Ultrafast fluorescence upconversion technique and its applications to proteins

Microscopic time-resolved spectroscopy of organic crystals at the nanometer and micrometer scale

How can the photoexcitation dynamics processes of solid substances be measured at the microscopic level? This is a popular topic in many fields of basic and applied sciences. Organic crystals are one of many materials, and understanding their intrinsic properties at the microscopic level is the focus of this discussion. Microscopic time-resolved spectroscopy can study the morphology-dependent photoexcitation dynamics and energy spatial transport processes in organic crystals. In this tutorial review, we introduce the principles and methods of microscopic time-resolved photoluminescence and microscopic transient absorption techniques, which are currently or potentially used to study organic crystals at the nanometer and micrometer scale. Meanwhile, the research status of organic crystals investigated via microscopic time-resolved spectroscopy is discussed, with several examples provided. We then compare the advantages and disadvantages of different methods in detail, offering insights into potential improvements for instrument performance.

Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein

Photoactive yellow protein (PYP) is a signaling protein whose internal p-coumaric acid chromophore undergoes reversible, light-induced trans-to-cis isomerization, which triggers a sequence of structural changes that ultimately lead to a signaling state. Since its discovery nearly 40 years ago, PYP has attracted much interest and has become one of the most extensively studied proteins found in nature. The method of time-resolved crystallography, pioneered by Keith Moffat, has successfully characterized intermediates in the PYP photocycle at near atomic resolution over 12 decades of time down to the sub-picosecond time scale, allowing one to stitch together a movie and literally watch a protein as it functions. But how close to reality is this movie? To address this question, results from numerous complementary time-resolved techniques including x-ray crystallography, x-ray scattering, and spectroscopy are discussed. Emerging from spectroscopic studies is a general consensus that three time constants are required to model the excited state relaxation, with a highly strained ground-state cis intermediate formed in less than 2.4 ps. Persistent strain drives the sequence of structural transitions that ultimately produce the signaling state. Crystal packing forces produce a restoring force that slows somewhat the rates of interconversion between the intermediates. Moreover, the solvent composition surrounding PYP can influence the number and structures of intermediates as well as the rates at which they interconvert. When chloride is present, the PYP photocycle in a crystal closely tracks that in solution, which suggests the epic movie of the PYP photocycle is indeed based in reality.

Ultrafast Dynamics of Solute Molecules Probed by Resonant Optical Kerr Effect Spectroscopy

Ultrafast molecular dynamics in fluids is of great importance in many biological and chemical systems. Although such dynamics in bulk liquids has been explored by various methods, experimental tools that unveil the dynamics of solvated solutes are limited. In this work, we have developed resonant optical Kerr effect spectroscopy (ROKE), which is an analogue of optical Kerr effect spectroscopy that measures the reorientational relaxation of a dilute solute in solution. By adjusting the pump and probe wavelengths at the resonant absorption band of a solute, the time response of the solute was distinguished easily from the negligible signal of the solvent. The heterodyne detection of ROKE enables the determination of reorientational relaxation time constants with an accuracy of 2.6%. The signal-to-noise ratio was high enough (average ∼26.7) to obtain an adequate signal from even a 10 μM solution. Thus, ROKE is a powerful tool to study solute dynamics with high sensitivity in a broad range of applications.

Excited-State Barrier Controls E → Z Photoisomerization in p-Hydroxycinnamate Biochromophores

Molecules based on the deprotonated p-hydroxycinnamate moiety are widespread in nature, including serving as UV filters in the leaves of plants and as the biochromophore in photoactive yellow protein. The photophysical behavior of these chromophores is centered around a rapid E → Z photoisomerization by passage through a conical intersection seam. Here, we use photoisomerization and photodissociation action spectroscopies with deprotonated 4-hydroxybenzal acetone (pCK^-) to characterize a wavelength-dependent bifurcation between electron autodetachment (spontaneous ejection of an electron from the S₁ state because it is situated in the detachment continuum) and E → Z photoisomerization. While autodetachment occurs across the entire S₁(ππ*) band (370-480 nm), E → Z photoisomerization occurs only over a blue portion of the band (370-430 nm). No E → Z photoisomerization is observed when the ketone functional group in pCK^- is replaced with an ester or carboxylic acid. The wavelength-dependent bifurcation is consistent with potential energy surface calculations showing that a barrier separates the Franck-Condon region from the E → Z isomerizing conical intersection. The barrier height, which is substantially higher in the gas phase than in solution, depends on the functional group and governs whether E → Z photoisomerization occurs more rapidly than autodetachment.

What Does Time-Dependent Fluorescence Shift (TDFS) in Biomembranes (and Proteins) Report on?

The organization of biomolecules and bioassemblies is highly governed by the nature and extent of their interactions with water. These interactions are of high intricacy and a broad range of methods based on various principles have been introduced to characterize them. As these methods view the hydration phenomena differently (e.g., in terms of time and length scales), a detailed insight in each particular technique is to promote the overall understanding of the stunning “hydration world.” In this prospective mini-review we therefore critically examine time-dependent fluorescence shift (TDFS)—an experimental method with a high potential for studying the hydration in the biological systems. We demonstrate that TDFS is very useful especially for phospholipid bilayers for mapping the interfacial region formed by the hydrated lipid headgroups. TDFS, when properly applied, reports on the degree of hydration and mobility of the hydrated phospholipid segments in the close vicinity of the fluorophore embedded in the bilayer. Here, the interpretation of the recorded TDFS parameters are thoroughly discussed, also in the context of the findings obtained by other experimental techniques addressing the hydration phenomena (e.g., molecular dynamics simulations, NMR spectroscopy, scattering techniques, etc.). The differences in the interpretations of TDFS outputs between phospholipid biomembranes and proteins are also addressed. Additionally, prerequisites for the successful TDFS application are presented (i.e., the proper choice of fluorescence dye for TDFS studies, and TDFS instrumentation). Finally, the effects of ions and oxidized phospholipids on the bilayer organization and headgroup packing viewed from TDFS perspective are presented as application examples.

Fluorescence-Detected Pump-Probe Spectroscopy

We introduce a new approach to transient spectroscopy, fluorescence-detected pump-probe (F-PP) spectroscopy, that overcomes several limitations of traditional PP. F-PP suppresses excited-state absorption, provides background-free detection, removes artifacts resulting from pump-pulse scattering, from non-resonant solvent response, or from coherent pulse overlap, and allows unique extraction of excited-state dynamics under certain conditions. Despite incoherent detection, time resolution of F-PP is given by the duration of the laser pulses, independent of the fluorescence lifetime. We describe the working principle of F-PP and provide its theoretical description. Then we illustrate specific features of F-PP by direct comparison with PP, theoretically and experimentally. For this purpose, we investigate, with both techniques, a molecular squaraine heterodimer, core-shell CdSe/ZnS quantum dots, and fluorescent protein mCherry. F-PP is broadly applicable to chemical systems in various environments and in different spectral regimes.

Revealing the origin of multiphasic dynamic behaviors in cyanobacteriochrome

Cyanobacteriochromes are photoreceptors in cyanobacteria that exhibit a wide spectral coverage and unique photophysical properties from the photoinduced isomerization of a linear tetrapyrrole chromophore. Here, we integrate femtosecond-resolved fluorescence and transient-absorption methods and unambiguously showed the significant solvation dynamics occurring at the active site from a few to hundreds of picoseconds. These motions of local water molecules and polar side chains are continuously convoluted with the isomerization reaction, leading to a nonequilibrium processes with continuous active-site motions. By mutations of critical residues at the active site, the modified local structures become looser, resulting in faster solvation relaxations and isomerization reaction. The observation of solvation dynamics is significant and critical to the correct interpretation of often-observed multiphasic dynamic behaviors, and thus the previously invoked ground-state heterogeneity may not be relevant to the excited-state isomerization reaction.

Dipole-dipole interactions between tryptophan side chains and hydration water molecules dominate the observed dynamic stokes shift of lysozyme

The fluorescence intensity of tryptophan residues in hen egg-white lysozyme was measured up to 500 ps after the excitation by irradiation pulses at 290 nm. From the time-dependent variation of fluorescence intensity in a wavelength range of 320-370 nm, the energy relaxation in the dynamic Stokes shift was reconstructed as the temporal variation in wavenumber of the estimated fluorescence maximum. The relaxation was approximated by two exponential curves with decay constants of 1.2 and 26.7 ps. To interpret the relaxation, a molecular dynamics simulation of 75 ns was conducted for lysozyme immersed in a water box. From the simulation, the energy relaxation in the electrostatic interactions of each tryptophan residue was evaluated by using a scheme derived from the linear response theory. Dipole-dipole interactions between each of the Trp62 and Trp123 residues and hydration water molecules displayed an energy relaxation similar to that experimentally observed regarding time constants and magnitudes. The side chains of these residues were partly or fully exposed to the solvent. In addition, by inspecting the variation in dipole moments of the hydration water molecules around lysozyme, it was suggested that the observed relaxation could be attributed to the orientational relaxation of hydration water molecules participating in the hydrogen-bond network formed around each of the two tryptophan residues.

Ultrafast Spectroscopic Dynamics of Quinacrine-Riboflavin Binding Protein Interactions

Redox active cofactors play a dynamic role inside protein binding active sites because the amino acids responsible for binding participate in electron transfer (ET) reactions. Here, we use femtosecond transient absorption (FsTA) spectroscopy to examine the ultrafast ET between quinacrine (Qc), an antimalarial drug with potential anticancer activity, and riboflavin binding protein (RfBP) with a known K_d = 264 nM. Steady-state absorption reveals a ∼ 10 nm red-shift in the ground state when QcH₃²⁺ is titrated with RfBP, and a Stern-Volmer analysis shows ∼84% quenching and a blue-shift of the QcH₃²⁺ photoluminescence to form a 1:1 binding ratio of the QcH₃²⁺-RfBP complex. Upon selective photoexcitation of QcH₃²⁺ in the QcH₃²⁺-RfBP complex, we observe charge separation in 7 ps to form ¹[QcH_{3_red}^•+-RfBP^•+], which persists for 138 ps. The FsTA spectra show the spectroscopic identification of QcH_{3_red}^•+, determined from spectroelectrochemical measurements in DMSO. We correlate our results to literature and report lifetimes that are 10-20× slower than the natural riboflavin, Rf-RfBP, complex and are oxygen independent. Driving force (ΔG) calculations, corrected for estimated dielectric constants for protein hydrophobic pockets, and Marcus theory depict a favorable one-electron ET process between QcH₃²⁺ and nearby redox active tyrosine (Tyr) or tryptophan (Trp) residues.