Ultrafast excited-state isomerization in phytochrome revealed by femtosecond stimulated Raman spectroscopy

Effect of the protein environment on the excited state phenomena in a bacteriophytochrome

The excited state processes of a bacteriophytochrome are studied using high-level multireference methods. The various non-radiative channels of deactivation are identified for the chromophore. The effects of the protein environment and substituents are elucidated for these excited state processes. It is observed that while the excited states are completely delocalized in the Franck-Condon (FC) region, they acquire significant charge transfer character near the conical intersections. Earlier studies have emphasized the delocalized nature of the excited states in the FC region, which leads to absorption spectra with minimal Stokes shift [Rumyantsev et al., Sci. Rep., 2015, 5, 18348]. The effect of the protein environment on the vertical excitation energies was minimal, while that on the conical intersection (CI) energetics was significant. This may lead one to believe that it is charge transfer driven. However, energy decomposition analysis shows that it is the effect of the dispersion of nearby residues and the steric effect on the rings and substituents that lead to the large effect of proteins on the energetics of the CIs.

New Insight Into Phytochromes: Connecting Structure to Function

Red and far-red light-sensing phytochromes are widespread in nature, occurring in plants, algae, fungi, and prokaryotes. Despite at least a billion years of evolution, their photosensory modules remain structurally and functionally similar. Conversely, nature has found remarkably different ways of transmitting light signals from the photosensor to diverse physiological responses. We summarize key features of phytochrome structure and function and discuss how these are correlated, from how the bilin environment affects the chromophore to how light induces cellular signals. Recent advances in the structural characterization of bacterial and plant phytochromes have resulted in paradigm changes in phytochrome research that we discuss in the context of present-day knowledge. Finally, we highlight questions that remain to be answered and suggest some of the benefits of understanding phytochrome structure and function.

Dynamics-driven allosteric stimulation of diguanylate cyclase activity in a red light-regulated phytochrome

Sensor-effector proteins integrate information from different stimuli and transform this into cellular responses. Some sensory domains, like red-light responsive bacteriophytochromes, show remarkable modularity regulating a variety of effectors. One effector domain is the GGDEF diguanylate cyclase catalyzing the formation of the bacterial second messenger cyclic-dimeric-guanosine monophosphate. While critical signal integration elements have been described for different phytochromes, a generalized understanding of signal processing and communication over large distances, roughly 100 Å in phytochrome diguanylate cyclases, is missing. Here we show that dynamics-driven allostery is key to understanding signal integration on a molecular level. We generated protein variants stabilized in their far-red-absorbing Pfr state and demonstrated by analysis of conformational dynamics using hydrogen-deuterium exchange coupled to mass spectrometry that single amino acid replacements are accompanied by altered dynamics of functional elements throughout the protein. We show that the conformational dynamics correlate with the enzymatic activity of these variants, explaining also the increased activity of a non-photochromic variant. In addition, we demonstrate the functional importance of mixed Pfr/intermediate state dimers using a fast-reverting variant that still enables wild-type-like fold-changes of enzymatic stimulation by red light. This supports the functional role of single protomer activation in phytochromes, a property that might correlate with the non-canonical mixed Pfr/intermediate-state spectra observed for many phytochrome systems. We anticipate our results to stimulate research in the direction of dynamics-driven allosteric regulation of different bacteriophytochrome-based sensor-effectors. This will eventually impact design strategies for the creation of novel sensor-effector systems for enriching the optogenetic toolbox.

Mastering Femtosecond Stimulated Raman Spectroscopy: A Practical Guide

Femtosecond stimulated Raman spectroscopy (FSRS) is a powerful nonlinear spectroscopic technique that probes changes in molecular and material structure with high temporal and spectral resolution. With proper spectral interpretation, this is equivalent to mapping out reactive pathways on highly anharmonic excited-state potential energy surfaces with femtosecond to picosecond time resolution. FSRS has been used to examine structural dynamics in a wide range of samples, including photoactive proteins, photovoltaic materials, plasmonic nanostructures, polymers, and a range of others, with experiments performed in multiple groups around the world. As the FSRS technique grows in popularity and is increasingly implemented in user facilities, there is a need for a widespread understanding of the methodology and best practices. In this review, we present a practical guide to FSRS, including discussions of instrumentation, as well as data acquisition and analysis. First, we describe common methods of generating the three pulses required for FSRS: the probe, Raman pump, and actinic pump, including a discussion of the parameters to consider when selecting a beam generation method. We then outline approaches for effective and efficient FSRS data acquisition. We discuss common data analysis techniques for FSRS, as well as more advanced analyses aimed at extracting small signals on a large background. We conclude with a discussion of some of the new directions for FSRS research, including spectromicroscopy. Overall, this review provides researchers with a practical handbook for FSRS as a technique with the aim of encouraging many scientists and engineers to use it in their research.

Optical control of ultrafast structural dynamics in a fluorescent protein

The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

Current Trends of Bacterial and Fungal Optoproteins for Novel Optical Applications

Photoproteins, luminescent proteins or optoproteins are a kind of light-response protein responsible for the conversion of light into biochemical energy that is used by some bacteria or fungi to regulate specific biological processes. Within these specific proteins, there are groups such as the photoreceptors that respond to a given light wavelength and generate reactions susceptible to being used for the development of high-novel applications, such as the optocontrol of metabolic pathways. Photoswitchable proteins play important roles during the development of new materials due to their capacity to change their conformational structure by providing/eliminating a specific light stimulus. Additionally, there are bioluminescent proteins that produce light during a heatless chemical reaction and are useful to be employed as biomarkers in several fields such as imaging, cell biology, disease tracking and pollutant detection. The classification of these optoproteins from bacteria and fungi as photoreceptors or photoresponse elements according to the excitation-emission spectrum (UV-Vis-IR), as well as their potential use in novel applications, is addressed in this article by providing a structured scheme for this broad area of knowledge.

Vibrational Spectroscopy of Phytochromes

Phytochromes are biological photoswitches that translate light into physiological functions. Spectroscopic techniques are essential tools for molecular research into these photoreceptors. This review is directed at summarizing how resonance Raman and IR spectroscopy contributed to an understanding of the structure, dynamics, and reaction mechanism of phytochromes, outlining the substantial experimental and theoretical challenges and describing the strategies to master them. It is shown that the potential of the various vibrational spectroscopic techniques can be most efficiently exploited using integral approaches via a combination of theoretical methods as well as other experimental techniques.

The Role of H-Bonds in the Excited-State Properties of Multichromophoric Systems: Static and Dynamic Aspects

Given their importance, hydrogen bonds (H-bonds) have been the subject of intense investigation since their discovery. Indeed, H-bonds play a fundamental role in determining the structure, the electronic properties, and the dynamics of complex systems, including biologically relevant materials such as DNA and proteins. While H-bonds have been largely investigated for systems in their electronic ground state, fewer studies have focused on how the presence of H-bonds could affect the static and dynamic properties of electronic excited states. This review presents an overview of the more relevant progress in studying the role of H-bond interactions in modulating excited-state features in multichromophoric biomimetic complex systems. The most promising spectroscopic techniques that can be used for investigating the H-bond effects in excited states and for characterizing the ultrafast processes associated with their dynamics are briefly summarized. Then, experimental insights into the modulation of the electronic properties resulting from the presence of H-bond interactions are provided, and the role of the H-bond in tuning the excited-state dynamics and the related photophysical processes is discussed.

Ultrafast motion in a third generation photomolecular motor

Controlling molecular translation at the nanoscale is a key objective for development of synthetic molecular machines. Recently developed third generation photochemically driven molecular motors (3GMs), comprising pairs of overcrowded alkenes capable of cooperative unidirectional rotation offer the possibility of converting light energy into translational motion. Further development of 3GMs demands detailed understanding of their excited state dynamics. Here we use time-resolved absorption and emission to track population and coherence dynamics in a 3GM. Femtosecond stimulated Raman reveals real-time structural dynamics as the excited state evolves from a Franck-Condon bright-state through weakly-emissive dark-state to the metastable product, yielding new insight into the reaction coordinate. Solvent polarity modifies the photoconversion efficiency suggesting charge transfer character in the dark-state. The enhanced quantum yield correlates with suppression of a low-frequency flapping motion in the excited state. This detailed characterization facilitates development of 3GMs, suggesting exploitation of medium and substituent effects to modulate motor efficiency.

Investigation of Ultrafast Configurational Photoisomerization of Bilirubin Using Femtosecond Stimulated Raman Spectroscopy

Phototherapy is an efficient and safe way to reduce high levels of free 4Z,15Z-bilirubin (ZZ-BR) in the serum of newborns. The success of BR phototherapy lies in photoinduced configurational and structural isomerization processes that form excretable isomers. However, the physical picture of photoinduced photoisomerization of ZZ-BR is still unclear. Here, we strategically implement tunable femtosecond stimulated Raman spectroscopy and several time-resolved electronic spectroscopies, assisted by quantum chemical calculations, to dissect the detailed primary configurational isomerization dynamics of free ZZ-BR in organic solvents. The results of this study demonstrate that upon photoexcitation, ultrafast configurational isomerization proceeds by a volume-conserving "hula twist", followed by intramolecular hydrogen-bond distortion and large-scale rotation of the two dipyrrinone halves of the ZZ-BR isomer in a few picoseconds. After that, most of the population recovers back to ZZ-BR, and a very small amount is converted into stable BR isomers via structural isomerization.

Mapping the Complete Photocycle that Powers a Large Stokes Shift Red Fluorescent Protein

Large Stokes shift (LSS) red fluorescent proteins (RFPs) are highly desirable for bioimaging advances. The RFP mKeima, with coexisting cis- and trans-isomers, holds significance as an archetypal system for LSS emission due to excited-state proton transfer (ESPT), yet the mechanisms remain elusive. We implemented femtosecond stimulated Raman spectroscopy (FSRS) and various time-resolved electronic spectroscopies, aided by quantum calculations, to dissect the cis- and trans-mKeima photocycle from ESPT, isomerization, to ground-state proton transfer in solution. This work manifests the power of FSRS with global analysis to resolve Raman fingerprints of intermediate states. Importantly, the deprotonated trans-isomer governs LSS emission at 620 nm, while the deprotonated cis-isomer's 520 nm emission is weak due to an ultrafast cis-to-trans isomerization. Complementary spectroscopic techniques as a table-top toolset are thus essential to study photochemistry in physiological environments.

From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions

This review discusses how ultrafast organic photochemical reactions are controlled by conical intersections, highlighting that decay to the ground-state at multiple points of the intersection space results in their multi-mode character.

Photoisomerization of phytochrome chromophore models: an XMS-CASPT2 study

Phytochromes are a superfamily of photoreceptors that harbor linear tetrapyrroles as chromophores. Upon light illumination, the linear tetrapyrrole chromophore undergoes a double bond isomerization which starts a photocycle. In this work, we studied the photoisomerization of chromophore models designed based on the C- and D-rings of the phycocyanobilin (PCB) chromophore. In total, five different models with varying substitutions were investigated. Firstly, the vertical excitation energies were benchmarked using different computational methods to establish the relative order of the excited states. Based on these calculations, we computed the photoisomerization profiles using the extended multi-state (XMS) version of the CASPT2 method. The profiles were obtained for both the clockwise and counterclockwise rotations of the C₁₅C₁₆ bond in the Z and E isomers using a linear interpolation of internal coordinates between the Franck-Condon and MECI geometries. In the minimal chromophore model that lacks the substitutions at the pyrrole rings, the isomerization involves both C₁₄-C₁₅ and C₁₅C₁₆ bonds of the methine bridge between the C- and D-rings, resembling the hula-twist motion. The MECIs are characterized by a partial charge transfer between the two pyrrole rings pointing towards a twisted intramolecular charge transfer. Systematic introduction of substituents leads to an increase in the steric repulsion between the two pyrrole rings causing a pretwist of the dihedral around the C₁₅C₁₆ bond, which creates a preference for the counterclockwise isomerization. An introduction of the carbonyl group at the D-ring increases the extent of charge transfer which changes the isomerization mechanism from hula-twist to one-bond flip.

Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives

Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.

Excitation energy transfer and vibronic coherence in intact phycobilisomes

The phycobilisome is an oligomeric chromoprotein complex that serves as the principal mid-visible light-harvesting system in cyanobacteria. Here we report the observation of excitation-energy-transfer pathways involving delocalized optical excitations of the bilin (linear tetrapyrrole) chromophores in intact phycobilisomes isolated from Fremyella diplosiphon. By using broadband multidimensional electronic spectroscopy with 6.7-fs laser pulses, we are able to follow the progress of excitation energy from the phycoerythrin disks at the ends of the phycobilisome's rods to the C-phycocyanin disks along their length in <600 fs. Oscillation maps show that coherent wavepacket motions prominently involving the hydrogen out-of-plane vibrations of the bilins mediate non-adiabatic relaxation of a manifold of vibronic exciton states. However, the charge-transfer character of the bilins in the allophycocyanin-containing segments localizes the excitations in the core of the phycobilisome, yielding a kinetic bottleneck that enables photoregulatory mechanisms to operate efficiently on the >10-ps timescale.

Vibrational couplings between protein and cofactor in bacterial phytochrome Agp1 revealed by 2D-IR spectroscopy

Phytochromes are ubiquitous photoreceptor proteins that undergo a significant refolding of secondary structure in response to initial photoisomerization of the chromophoric group. This process is important for the signal transduction through the protein and thus its regulatory function in different organisms. Here, we employ two-dimensional infrared absorption (2D-IR) spectroscopy, an ultrafast spectroscopic technique that is sensitive to vibrational couplings, to study the photoreaction of bacterial phytochrome Agp1. By calculating difference spectra with respect to the photoactivation, we are able to isolate sharp difference cross-peaks that report on local changes in vibrational couplings between different sites of the chromophore and the protein. These results indicate inter alia that a dipole coupling between the chromophore and the so-called tongue region plays a role in stabilizing the protein in the light-activated state.

Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome

Phytochromes are red light-sensing photoreceptor proteins that bind a bilin chromophore. Here, we investigate the role of a conserved histidine (H260) and tyrosine (Y263) in the chromophore-binding domain (CBD) of Deinococcus radiodurans phytochrome (DrBphP). Using crystallography, we show that in the H260A variant, the missing imidazole side chain leads to increased water content in the binding pocket. On the other hand, Y263F mutation reduces the water occupancy around the chromophore. Together, these changes in water coordination alter the protonation and spectroscopic properties of the biliverdin. These results pinpoint the importance of this conserved histidine and tyrosine, and the related water network, for the function and applications of phytochromes.

Photoswitchable Fluorescent Proteins: Mechanisms on Ultrafast Timescales

The advancement of super-resolution imaging (SRI) relies on fluorescent proteins with novel photochromic properties. Using light, the reversibly switchable fluorescent proteins (RSFPs) can be converted between bright and dark states for many photocycles and their emergence has inspired the invention of advanced SRI techniques. The general photoswitching mechanism involves the chromophore cis-trans isomerization and proton transfer for negative and positive RSFPs and hydration-dehydration for decoupled RSFPs. However, a detailed understanding of these processes on ultrafast timescales (femtosecond to millisecond) is lacking, which fundamentally hinders the further development of RSFPs. In this review, we summarize the current progress of utilizing various ultrafast electronic and vibrational spectroscopies, and time-resolved crystallography in investigating the on/off photoswitching pathways of RSFPs. We show that significant insights have been gained for some well-studied proteins, but the real-time "action" details regarding the bidirectional cis-trans isomerization, proton transfer, and intermediate states remain unclear for most systems, and many other relevant proteins have not been studied yet. We expect this review to lay the foundation and inspire more ultrafast studies on existing and future engineered RSFPs. The gained mechanistic insights will accelerate the rational development of RSFPs with enhanced two-way switching rate and efficiency, better photostability, higher brightness, and redder emission colors.

The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization

Photoactivation of bacteriophytochrome involves a cis-trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the chromophore to adopt a more planar configuration, which we assign to the early Lumi-R state. The isomerization process is completed via helix inversion of the biliverdin chromophore to form the late Lumi-R state. The mechanistic insights into the photoisomerization process are essential to understand how bacteriophytochrome has evolved to mediate photoactivation and to engineer this protein for new applications.

Photoinduced reaction mechanisms in prototypical and bathy phytochromes

Phytochromes, found in plants, fungi, and bacteria, exploit light as a source of information to control physiological processes via photoswitching between two states of different physiological activity, i.e. a red-absorbing Pr and a far-red-absorbing Pfr state. Depending on the relative stability in the dark, bacterial phytochromes are divided into prototypical and bathy phytochromes, where the stable state is Pr and Pfr, respectively. In this work we studied representatives of these groups (prototypical Agp1 and bathy Agp2 from Agrobacterium fabrum) together with the bathy-like phytochrome XccBphP from Xanthomonas campestris by resonance Raman and IR difference spectroscopy. In all three phytochromes, the photoinduced conversions display the same mechanistic pattern as reflected by the chromophore structures in the various intermediate states. We also observed in each case the secondary structure transition of the tongue, which is presumably crucial for the function of phytochrome. The three phytochromes differ in details of the chromophore conformation in the various intermediates and the energetic barrier of their respective decay reactions. The specific protein environment in the chromophore pocket, which is most likely the origin for these small differences, also controls the proton transfer processes concomitant to the photoconversions. These proton translocations, which are tightly coupled to the structural transition of the tongue, presumably proceed via the same mechanism along the Pr → Pfr conversion whereas the reverse Pfr → Pr photoconversion includes different proton transfer pathways. Finally, classification of phytochromes in prototypical and bathy (or bathy-like) phytochromes is discussed in terms of molecular structure and mechanistic properties.

Ultrafast proton-coupled isomerization in the phototransformation of phytochrome

The biological function of phytochromes is triggered by an ultrafast photoisomerization of the tetrapyrrole chromophore biliverdin between two rings denoted C and D. The mechanism by which this process induces extended structural changes of the protein is unclear. Here we report ultrafast proton-coupled photoisomerization upon excitation of the parent state (Pfr) of bacteriophytochrome Agp2. Transient deprotonation of the chromophore's pyrrole ring D or ring C into a hydrogen-bonded water cluster, revealed by a broad continuum infrared band, is triggered by electronic excitation, coherent oscillations and the sudden electric-field change in the excited state. Subsequently, a dominant fraction of the excited population relaxes back to the Pfr state, while ~35% follows the forward reaction to the photoproduct. A combination of quantum mechanics/molecular mechanics calculations and ultrafast visible and infrared spectroscopies demonstrates how proton-coupled dynamics in the excited state of Pfr leads to a restructured hydrogen-bond environment of early Lumi-F, which is interpreted as a trigger for downstream protein structural changes.

Fluorescence Modulation by Ultrafast Chromophore Twisting Events: Developing a Powerful Toolset for Fluorescent-Protein-Based Imaging

The advancement of modern life sciences has benefited tremendously from the discovery and development of fluorescent proteins (FPs), widely expressed in live cells to track a myriad of cellular events. The chromophores of various FPs can undergo many ultrafast photophysical and/or photochemical processes in the electronic excited state and emit fluorescence with different colors. However, the chromophore becomes essentially nonfluorescent in solution environment due to its intrinsic twisting capability upon photoexcitation. To study "microscopic" torsional events and their effects on "macroscopic" fluorescence, we have developed an integrated ultrafast characterization platform involving femtosecond transient absorption (fs-TA) and wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS). A wide range of naturally occurring, circularly permuted, non-canonical amino-acid-decorated FPs and FP-based optical highlighters with photochromicity, photoconversion, and/or photoswitching capabilities have been recently investigated in great detail. Twisting conformational motions were elucidated to exist in all of these systems but to various extents. The associated different ultrafast pathways can be monitored via frequency changes of characteristic Raman bands during primary events and functional processes. The mapped electronic and structural dynamics information is crucial and has shown great potential and initial success for the rational design of proteins and other photoreceptors with novel functions and fluorescence properties.

Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level

Phytochromes constitute a widespread photoreceptor family that typically interconverts between two photostates called Pr (red light–absorbing) and Pfr (far-red light–absorbing). The lack of full-length structures solved at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here, we present the crystallographic structures of three versions from the plant pathogen Xanthomonas campestris virulence regulator XccBphP bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structures show a reorganization of the interaction networks within and around the chromophore-binding pocket, an α-helix/β-sheet tongue transition, and specific domain reorientations, along with interchanging kinks and breaks at the helical spine as a result of the photoswitching, which subsequently affect the quaternary assembly. These structural findings, combined with multidisciplinary studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level.

Ultrafast Photoconversion Dynamics of the Knotless Phytochrome SynCph2

The family of phytochrome photoreceptors contains proteins with different domain architectures and spectral properties. Knotless phytochromes are one of the three main subgroups classified by their distinct lack of the PAS domain in their photosensory core module, which is in contrast to the canonical PAS-GAF-PHY array. Despite intensive research on the ultrafast photodynamics of phytochromes, little is known about the primary kinetics in knotless phytochromes. Here, we present the ultrafast P_r ⇆ P_fr photodynamics of SynCph2, the best-known knotless phytochrome. Our results show that the excited state lifetime of P_r* (~200 ps) is similar to bacteriophytochromes, but much longer than in most canonical phytochromes. We assign the slow P_r* kinetics to relaxation processes of the chromophore-binding pocket that controls the bilin chromophore’s isomerization step. The P_fr photoconversion dynamics starts with a faster excited state relaxation than in canonical phytochromes, but, despite the differences in the respective domain architectures, proceeds via similar ground state intermediate steps up to Meta-F. Based on our observations, we propose that the kinetic features and overall dynamics of the ultrafast photoreaction are determined to a great extent by the geometrical context (i.e., available space and flexibility) within the binding pocket, while the general reaction steps following the photoexcitation are most likely conserved among the red/far-red phytochromes.

Light- and temperature-dependent dynamics of chromophore and protein structural changes in bathy phytochrome Agp2

Bacterial phytochromes are sensoric photoreceptors that transform light absorbed by the photosensor core module (PCM) to protein structural changes that eventually lead to the activation of the enzymatic output module. The underlying photoinduced reaction cascade in the PCM starts with the isomerization of the tetrapyrrole chromophore, followed by conformational relaxations, proton transfer steps, and a secondary structure transition of a peptide segment (tongue) that is essential for communicating the signal to the output module. In this work, we employed various static and time-resolved IR and resonance Raman spectroscopic techniques to study the structural and reaction dynamics of the Meta-F intermediate of both the PCM and the full-length (PCM and output module) variant of the bathy phytochrome Agp2 from Agrobacterium fabrum. In both cases, this intermediate represents a branching point of the phototransformation, since it opens an unproductive reaction channel back to the initial state and a productive pathway to the final active state, including the functional protein structural changes. It is shown that the functional quantum yield, i.e. the events of tongue refolding per absorbed photons, is lower by a factor of ca. two than the quantum yield of the primary photochemical process. However, the kinetic data derived from the spectroscopic experiments imply an increased formation of the final active state upon increasing photon flux or elevated temperature under photostationary conditions. Accordingly, the branching mechanism does not only account for the phytochrome's function as a light intensity sensor but may also modulate its temperature sensitivity.

Tips and turns of bacteriophytochrome photoactivation

Phytochromes are ubiquitous photosensor proteins, which control the growth, reproduction and movement in plants, fungi and bacteria. Phytochromes switch between two photophysical states depending on the light conditions. In analogy to molecular machines, light absorption induces a series of structural changes that are transduced from the bilin chromophore, through the protein, and to the output domains. Recent progress towards understanding this structural mechanism of signal transduction has been manifold. We describe this progress with a focus on bacteriophytochromes. We describe the mechanism along three structural tiers, which are the chromophore-binding pocket, the photosensory module, and the output domains. We discuss possible interconnections between the tiers and conclude by presenting future directions and open questions. We hope that this review may serve as a compendium to guide future structural and spectroscopic studies designed to understand structural signaling in phytochromes.

An Engineered Biliverdin-Compatible Cyanobacteriochrome Enables a Unique Ultrafast Reversible Photoswitching Pathway

Cyanobacteriochromes (CBCRs) are promising optogenetic tools for their diverse absorption properties with a single compact cofactor-binding domain. We previously uncovered the ultrafast reversible photoswitching dynamics of a red/green photoreceptor AnPixJg2, which binds phycocyanobilin (PCB) that is unavailable in mammalian cells. Biliverdin (BV) is a mammalian cofactor with a similar structure to PCB but exhibits redder absorption. To improve the AnPixJg2 feasibility in mammalian applications, AnPixJg2_BV4 with only four mutations has been engineered to incorporate BV. Herein, we implemented femtosecond transient absorption (fs-TA) and ground state femtosecond stimulated Raman spectroscopy (GS-FSRS) to uncover transient electronic dynamics on molecular time scales and key structural motions responsible for the photoconversion of AnPixJg2_BV4 with PCB (Bpcb) and BV (Bbv) cofactors in comparison with the parent AnPixJg2 (Apcb). Bpcb adopts the same photoconversion scheme as Apcb, while BV4 mutations create a less bulky environment around the cofactor D ring that promotes a faster twist. The engineered Bbv employs a reversible clockwise/counterclockwise photoswitching that requires a two-step twist on ~5 and 35 picosecond (ps) time scales. The primary forward P_fr → P_o transition displays equal amplitude weights between the two processes before reaching a conical intersection. In contrast, the primary reverse P_o → P_fr transition shows a 2:1 weight ratio of the ~35 ps over 5 ps component, implying notable changes to the D-ring-twisting pathway. Moreover, we performed pre-resonance GS-FSRS and quantum calculations to identify the Bbv vibrational marker bands at ~659,797, and 1225 cm^-1. These modes reveal a stronger H-bonding network around the BV cofactor A ring with BV4 mutations, corroborating the D-ring-dominant reversible photoswitching pathway in the excited state. Implementation of BV4 mutations in other PCB-binding GAF domains like AnPixJg4, AM1_1870g3, and NpF2164g5 could promote similar efficient reversible photoswitching for more directional bioimaging and optogenetic applications, and inspire other bioengineering advances.

Tracking Ultrafast Structural Dynamics in a Dual-Emission Anti-Kasha-Active Fluorophore Using Femtosecond Stimulated Raman Spectroscopy

The anti-Kasha process provides the possibility of using high-energy excited states to develop novel applications. Our previous research (Nature communications, 2020, 11, 793) has demonstrated a dual-emission anti-Kasha-active fluorophore for bioimaging application, which exhibits near-infrared emissions from the S₁ state and visible anti-Kasha emissions from the S₂ state. Here, we applied tunable blue-side femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption spectroscopy, assisted by quantum calculations, to reveal the anti-Kasha dual emission mechanism, in which the emergence of two fluorescing states is due to the retardation of internal conversion from the S₂ state to the S₁ state. It has been demonstrated that the facts of anti-Kasha high-energy emission are commonly attributed to a large energy gap between the two excited states, leading to a decrease in the internal conversion rate due to a poor Franck-Condon factor. In this study, analysis of the calculation and FSRS experimental results provide us further insight into the dual-emission anti-Kasha mechanism, where the observation of hydrogen out-of-plane Raman modes from FSRS suggested that, in addition to the energy-gap law, the initial photoinduced molecular conformational change plays a key role in influencing the rate of internal conversion.

Excited State Structure Correlates with Efficient Photoconversion in Unidirectional Motors

The design of unidirectional photomolecular motors demands a critical understanding of an ultrafast photochemical isomerization. An intermediate dark excited state mediates the reaction via a conical intersection (CI) with the ground state, but a correlation between molecular structure and photoisomerization efficiency has remained elusive. Here femtosecond stimulated Raman spectroscopy captures vibrational spectra of the dark state in a set of molecular motors bearing different substituents. A direct correlation between isomerization quantum yield, dark state lifetime, and excited state vibrational spectrum is found. Electron withdrawing substituents lead to activity in lower frequency modes, which we correlate with a pyramidalization distortion at the ethylenic axle occurring within 100 fs. This structure is not formed with an electron donating substituent, where the axle retains double bond character. Further structural reorganization is observed and assigned to excited state reorganization and charge redistribution on the sub-picosecond time scale. The correlation of the dark state structure with photoconversion performance suggests guidelines for developing new more efficient motor derivatives.

Transient electronic and vibrational signatures during reversible photoswitching of a cyanobacteriochrome photoreceptor

Cyanobacteriochromes (CBCRs) are an emerging class of photoreceptors that are distant relatives of the phytochromes family. Unlike phytochromes, CBCRs have gained popularity in optogenetics due to their highly diverse spectral properties spanning the UV to near-IR region and only needing a single compact binding domain. AnPixJg2 is a CBCR that can reversibly photoswitch between its red-absorbing (^15ZP_r) and green-absorbing (^15EP_g) forms of the phycocyanobilin (PCB) cofactor. To reveal primary events of photoconversion, we implemented femtosecond transient absorption spectroscopy with a homemade LED box and a miniature peristaltic pump flow cell to track transient electronic responses of the photoexcited AnPixJg2 on molecular time scales. The 525 nm laser-induced P_g-to-P_r reverse conversion exhibits a ~3 ps excited-state lifetime before reaching the conical intersection (CI) and undergoing further relaxation on the 30 ps time scale to generate a long-lived Lumi-G ground state intermediate en route to P_r. The 650 nm laser-induced P_r-to-P_g forward conversion is less efficient than reverse conversion, showing a longer-lived excited state which requires two steps with ~13 and 217 ps time constants to enter the CI region. Furthermore, using a tunable ps Raman pump with broadband Raman probe on both the Stokes and anti-Stokes sides, we collected the pre-resonance ground-state femtosecond stimulated Raman spectroscopy (GS-FSRS) data with mode assignments aided by quantum calculations. Key vibrational marker bands at ~850, 1050, 1615, and 1649 cm^-1 of the P_r conformer exhibit a notable blueshift to those of the P_g conformer inside AnPixJg2, reflecting the PCB chromophore terminal D (major) and A (minor) ring twist along the primary photoswitching reaction coordinate. This integrated ultrafast spectroscopy and computational platform has the potential to elucidate photochemistry and photophysics of more CBCRs and photoactive proteins in general, providing the highly desirable mechanistic insights to facilitate the rational design of functional molecular sensors and devices.

Spectroscopic and Photophysical Investigation of Model Dipyrroles Common to Bilins: Exploring Natural Design for Steering Torsion to Divergent Functions

Biliproteins are a unique class of photosynthetic proteins in their diverse, and at times, divergent biophysical function. The two contexts of photosynthetic light harvesting and photoreception demonstrate characteristically opposite criteria for success, with light harvesting demanding structurally-rigid chromophores which minimize excitation quenching, and photoreception requiring structural flexibility to enable conformational isomerization. The functional plasticity borne out in these two biological contexts is a consequence of the structural plasticity of the pigments utilized by biliproteins―linear tetrapyrroles, or bilins. In this work, the intrinsic flexibility of the bilin framework is investigated in a bottom-up fashion by reducing the active nuclear degrees of freedom through model dipyrrole subunits of the bilin core and terminus free of external protein interactions. Steady-state spectroscopy was carried out on the dipyrrole (DPY) and dipyrrinone (DPN) subunits free in solution to characterize their intrinsic spectroscopic properties including absorption strengths and nonradiative activity. Transient absorption (TA) spectroscopy was utilized to determine the mechanism and kinetics of nonradiative decay of the dipyrrole subunits, revealing dynamics dominated by rapid internal conversion with some Z→E isomerization observable in DPY. Computational analysis of the ground state conformational landscapes indicates enhanced complexity in the asymmetric terminal subunit, and the prediction was confirmed by heterogeneity of species and kinetics observed in TA. Taken together, the large oscillator strengths (f ∼ 0.6) of the dipyrrolic derivatives and chemically-efficient spectral tunability seen through the ∼100 nm difference in absorption spectra, validate Nature's "selection" of multi-pyrrole pigments for light capture applications. However, the rapid deactivation of the excited state via their natural torsional activity when free in solution would limit their effective biological function. Comparison with phytochrome and phycocyanin 645 crystal structures reveals binding motifs within the in vivo bilin environment that help to facilitate or inhibit specific inter-pyrrole twisting vital for protein operation.

Effect of the PHY Domain on the Photoisomerization Step of the Forward Pr →Pfr Conversion of a Knotless Phytochrome

Phytochrome photoreceptors operate via photoisomerization of a bound bilin chromophore. Their typical architecture consists of GAF, PAS and PHY domains. Knotless phytochromes lack the PAS domain, while retaining photoconversion abilities, with some being able to photoconvert with just the GAF domain. Therefore, we investigated the ultrafast photoisomerization of the Pr state of a knotless phytochrome to reveal the effect of the PHY domain and its "tongue" region on the transduction of the light signal. We show that the PHY domain does not affect the initial conformational dynamics of the chromophore. However, it significantly accelerates the consecutively induced reorganizational dynamics of the protein, necessary for the progression of the photoisomerization. Consequently, the PHY domain keeps the bilin and its binding pocket in a more reactive conformation, which decreases the extent of protein reorganization required for the chromophore isomerization. Thereby, less energy is lost along nonproductive reaction pathways, resulting in increased efficiency.

Probing the allostery in dimeric near-infrared biomarkers derived from the bacterial phytochromes: The impact of the T204A substitution on the inter-monomer interaction

In dimeric near-infrared (NIR) biomarkers engineered from bacterial phytochromes the covalent binding of BV to the cysteine residue in one monomer of a protein allosterically prevents the chromophore embedded into the pocket of the other monomer from the covalent binding to the cysteine residue. In this work, we analyzed the impact on inter-monomeric allosteric effects in dimeric NIR biomarkers of substitutions at position 204, one of the target residues of mutagenesis at the evolution of these proteins. The T204A substitution in iRFP713, developed on the basis of RpBphP2, and in its mutant variant iRFP713/C15S/V256C, in which the ligand covalent attachment site was changed, resulted in the rearrangement of the hydrogen bond network joining the chromophore with the adjacent amino acids and bound water molecules in its local environment. The change in the intramolecular contacts between the chromophore and its protein environment in iRFP713/C15S/V256C caused by the T204A substitution reduced the negative cooperativity of cofactor binding. We discuss the possible influence of cross-talk between monomers the functioning of full-length phytochromes.

Engineering Photosensory Modules of Non-Opsin-Based Optogenetic Actuators

Optogenetic (photo-responsive) actuators engineered from photoreceptors are widely used in various applications to study cell biology and tissue physiology. In the toolkit of optogenetic actuators, the key building blocks are genetically encodable light-sensitive proteins. Currently, most optogenetic photosensory modules are engineered from naturally-occurring photoreceptor proteins from bacteria, fungi, and plants. There is a growing demand for novel photosensory domains with improved optical properties and light-induced responses to satisfy the needs of a wider variety of studies in biological sciences. In this review, we focus on progress towards engineering of non-opsin-based photosensory domains, and their representative applications in cell biology and physiology. We summarize current knowledge of engineering of light-sensitive proteins including light-oxygen-voltage-sensing domain (LOV), cryptochrome (CRY2), phytochrome (PhyB and BphP), and fluorescent protein (FP)-based photosensitive domains (Dronpa and PhoCl).

Direct observation of o-benzyne formation in photochemical hexadehydro-Diels-Alder (hν-HDDA) reactions

Reactive ortho-benzyne derivatives are believed to be the initial products of liquid-phase [4 + 2]-cycloadditions between a 1,3-diyne and an alkyne via what is known as a hexadehydro-Diels–Alder (HDDA) reaction. The UV/VIS spectroscopic observation of o-benzyne derivatives and their photochemical dynamics in solution, however, have not been reported previously. Herein, we report direct UV/VIS spectroscopic evidence for the existence of an o-benzyne in solution, and establish the dynamics of its formation in a photoinduced reaction. For this purpose, we investigated a bis-diyne compound using femtosecond transient absorption spectroscopy in the ultraviolet/visible region. In the first step, we observe excited-state isomerization on a sub-10 ps time scale. For identification of the o-benzyne species formed within 50–70 ps, and the corresponding photochemical hexadehydro-Diels–Alder (hν-HDDA) reactions, we employed two intermolecular trapping strategies. In the first case, the o-benzyne was trapped by a second bis-diyne, i.e., self-trapping. The self-trapping products were then identified in the transient absorption experiments by comparing their spectral features to those of the isolated products. In the second case, we used perylene for trapping and reconstructed the spectrum of the trapping product by removing the contribution of irrelevant species from the experimentally observed spectra. Taken together, the UV/VIS spectroscopic data provide a consistent picture for o-benzyne derivatives in solution as the products of photo-initiated HDDA reactions, and we deduce the time scales for their formation.

We report the transient ultraviolet/visible absorption spectrum of an o-benzyne species in solution for the first time.

The Origin of Ultrafast Multiphasic Dynamics in Photoisomerization of Bacteriophytochrome

Red-light bacteriophytochromes regulate many physiological functions through photoisomerization of a linear tetrapyrrole chromophore. In this work, we mapped out femtosecond-resolved fluorescence spectra of the excited Pr state and observed unique active-site relaxations on the picosecond time scale with unusual spectral tuning of rises on the blue side and decays on the red side of the emission. We also observed initial wavepacket dynamics in femtoseconds with two low-frequency modes of 38 and 181 cm^-1 as well as the intermediate product formation after isomerization in hundreds of picoseconds. With critical mutations at the active site, we observed similar dynamic patterns with different times for both relaxation and isomerization, consistent with the structural and chemical changes induced by the mutations. The observed multiphasic dynamics clearly represents the active-site relaxation, not different intermediate reactions or excitation of heterogeneous ground states. The active-site relaxation must be considered in understanding overall isomerization reactions in phytochromes, and such a molecular mechanism should be general.

Two Distinct Photoprocesses in Cyanobacterial Bilin Pigments: Energy Migration in Light‐Harvesting Phycobiliproteins versus Photoisomerization in Phytochromes

The evolution of oxygenic photosynthesis, respiration and photoperception are connected with the appearance of cyanobacteria. The key compounds, which are involved in these processes, are tetrapyrroles: open chain — bilins and cyclic — chlorophylls and heme. The latter are characterized by their covalent bond with the apoprotein resulting in the formation of biliproteins. This type of photoreceptors is unique in that it can perform important and opposite functions—light‐harvesting in photosynthesis with the participation of phycobiliproteins and photoperception mediated by phycochromes and phytochromes. In this review, cyanobacterial phycobiliproteins and phytochrome Cph1 are considered from a comparative point of view. Structural features of these pigments, which provide their contrasting photophysical and photochemical characteristics, are analyzed. The determining factor in the case of energy migration with the participation of phycobiliproteins is blocking the torsional relaxations of the chromophore, its D‐ring, in the excited state and their freedom, in the case of phytochrome photoisomerization. From the energetics point of view, this distinction is preconditioned by the height of the activation barrier for the photoreaction and relaxation in the excited state, which depends on the degree of the chromophore fixation by its protein surroundings.

The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome

Phytochromes are a diverse family of bilin-binding photoreceptors that regulate a wide range of physiological processes. Their photochemical properties make them attractive for applications in optogenetics and superresolution microscopy. Phytochromes undergo reversible photoconversion triggered by the Z ⇄ E photoisomerization about the double bond in the bilin chromophore. However, it is not fully understood at the molecular level how the protein framework facilitates the complex photoisomerization dynamics. We have studied a single-domain bilin-binding photoreceptor All2699g1 (Nostoc sp. PCC 7120) that exhibits photoconversion between the red light-absorbing (P_r) and far red-absorbing (P_fr) states just like canonical phytochromes. We present the crystal structure and examine the photoisomerization mechanism of the P_r form as well as the formation of the primary photoproduct Lumi-R using time-resolved spectroscopy and hybrid quantum mechanics/molecular mechanics simulations. We show that the unusually long excited state lifetime (broad lifetime distribution centered at ∼300 picoseconds) is due to the interactions between the isomerizing pyrrole ring D and an adjacent conserved Tyr142. The decay kinetics shows a strongly distributed character which is imposed by the nonexponential protein dynamics. Our findings offer a mechanistic insight into how the quantum efficiency of the bilin photoisomerization is tuned by the protein environment, thereby providing a structural framework for engineering bilin-based optical agents for imaging and optogenetics applications.

The Lumi-R Intermediates of Prototypical Phytochromes

Phytochromes are photoreceptors that upon light absorption initiate a physiological reaction cascade. The starting point is the photoisomerization of the tetrapyrrole cofactor in the parent Pr state, followed by thermal relaxation steps culminating in activation of the physiological signal. Here we have employed resonance Raman (RR) spectroscopy to study the chromophore structure in the primary photoproduct Lumi-R, trapped between 130 and 200 K. The investigations covered phytochromes from plants (phyA) and prokaryotes (Cph1, Agp1, CphB, and RpBphP2) including phytochromobilin (PΦB), phycocyanobilin (PCB), and biliverdin (BV). In PΦB- and PCB-binding phyA and Cph1, two Lumi-R states (Lumi-R1, Lumi-R2) were identified and discussed in terms of sequential and parallel reaction models. In Lumi-R1, the chromophore structural changes are restricted to the C-D methine bridge isomerization site but extended throughout the chromophore in Lumi-R2. Formation and decay kinetics as well as photochemical activity depend on the specific protein-chromophore interactions and thus account for the different distribution between Lumi-R1 and Lumi-R2 in the photostationary mixtures of the various PΦB(PCB)-binding phytochromes. For BV-binding bacteriophytochromes, only a single Lumi-R(BV) state was found. In this state, which is similar for Agp1, CphB, and RpBphP2, the chromophore structural changes comprise major torsions of the C-D methine bridge but also perturbations at the A-B methine bridge remote from the isomerization site. The different structures of the photoproducts in PΦB(PCB)-binding phytochromes and BV-binding bacteriophytochromes are attributed to the different disposition of ring D upon isomerization, which leads to distinct protein-chromophore interactions in the Lumi-R states of these two classes of phytochromes.

Time-Resolved Impulsive Stimulated Raman Spectroscopy with Synchronized Triple Mode-Locked Lasers

A complete understanding of a photochemical reaction dynamics begins with real-time measurements of both electronic and vibrational structures of photoexcited molecules. Time-resolved impulsive stimulated Raman spectroscopy (TR-ISRS) with femtosecond actinic pump, Raman pump, and Raman probe pulses is one of the incisive techniques enabling one to investigate the structural changes of photoexcited molecules. Herein, we demonstrate that such femtosecond TR-ISRS is feasible with synchronized triple mode-locked lasers without using any time-delay devices. Taking advantage of precise control of the three repetition rates independently, we could achieve automatic scanning of two delay times between the three pulses, which makes both rapid data acquisition and wide dynamic range measurement of the fifth-order TR-ISRS signal achievable. We thus anticipate that the present triple mode-locked laser-based TR-ISRS technique will be of critical use for long-term monitoring of photochemical reaction dynamics in condensed phases and biological systems.

The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.

Plants adapt to the availability of light throughout their lives because it regulates so many aspects of their growth and reproduction. To detect the level of light, plant cells use proteins called phytochromes, which are also found in some bacteria and fungi. Phytochrome proteins change shape when they are exposed to red light, and this change alters the behaviour of the cell. The red light is absorbed by a molecule known as chromophore, which is connected to a region of the phytochrome called the PHY-tongue. This region undergoes one of the key structural changes that occur when the phytochrome protein absorbs light, turning from a flat sheet into a helix.

Claesson, Wahlgren, Takala et al. studied the structure of a bacterial phytochrome protein almost immediately after shining a very brief flash of red light using a laser. The experiments revealed that the structure of the protein begins to change within a trillionth of a second: specifically, the chromophore twists, which disrupts its attachment to the protein, freeing the protein to change shape. Claesson, Wahlgren, Takala et al. note that this structure is likely a very short-lived intermediate state, which however triggers more changes in the overall shape change of the protein.

One feature of the rearrangement is the disappearance of a particular water molecule. This molecule can be found at the core of many different phytochrome structures and interacts with several parts of the chromophore and the phytochrome protein. It is unclear why the water molecule is lost, but given how quickly this happens after the red light is applied it is likely that this disappearance is an integral part of the reshaping process.

Together these events disrupt the interactions between the chromophore and the PHY-tongue, enabling the PHY-tongue to change shape and alter the structure of the phytochrome protein. Understanding and controlling this process could allow scientists to alter growth patterns in plants, such as crops or weeds.

Mapping Structural Dynamics of Proteins with Femtosecond Stimulated Raman Spectroscopy

The structure-function relationships of biomolecules have captured the interest and imagination of the scientific community and general public since the field of structural biology emerged to enable the molecular understanding of life processes. Proteins that play numerous functional roles in cellular processes have remained in the forefront of research, inspiring new characterization techniques. In this review, we present key theoretical concepts and recent experimental strategies using femtosecond stimulated Raman spectroscopy (FSRS) to map the structural dynamics of proteins, highlighting the flexible chromophores on ultrafast timescales. In particular, wavelength-tunable FSRS exploits dynamic resonance conditions to track transient-species-dependent vibrational motions, enabling rational design to alter functions. Various ways of capturing excited-state chromophore structural snapshots in the time and/or frequency domains are discussed. Continuous development of experimental methodologies, synergistic correlation with theoretical modeling, and the expansion to other nonequilibrium, photoswitchable, and controllable protein systems will greatly advance the chemical, physical, and biological sciences.

Elucidating the role of structural fluctuations, and intermolecular and vibronic interactions in the spectroscopic response of a bacteriophytochrome

Molecular dynamics and a multiscale polarizable QM/MM strategy allow reproducing absorption, circular dichroism, and resonance Raman spectra of a bacteriophytochrome.

Transient IR spectroscopy identifies key interactions and unravels new intermediates in the photocycle of a bacterial phytochrome

Infra-red spectroscopy advances our understanding of how photosensory proteins carry their function.

Two Distinct Photoprocesses in Cyanobacterial Bilin Pigments: Energy Migration in Light-Harvesting Phycobiliproteins versus Photoisomerization in Phytochromes

The evolution of oxygenic photosynthesis, respiration and photoperception are connected with the appearance of cyanobacteria. The key compounds, which are involved in these processes, are tetrapyrroles: open chain - bilins and cyclic - chlorophylls and heme. The latter are characterized by their covalent bond with the apoprotein resulting in the formation of biliproteins. This type of photoreceptors is unique in that it can perform important and opposite functions-light-harvesting in photosynthesis with the participation of phycobiliproteins and photoperception mediated by phycochromes and phytochromes. In this review, cyanobacterial phycobiliproteins and phytochrome Cph1 are considered from a comparative point of view. Structural features of these pigments, which provide their contrasting photophysical and photochemical characteristics, are analyzed. The determining factor in the case of energy migration with the participation of phycobiliproteins is blocking the torsional relaxations of the chromophore, its D-ring, in the excited state and their freedom, in the case of phytochrome photoisomerization. From the energetics point of view, this distinction is preconditioned by the height of the activation barrier for the photoreaction and relaxation in the excited state, which depends on the degree of the chromophore fixation by its protein surroundings.

Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy

The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.

Elucidating the Molecular Mechanism of Ultrafast Pfr-State Photoisomerization in Bathy Bacteriophytochrome PaBphP

Bacteriophytochromes are photoreceptors that regulate various physiological processes induced by photoisomerization in a linear tetrapyrrole chromophore upon red/far-red light absorption. Here, we investigate the photoinduced Pfr-state isomerization mechanism of a bathy bacteriophytochrome from Pseudomonas aeruginosa combining femtosecond-resolved fluorescence and absorption methods. We observed initial coherent oscillation motions in the first 1 ps with low-frequency modes below 60 cm^-1, then a bifurcation of the wavepacket with the distinct excited-state lifetimes in a few picoseconds, and finally chromophore-protein coupled ground-state conformational evolution on nanosecond time scales. Together with systematic mutational studies, we revealed the critical roles of hydrogen bonds in tuning the photoisomerization dynamics. These results provide a clear molecular picture of the Pfr-state photoisomerization, a mechanism likely applicable to the other phytochromes.