc.M103114200
Kottke, 2003, Phot LOV1: photocycle of a blue-light receptor domain from the green alga Chlamydomonas reinhardtii, Biophys. J., 84, 1192, 10.1016/S0006-3495(03)74933-9
Schüttrigkeit, 2003, Primary photophysics of the FMN binding LOV2 domain of the plant blue light receptor phototropin of Avena sativa, Chem. Phys., 294, 501, 10.1016/S0301-0104(03)00390-2
Kennis, 2003, Primary reactions of the LOV2 domain of phototropin, a plant blue-light photoreceptor, Biochemistry, 42, 3385, 10.1021/bi034022k
Schleicher, 2004, On the reaction mechanism of adduct formation in LOV domains of the plant blue-light receptor phototropin, J. Am. Chem. Soc., 126, 11067, 10.1021/ja049553q
Folta, 2001, Unexpected roles for cryptochrome 2 and phototropin revealed by high-resolution analysis of blue light-mediated hypocotyl growth inhibition, Plant J., 26, 471, 10.1046/j.1365-313x.2001.01038.x
Fedorov, 2003, Crystal structures and molecular mechanism of a light-induced signaling switch: the Phot-LOV1 domain from Chlamydomonas reinhardtii, Biophys. J., 84, 2492, 10.1016/S0006-3495(03)75052-8
Crosson, 2001, Structure of a flavin-binding plant photoreceptor domain: insights into light-mediated signal transduction, Proc. Natl Acad. Sci. USA, 98, 2995, 10.1073/pnas.051520298
Crosson, 2002, Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch, Plant Cell, 14, 1067, 10.1105/tpc.010475
Swartz, 2002, Vibration spectroscopy reveals light-induced chromophore and protein structural changes in the LOV2 domain of the plant blue-light receptor phototropin 1, Biochemistry, 41, 7183, 10.1021/bi025861u
Fedorov, 2003, Crystal structures and molecular mechanism of a light-induced signaling switch: the Phot-LOV1 domain from Chlamydomonas reinhardtii, Biophys. J., 84, 2492, 10.1016/S0006-3495(03)75052-8
Iwata, 2005, Comparative investigation of the LOV1 and LOV2 domains in adiantum phytochrome3, Biochemistry, 44, 7427, 10.1021/bi047281y
Harper, 2003, Structural basis of a phototropin light switch, Science, 301, 1541, 10.1126/science.1086810
Harper, 2004, Disruption of the LOV-J helix interaction activates phototropin kinase activity, Biochemistry, 43, 16184, 10.1021/bi048092i
Nakasako, 2004, Light-induced structural changes of LOV domain-containing polypeptides from arabidopsis phototropin 1 and 2 studied by small-angle X-ray scattering, Biochemistry, 43, 14881, 10.1021/bi0485530
Losi, 2004, Recording of blue light-induced energy and volume changes within the wild-type and mutated phot-LOV1 domain from Chlamydomonas reinhardtii, Biophys. J., 86, 1051, 10.1016/S0006-3495(04)74180-6
Corchnoy, 2003, Intramolecular proton transfers and structural changes during the photocycle of the LOV2 domain of phototropin 1, J. Biol. Chem., 278, 724, 10.1074/jbc.M209119200
Guo, 2005, The Phot LOV2 domain and its interaction with LOV1, Biophys. J., 89, 402, 10.1529/biophysj.104.058230
Alexandre, 2009, Primary reactions of the LOV2 domain of phototropin studied with ultrafast mid-infrared spectroscopy and quantum chemistry, Biophys. J., 97, 227, 10.1016/j.bpj.2009.01.066
Alexandre, 2009, Conformational heterogeneity and propagation of structural changes in the LOV2/Ja domain from Avena sativa Phototropin 1 as recorded by temperature-dependent FTIR spectroscopy, Biophys. J., 97, 238, 10.1016/j.bpj.2009.03.047
Koyama, 2009, Different role of the Jalpha helix in the light-induced activation of the LOV2 domains in various phototropins, Biochemistry, 48, 7621, 10.1021/bi9009192
Pfeifer, 2010, Blue light induces global and localized conformational changes in the kinase domain of full-length phototropin, Biochemistry, 49, 1024, 10.1021/bi9016044
Losi, 2003, Listening to the blue: the time-resolved thermodynamics of the bacterial blue-light receptor YtvA and its isolated LOV domain, Photochem. Photobiol. Aci., 2, 759, 10.1039/B301782F
Pfeifer, 2009, Time-resolved Fourier Transform Infrared study on photoadduct formation and secondary structural Changes within the phototropin LOV domain, Biophys. J., 96, 1462, 10.1016/j.bpj.2008.11.016
Yao, 2008, Estimation of the available free energy in a LOV2-J alpha photoswitch, Nat. Chem. Biol., 4, 491, 10.1038/nchembio.99
Strickland, 2010, Rationally improving LOV domain–based photoswitches, Nat. Methods, 7, 623, 10.1038/nmeth.1473
Terazima, 1996, Energetic and molecular dynamics in solution studied by the third order nonlinear optical spectroscopies; Transient lens and transient grating, Vol. 10, 1
Terazima, 1998, Transient lens spectroscopy in a fast time scale, Israel J. Chem., 38, 143, 10.1002/ijch.199800016
Bialkowski, 1996