Dissecting Optical Response and Molecular Structure of Fluorescent Proteins With Non-canonical Chromophores.

Tracking the structural dynamics of fluorescent protein chromophores holds the key to unlocking the fluorescence mechanisms in real time and enabling rational design principles of these powerful and versatile bioimaging probes. By combining recent chemical biology and ultrafast spectroscopy advances, we prepared the superfolder green fluorescent protein (sfGFP) and its non-canonical amino acid (ncAA) derivatives with a single chlorine, bromine, and nitro substituent at the ortho site to the phenolate oxygen of the embedded chromophore, and characterized them using an integrated toolset of femtosecond transient absorption and tunable femtosecond stimulated Raman spectroscopy (FSRS), aided by quantum calculations of the vibrational normal modes. A dominant vibrational cooling time constant of ~4 and 11 ps is revealed in Cl-GFP and Br-GFP, respectively, facilitating a ~30 and 12% increase of the fluorescent quantum yield vs. the parent sfGFP. Similar time constants were also retrieved from the transient absorption spectra, substantiating the correlated electronic and vibrational motions on the intrinsic molecular timescales. Key carbon-halogen stretching motions coupled with phenolate ring motions of the deprotonated chromophores at ca. 908 and 890 cm-1 in Cl-GFP and Br-GFP exhibit enhanced activities in the electronic excited state and blue-shift during a distinct vibrational cooling process on the ps timescale. The retrieved structural dynamics change due to targeted site-specific halogenation of the chromophore thus provides an effective means to design new GFP derivatives and enrich the bioimaging probe toolset for life and medical sciences.

Capturing Structural Snapshots during Photochemical Reactions with Ultrafast Raman Spectroscopy: From Materials Transformation to Biosensor Responses.

Chemistry studies the composition, structure, properties, and transformation of matter. A mechanistic understanding of the pertinent processes is required to translate fundamental knowledge into practical applications. The current development of ultrafast Raman as a powerful time-resolved vibrational technique, particularly femtosecond stimulated Raman spectroscopy (FSRS), has shed light on the structure-energy-function relationships of various photosensitive systems. This Perspective reviews recent work incorporating optical innovations, including the broad-band up-converted multicolor array (BUMA) into a tunable FSRS setup, and demonstrates its resolving power to watch metal speciation and photolysis, leading to high-quality thin films, and fluorescence modulation of chimeric protein biosensors for calcium ion imaging. We discuss advantages of performing FSRS in the mixed time-frequency domain and present strategies to delineate mechanisms by tracking low-frequency modes and systematically modifying chemical structures with specific functional groups. These unique insights at the chemical-bond level have started to enable the rational design and precise control of functional molecular machines in optical, materials, energy, and life sciences.

Dynamic Raman Line Shapes on an Evolving Excited-State Landscape: Insights from Tunable Femtosecond Stimulated Raman Spectroscopy.

Tracking molecular motions in real time remains a formidable challenge in science and engineering fields because the experimental methodology requires simultaneously high spatial and temporal resolutions. Building on early successes and future potential of femtosecond stimulated Raman spectroscopy (FSRS) as a structural dynamics technique, we present a comprehensive study of stimulated Raman line shapes of a photosensitive molecule in solution with tunable Raman pump and probe pulses. Following femtosecond 400 nm electronic excitation, the model photoacid pyranine exhibits dynamic and mode-dependent Raman line shapes when the Raman pump is tuned from the red side toward and across the excited-state absorption (ESA) band (e.g., from S1) with varying resonance conditions. On the anti-Stokes FSRS side, low-frequency modes below ∼1000 cm-1 exhibit a line shape change from gain to dispersive to loss, whereas the dispersive intermediate is much less notable for high-frequency modes. The characteristic mode frequency blue shift involving vibrationally hot states in S1 with time constants of ∼9.6 and 58.6 ps reveals the sensitivity of anti-Stokes FSRS to vibrational cooling and solvation. This work lays the foundation for expanding tunable FSRS technology on both the Stokes and anti-Stokes sides to investigate a variety of photoinduced processes in solution with sufficient resolution to expose functional motions and increased sensitivity to monitor vibrational cooling.

Tracking Ultrafast Vibrational Cooling during Excited-State Proton Transfer Reaction with Anti-Stokes and Stokes Femtosecond Stimulated Raman Spectroscopy.

Energy dissipation following photoexcitation is foundational to photophysics and chemistry. Consequently, understanding such processes on molecular time scales holds paramount importance. Femtosecond stimulated Raman spectroscopy (FSRS) has been used to study the molecular structure-function relationships but usually on the Stokes side. Here, we perform both Stokes and anti-Stokes FSRS to track energy dissipation and excited-state proton transfer (ESPT) for the photoacid pyranine in aqueous solution. We reveal biphasic vibrational cooling on fs-ps time scales during ESPT. Characteristic low-frequency motions (<800 cm-1) exhibit initial energy dissipation (∼2 ps) that correlates with functional events of forming contact ion pairs via H-bonds between photoacid and water, which lengthens to ∼9 ps in methanol where ESPT is inhibited. The interplay between photoinduced dissipative and reactive channels is implied. Thermal cooling to bulk solvent occurs on the ∼50 ps time scale. These results demonstrate the combined Stokes and anti-Stokes FSRS as a powerful toolset to elucidate structural dynamics.

Ultrafast intermolecular proton transfer to a proton scavenger in an organic solvent.

Proton transfer reactions are functionally important in numerous chemical and biological processes. To unravel proton scavengers in action with atomistic details, we studied excited-state proton transfer (ESPT) from photoacid pyranine to the weak base acetate in methanol using transient absorption and wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS). Proton transfer is inhibited in neat methanol, but coherent proton motions and the formation of a charge-separated state occur on the sub-picosecond (sub-ps) timescale, accompanied by chromophore solvation wherein the longitudinal relaxation time of methanol (∼9 ps) dominates. With acetate ions added, bimolecular diffusion-controlled ESPT from the photoacid to acetate occurs on the ∼30 ps timescale, followed by ∼600 ps diffusion-assisted charge separation and solvation in the methanol H-bonding network. Besides intensity dynamics, frequency redshift and blueshift of the transient ∼285 and 1525 cm-1 modes track ESPT after 400 nm photoexcitation. Tunable FSRS exploits resonance Raman enhancement with optimal wavelengths, extends the detection window of excited-state vibrational modes to low frequency, and enables a deeper mechanistic understanding of the proton transfer reaction to proton scavengers in an organic solvent.

Panoramic portrait of primary molecular events preceding excited state proton transfer in water.

Photochemistry powers numerous processes from luminescence and human vision, to light harvesting. However, the elucidation of multidimensional photochemical reaction coordinates on molecular timescales remains challenging. We developed wavelength-tunable femtosecond stimulated Raman spectroscopy to simultaneously achieve pre-resonance enhancement for transient reactant and product species of the widely used photoacid pyranine undergoing excited-state proton transfer (ESPT) reaction in solution. In the low-frequency region, the 280 cm-1 ring deformation mode following 400 nm photoexcitation exhibits pronounced intensity oscillations on the sub-picosecond timescale due to anharmonic vibrational coupling to the 180 cm-1 hydrogen-bond stretching mode only in ESPT-capable solvents, indicating a primary event of functional relevance. This leads to the contact ion pair formation on the 3 ps timescale before diffusion-controlled separation. The intermolecular 180 cm-1 mode also reveals vibrational cooling time constants, ∼500 fs and 45 ps in both H2O and D2O, which differ from ESPT time constants of ∼3/8 and 90/250 ps in H2O/D2O, respectively. Spectral results using H218O further substantiate the functional role of the intermolecular 180 cm-1 mode in modulating the distance between proton donor and acceptor and forming the transient ion pair. The direct observation of molecular structural evolution across a wide spectral region during photochemical reactions enriches our fundamental understanding of potential energy surface and holds the key to advancing energy and biological sciences with exceptional atomic and temporal precision.

Unraveling ultrafast photoinduced proton transfer dynamics in a fluorescent protein biosensor for Ca(2+) imaging.

Imaging Ca(2+) dynamics in living systems holds great potential to advance neuroscience and cellular biology. G-GECO1.1 is an intensiometric fluorescent protein Ca(2+) biosensor with a Thr-Tyr-Gly chromophore. The protonated chromophore emits green upon photoexcitation via excited-state proton transfer (ESPT). Upon Ca(2+) binding, a significant population of the chromophores becomes deprotonated. It remains elusive how the chromophore structurally evolves prior to and during ESPT, and how it is affected by Ca(2+) . We use femtosecond stimulated Raman spectroscopy to dissect ESPT in both the Ca(2+) -free and bound states. The protein chromophores exhibit a sub-200 fs vibrational frequency shift due to coherent small-scale proton motions. After wavepackets move out of the Franck-Condon region, ESPT gets faster in the Ca(2+) -bound protein, indicative of the formation of a more hydrophilic environment. These results reveal the governing structure-function relationship of Ca(2+) -sensing protein biosensors.

Excited state structural events of a dual-emission fluorescent protein biosensor for Ca²âº imaging studied by femtosecond stimulated Raman spectroscopy.

Fluorescent proteins (FPs) are luminescent biomolecules that emit characteristic hues upon irradiation. A group of calmodulin (CaM)-green FP (GFP) chimeras have been previously engineered to enable the optical detection of calcium ions (Ca(2+)). We investigate one of these genetically encoded Ca(2+) biosensors for optical imaging (GECOs), GEM-GECO1, which fluoresces green without Ca(2+) but blue with Ca(2+), using femtosecond stimulated Raman spectroscopy (FSRS). The time-resolved FSRS data (<800 cm(-1)) reveal that initial structural evolution following 400 nm photoexcitation involves small-scale coherent proton motions on both ends of the chromophore two-ring system with a <250 fs time constant. Upon Ca(2+) binding, the chromophore adopts a more twisted conformation in the protein pocket with increased hydrophobicity, which inhibits excited-state proton transfer (ESPT) by effectively trapping the protonated chromophore in S1. Both the chromophore photoacidity and local environment form the ultrafast structural dynamics basis for the dual-emission properties of GEM-GECO1. Its photochemical transformations along multidimensional reaction coordinates are evinced by distinct stages of FSRS spectral evolution, particularly related to the ∼460 and 504 cm(-1) modes. The direct observation of lower frequency modes provides crucial information about the nuclear motions preceding ESPT, which enriches our understanding of photochemistry and enables the rational design of new biosensors.

Excited-state structural dynamics of a dual-emission calmodulin-green fluorescent protein sensor for calcium ion imaging.

Fluorescent proteins (FPs) have played a pivotal role in bioimaging and advancing biomedicine. The versatile fluorescence from engineered, genetically encodable FP variants greatly enhances cellular imaging capabilities, which are dictated by excited-state structural dynamics of the embedded chromophore inside the protein pocket. Visualization of the molecular choreography of the photoexcited chromophore requires a spectroscopic technique capable of resolving atomic motions on the intrinsic timescale of femtosecond to picosecond. We use femtosecond stimulated Raman spectroscopy to study the excited-state conformational dynamics of a recently developed FP-calmodulin biosensor, GEM-GECO1, for calcium ion (Ca(2+)) sensing. This study reveals that, in the absence of Ca(2+), the dominant skeletal motion is a ∼ 170 cm(-1) phenol-ring in-plane rocking that facilitates excited-state proton transfer (ESPT) with a time constant of ∼ 30 ps (6 times slower than wild-type GFP) to reach the green fluorescent state. The functional relevance of the motion is corroborated by molecular dynamics simulations. Upon Ca(2+) binding, this in-plane rocking motion diminishes, and blue emission from a trapped photoexcited neutral chromophore dominates because ESPT is inhibited. Fluorescence properties of site-specific protein mutants lend further support to functional roles of key residues including proline 377 in modulating the H-bonding network and fluorescence outcome. These crucial structural dynamics insights will aid rational design in bioengineering to generate versatile, robust, and more sensitive optical sensors to detect Ca(2+) in physiologically relevant environments.