Diverse Fluorescence Resonance Energy Transfer Processes Originating from the Conformational Heterogeneity of the Calcium Indicator Yellow Cameleon YC3.60.

By combining time-resolved fluorescence spectroscopy and molecular biology, we have clearly elucidated the fluorescence mechanism of yellow cameleon YC3.60. YC3.60 is one of the most widely used fundamental calcium ion indicator proteins and is a tandem protein consisting of cyan fluorescent protein, calmodulin, and yellow fluorescent protein. Our results show that the conformational heterogeneity of YC3.60 leads to multiple FRET (fluorescence resonance energy transfer) processes occurring in a variety of structures. In the presence of calcium ions, FRET occurs in 75% of all YC3.60 molecules, and the intramolecular FRET faster than 20 ps is dominant among the three different FRET processes. Even in the absence of calcium ions, FRET occurs in 28% of YC3.60, where intra- and intermolecular FRET with a time constant of 160 ps is dominant among the four different FRET processes. YC3.60 with the immature chromophore, which is 25% of the total, would result in lower contrast on imaging. Conformational heterogeneity arises from the specific association of the two fluorescent proteins. It was clearly shown that the association of fluorescent proteins has a significant impact on the fluorescence mechanism. These observations lead to the promotion of research that elucidates the relationship between the higher-order structure and function of proteins.

Excited-State Proton Transfer Dynamics in LSSmOrange Studied by Time-Resolved Impulsive Stimulated Raman Spectroscopy.

LSSmOrange is a fluorescent protein that exhibits a large energy gap between absorption and emission, which makes it a useful tool for multicolor bioimaging. This characteristic of LSSmOrange originates from excited-state proton transfer (ESPT): The neutral chromophore is predominantly present in the ground state while the bright fluorescence is emitted from the anionic excited state after ESPT. Interestingly, it was reported that this ESPT process follows bimodal dynamics, but its origin has not clearly been understood. We investigate ESPT of LSSmOrange using time-resolved impulsive stimulated Raman spectroscopy (TR-ISRS) that provides femtosecond time-resolved Raman spectra. The results indicate that the bimodal ESPT dynamics originates from the structural heterogeneity of the chromophore. Species-associated Raman spectra obtained by spectral analysis based on singular value decomposition (SVD) suggest that cis and trans chromophores coexist in the ground state. It is considered that these two forms are photoexcited and undergo ESPT in parallel, resulting in the bimodal dynamics of ESPT in LSSmOrange.

Three Simultaneous Fluorescence Resonance Energy Transfer Processes and Structural Relaxation of Enhanced Yellow Fluorescent Protein Observed by Picosecond Time-Resolved Fluorescence Anisotropy.

Fluorescent proteins (FPs) have been widely used to visualize biological processes in living cells. It is essential to understand the underlying fluorescence mechanism to develop novel FPs and to interpret imaging data appropriately. Enhanced yellow fluorescent protein (eYFP) is one of the most typical FPs; however, several reports to date have been limited to individual discussion, which is insufficient to understand the full picture of the dynamics involved. In this study, we focused on the fluorescence resonance energy transfer (FRET) and dimerization behavior and performed picosecond time-resolved fluorescence measurements of eYFP and its A206K mutant, which does not form a dimer. The combination of the dissociation constant and the acid dissociation constant rationally explains the mechanism of ultrafast homo-FRET and ultrafast hetero-FRET. It is also shown that structural relaxation occurs in the dimer after excited-state proton transfer. The formation efficiencies and quaternary structures of dimers consisting of different protonation states are shown to be different. Furthermore, under high-concentration conditions, "slow" homo-FRET with tens of nanoseconds timescale occurs between monomers and dimers. The findings from this study will be applied to other fluorescent proteins such as Aequorea victoria green FP and its mutants and various red FPs with longer conjugation lengths.

Role of Coherent Low-Frequency Motion in Excited-State Proton Transfer of Green Fluorescent Protein Studied by Time-Resolved Impulsive Stimulated Raman Spectroscopy.

Green fluorescent protein (GFP) from jellyfish Aequorea victoria, an essential bioimaging tool, luminesces via excited-state proton transfer (ESPT) in which the phenolic proton of the p-hydroxybenzylideneimidazolinone chromophore is transferred to Glu222 through a hydrogen-bond network. In this process, the ESPT mediated by the low-frequency motion of the chromophore has been proposed. We address this issue using femtosecond time-resolved impulsive stimulated Raman spectroscopy. After coherently exciting low-frequency modes (<300 cm(-1)) in the excited state of GFP, we examined the excited-state structural evolution and the ESPT dynamics within the dephasing time of the low-frequency vibration. A clear anharmonic vibrational coupling is found between one high-frequency mode of the chromophore (phenolic CH bend) and a low-frequency mode at ∼104 cm(-1). However, the data show that this low-frequency motion does not substantially affect the ESPT dynamics.

Direct observation of time-dependent photoluminescence spectral shift in CdS nanoparticles synthesized in polymer solutions.

Direct observation of time-resolved emission spectra (TRESs) of cadmium sulfide nanoparticles in polymer solutions was carried out with picosecond resolution using a streak camera. The TRESs were found to undergo a pronounced time-dependent Stokes shift, eventually coinciding with the steady-state photoluminescence spectra within an approximately 40 ns delay time. Moreover, approximately 90% of the shift was complete within the first 1 ns after excitation, in contrast to the fact that overall photoluminescence involves very long time constants of 10-100 ns. The observed Stokes shift dynamics was very similar in CdS nanoparticles stabilized in two very different types of polymer solutions. Thus the solvent and/or polymeric stabilizer appeared to have a minimal effect on the shift. We propose that the relaxation proceeds through an internal mechanism involving the fast decay of high-energy traps into relatively slow-decaying low-energy traps. Time-dependent photoluminescence anisotropy experiments also revealed an approximately 1 ns decay component appearing only in the higher-energy end of the photoluminescence spectrum. Because this time constant is too short to represent rotational diffusion of the nanometer-sized particles, it was associated with the rapid relaxation of the high-energy trap states.

Hidden electronic excited state of enhanced green fluorescent protein.

Precise two-photon absorption spectra of the green fluorescent protein (GFP) and the mutants sapphire-GFP (T203I) and enhanced GFP (S65T/F64L), as well as a model compound for the chromophore, 4'-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) were measured by multiplex two-photon absorption spectroscopy. The observed TPA bands of the anionic forms of enhanced GFP and HBDI were significantly shifted to the higher energy compared with the lowest-energy bands in one-photon absorption spectra. This result indicated the existence of a hidden electronic excited state in the vicinity of the lowest excited singlet (S1) state of the anionic form of the GFP chromophore, which is the origin of the blue shift of the two-photon absorption spectra as well as two-photon fluorescence excitation spectra.

Femtosecond/picosecond time-resolved fluorescence study of hydrophilic polymer fine particles.

Femtosecond/picosecond time-resolved fluorescence study of hydrophilic polymer fine particles (polyacrylamide, PAAm) was reported. Ultrafast fluorescence dynamics of polymer/water solution was monitored using a fluorescent probe molecule (C153). In the femtosecond time-resolved fluorescence measurement at 480 nm, slowly decay components having lifetimes of tau(1) approximately 53 ps and tau(2) approximately 5 ns were observed in addition to rapid fluorescence decay. Picosecond time-resolved fluorescence spectra of C153/PAAm/H2O solution were also measured. In the time-resolved fluorescence spectra of C153/PAAm/H2O, a peak shift from 490 to 515 nm was measured, which can be assigned to the solvation dynamics of polymer fine particles. The fluorescence peak shift was related to the solvation response function and two time constants were determined (tau(3) approximately 50 ps and tau(4) approximately 467 ps). Therefore, the tau(1) component observed in the femtosecond time-resolved fluorescence measurement was assigned to the solvation dynamics that was observed only in the presence of polymer fine particles. Rotational diffusion measurements were also carried out on the basis of the picosecond time-resolved fluorescence spectra. In the C153/PAAm/H2O solution, anisotropy decay having two different time constants was also derived (tau(6) approximately 76 ps and tau(7) approximately 676 ps), indicating the presence of two different microscopic molecular environments around the polymer surface. Using the Stokes-Einstein-Debye (SED) equation, microscopic viscosity around the polymer surface was evaluated. For the area that gave a rotational diffusion time of tau(6) approximately 76 ps, the calculated viscosity is approximately 1.1 cP and for tau(7) approximately 676 ps, it is approximately 10 cP. The calculated viscosity values clearly revealed that there are two different molecular environments around the polyacrylamide fine particles.

Excited-state structure and dynamics of 1,3,5-tris(phenylethynyl)benzene as studied by Raman and time-resolved fluorescence spectroscopy.

Excited-state structure and dynamics of 1,3,5-tris(phenylethynyl)benzene (TPB) have been studied in n-hexane and n-heptane solutions. Time-resolved fluorescence spectra, fluorescence anisotropy, and lifetime of TPB were recorded with femtosecond to nanosecond time resolution. Raman depolarization ratio was also measured to elucidate a nonplanar structure of the ground state. Two fluorescence components, the short-lived component with 150 fs lifetime and the long-lived component with 10 ns lifetime, were observed. The analysis of the fluorescence anisotropy values combined with the Raman depolarization data has led to a conclusion that TPB is primarily excited to a short-lived excited singlet state with a nonplanar structure, and then it relaxes to a long-lived excited singlet state with a 3-fold axis. A rapid structural change from a nonplanar to a planar structure is suggested to take place in the process of relaxation.

Competition between energy and proton transfer in ultrafast excited-state dynamics of an oligomeric fluorescent protein red Kaede.

We investigated femtosecond and picosecond time-resolved fluorescence dynamics of a tetrameric fluorescent protein Kaede with a red chromophore (red Kaede) to examine a relationship between the excited-state dynamics and a quaternary structure of the fluorescent protein. Red Kaede was obtained by photoconversion from green Kaede that was cloned from a stony coral Trachyphyllia geoffroyi. In common with other typical fluorescent proteins, a chromophore of red Kaede has two protonation states, the neutral and the anionic forms in equilibrium. Time-resolved fluorescence measurements clarified that excitation of the neutral form gives the anionic excited state with a time constant of 13 ps at pH 7.5. This conversion process was attributed to fluorescence resonance energy transfer (FRET) from the photoexcited neutral form to the ground-state anionic form that is located in an adjacent subunit in the tetramer. The time-resolved fluorescence data measured at different pH revealed that excited-state proton transfer (ESPT) also occurs with a time constant of 300 ps and hence that the FRET and ESPT take place simultaneously in the fluorescent protein as competing processes. The ESPT rate in red Kaede was significantly slower than the rate in Aequorea GFP, which highly likely arises from the different hydrogen bond network around the chromophore.

Concatenation of cyan and yellow fluorescent proteins for efficient resonance energy transfer.

Highly efficient fluorescence resonance energy transfer between cyan(CFP) and yellow fluorescent proteins (YFP), the cyan- and yellow-emitting variants of the Aequorea green fluorescent protein, respectively, was achieved by tightly concatenating the two proteins. After the C-terminus of CFP and the N-terminus of YFP were truncated by 11 and 5 amino acids, respectively, the proteins were fused through a leucine-glutamate dipeptide. The resulting chimeric protein, which we called Cy11.5, exhibited a simple emission spectrum that peaked at 527 nm when the protein was excited at 436 nm. The time-resolved emission of Cy11.5 was measured using a streak camera. After excitation of Cy11.5 with a 400 nm ultrashort pulse, a fast decay of the CFP emission and a concomitant rise of the YFP emission were observed with a lifetime of 66 ps. By contrast, the emission from CFP alone showed a decay component with a lifetime of 2.9 ns. We concluded that in fully folded Cy11.5 molecules, intramolecular FRET occurred with an efficiency of 98%. Importantly, most Cy11.5 molecules were properly folded, and the protein was highly resistant to all of the tested proteases. In living cells, therefore, Cy11.5 behaved as a single fluorescent protein with a broad excitation spectrum. Moreover, Cy11.5 was used as an optical highlighter after photobleaching of YFP. When HeLa cells expressing Cy11.5 were irradiated at 514.5 nm, a 10-fold increase in the 475 nm fluorescence intensity was observed. These features make Cy11.5 useful as an optical highlighter and a new-colored fluorescent protein for multicolor imaging.

Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus.

Small protein B (SmpB) is required for trans-translation, binding specifically to tmRNA. We show here the solution structure of SmpB from an extremely thermophilic bacterium, Thermus thermophilus HB8, determined by heteronuclear nuclear magnetic resonance methods. The core of the protein consists of an antiparallel beta-barrel twisted up from eight beta-strands, each end of which is capped with the second or third helix, and the first helix is located beside the barrel. Its C-terminal sequence (20 residues), which is rich in basic residues, shows a poorly structured form, as often seen in isolated ribosomal proteins. The results are discussed in relation to the oligonucleotide binding fold.