Ultrafast dynamics of phytochrome from the cyanobacterium synechocystis, reconstituted with phycocyanobilin and phycoerythrobilin

Conserved tyrosine in phytochromes controls the photodynamics through steric demand and hydrogen bonding capabilities

Using ultrafast spectroscopy and site-specific mutagenesis, we demonstrate the central role of a conserved tyrosine within the chromophore binding pocket in the forward (Pr → Pfr) photoconversion of phytochromes. Taking GAF1 of the knotless phytochrome All2699g1 from Nostoc as representative member of phytochromes, it was found that the mutations have no influence on the early (<30 ps) dynamics associated with conformational changes of the chromophore in the excited state. Conversely, they drastically impact the extended protein-controlled excited state decay (>100 ps). Thus, the steric demand, position and H-bonding capabilities of the identified tyrosine control the chromophore photoisomerization while leaving the excited state chromophore dynamics unaffected. In effect, this residue operates as an isomerization-steric-gate that tunes the excited state lifetime and the photoreaction efficiency by modulating the available space of the chromophore and by stabilizing the primary intermediate Lumi-R. Understanding the role of such a conserved structural element sheds light on a key aspect of phytochrome functionality and provides a basis for rational design of optimized photoreceptors for biotechnological applications.

Ultrafast protein response in the Pfr state of Cph1 phytochrome

Photoisomerization is a fundamental process in several classes of photoreceptors. Phytochromes sense red and far-red light in their Pr and Pfr states, respectively. Upon light absorption, these states react via individual photoreactions to the other state. Cph1 phytochrome shows a photoisomerization of its phycocyanobilin (PCB) chromophore in the Pfr state with a time constant of 0.7 ps. The dynamics of the PCB chromophore has been described, but whether or not the apoprotein exhibits an ultrafast response too, is not known. Here, we compare the photoreaction of ¹³C/¹⁵N labeled apoprotein with unlabeled apoprotein to unravel ultrafast apoprotein dynamics in Cph1. In the spectral range from 1750 to 1620 cm^-1 we assigned several signals due to ultrafast apoprotein dynamics. A bleaching signal at 1724 cm^-1 is tentatively assigned to deprotonation of a carboxylic acid, probably Asp207, and signals around 1670 cm^-1 are assigned to amide I vibrations of the capping helix close to the chromophore. These signals remain after photoisomerization. The apoprotein dynamics appear upon photoexcitation or concomitant with chromophore isomerization. Thus, apoprotein dynamics occur prior to and after photoisomerization on an ultrafast time-scale. We discuss the origin of the ultrafast apoprotein response with the 'Coulomb hammer' mechanism, i.e. an impulsive change of electric field and Coulombic force around the chromophore upon excitation.

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.

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.

Influence of the PHY domain on the ms-photoconversion dynamics of a knotless phytochrome

The ability of some knotless phytochromes to photoconvert without the PHY domain allows evaluation of the distinct effect of the PHY domain on their photodynamics. Here, we compare the ms dynamics of the single GAF domain (g1) and the GAF-PHY (g1g2) construct of the knotless phytochrome All2699 from cyanobacterium Nostoc punctiforme. While the spectral signatures and occurrence of the intermediates are mostly unchanged by the domain composition, the presence of the PHY domain slows down the early forward and reverse dynamics involving chromophore and protein binding pocket relaxation. We assign this effect to a more restricted binding pocket imprinted by the PHY domain. The photoproduct formation is also slowed down by the presence of the PHY domain but to a lesser extent than the early dynamics. This indicates a rate limiting step within the GAF and not the PHY domain. We further identify a pH dependence of the biphasic photoproduct formation hinting towards a pKa dependent tuning mechanism. Our findings add to the understanding of the role of the individual domains in the photocycle dynamics and provide a basis for engineering of phytochromes towards biotechnological applications.

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.

The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters

This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.

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.

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.

Conservation and Diversity in the Primary Reverse Photodynamics of the Canonical Red/Green Cyanobacteriochrome Family

In this report, we compare the femtosecond to nanosecond primary reverse photodynamics (^15EP_g → ^15ZP_r) of eight tetrapyrrole binding photoswitching cyanobacteriochromes in the canonical red/green family from the cyanobacterium Nostoc punctiforme. Three characteristic classes were identified on the basis of the diversity of excited-state and ground-state properties, including the lifetime, photocycle initiation quantum yield, photointermediate stability, spectra, and temporal properties. We observed a correlation between the excited-state lifetime and peak wavelength of the electronic absorption spectrum with higher-energy-absorbing representatives exhibiting both faster excited-state decay times and higher photoisomerization quantum yields. The latter was attributed to both an increased number of structural restraints and differences in H-bonding networks that facilitate photoisomerization. All three classes exhibited primary Lumi-G_o intermediates, with class II and III representatives evolving to a secondary Meta-G photointermediate. Class II Meta-G_R intermediates were orange absorbing, whereas class III Meta-G had structurally relaxed, red-absorbing chromophores that resemble their dark-adapted ^15ZP_r states. Differences in the reverse and forward reaction mechanisms are discussed within the context of structural constraints.

Bacteriophytochrome from Magnetospirillum magneticum affects phototactic behavior in response to light

Phytochromes are a class of photoreceptors found in plants and in some fungi, cyanobacteria, and photoautotrophic and heterotrophic bacteria. Although phytochromes have been structurally characterized in some bacteria, their biological and ecological roles in magnetotactic bacteria remain unexplored. Here, we describe the biochemical characterization of recombinant bacteriophytochrome (BphP) from magnetotactic bacteria Magnetospirillum magneticum AMB-1 (MmBphP). The recombinant MmBphP displays all the characteristic features, including the property of binding to biliverdin (BV), of a genuine phytochrome. Site-directed mutagenesis identified that cysteine-14 is important for chromophore covalent binding and photoreversibility. Arginine-240 and histidine-246 play key roles in binding to BV. The N-terminal photosensory core domain of MmBphP lacking the C-terminus found in other phytochromes is sufficient to exhibit the characteristic red/far-red-light-induced fast photoreversibility of phytochromes. Moreover, our results showed MmBphP is involved in the phototactic response, suggesting its conservative role as a stress protectant. This finding provided us a better understanding of the physiological function of this group of photoreceptors and photoresponse of magnetotactic bacteria.

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 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.

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.

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.

Protochromic absorption changes in the two-cysteine photocycle of a blue/orange cyanobacteriochrome

Cyanobacteriochromes (CBCRs) are phytochrome-related photosensors with diverse spectral sensitivities spanning the entire visible spectrum. They covalently bind bilin chromophores via conserved cysteine residues and undergo 15Z/15E bilin photoisomerization upon light illumination. CBCR subfamilies absorbing violet-blue light use an additional cysteine residue to form a second bilin-thiol adduct in a two-Cys photocycle. However, the process of second thiol adduct formation is incompletely understood, especially the involvement of the bilin protonation state. Here, we focused on the Oscil6304_2705 protein from the cyanobacterium Oscillatoria acuminata PCC 6304, which photoconverts between a blue-absorbing 15Z state ( ^15Z Pb) and orange-absorbing 15E state ( ^15E Po). pH titration analysis revealed that ^15Z Pb was stable over a wide pH range, suggesting that bilin protonation is stabilized by a second thiol adduct. As revealed by resonance Raman spectroscopy, ^15E Po harbored protonated bilin at both acidic and neutral pH, but readily converted to a deprotonated green-absorbing 15Z state ( ^15Z Pg) at alkaline pH. Site-directed mutagenesis revealed that the conserved Asp-71 and His-102 residues are required for second thiol adduct formation in ^15Z Pb and bilin protonation in ^15E Po, respectively. An Oscil6304_2705 variant lacking the second cysteine residue, Cys-73, photoconverted between deprotonated ^15Z Pg and protonated ^15E Pr, similarly to the protochromic photocycle of the green/red CBCR subfamily. Time-resolved spectroscopy revealed ^15Z Pg formation as an intermediate in the ^15E Pr-to- ^15Z Pg conversion with a significant solvent-isotope effect, suggesting the sequential occurrence of 15EP-to-15Z photoisomerization, deprotonation, and second thiol adduct formation. Our findings uncover the details of protochromic absorption changes underlying the two-Cys photocycle of violet-blue-absorbing CBCR subfamilies.

Forward Photodynamics of the Noncanonical Red/Green NpR3784 Cyanobacteriochrome from Nostoc punctiforme

Cyanobacteriochromes (CBCRs) make up a diverse family of cyanobacterial photoreceptors distantly related to the phytochrome photoreceptors of land plants. At least two lineages of CBCRs have reacquired red-absorbing dark states similar to the phytochrome P_r resting state but are coupled to green-absorbing light-adapted states rather than the canonical far-red-absorbing light-adapted state. One such lineage includes the canonical red/green (R/G) CBCRs that includes AnPixJg2 (UniProtKB Q8YXY7 ) and NpR6012g4 (UniProtKB B2IU14 ) that have been extensively characterized. Here we examine the forward P_r photodynamics of NpR3784 (UniProtKB B2J457 ), a representative member of the second R/G CBCR subfamily. Using broadband transient absorption pump-probe spectroscopy, we characterize both primary (100 fs to 10 ns) and secondary (10 ns to 1 ms) forward (P_r → P_g) photodynamics and compare the results to temperature-jump cryokinetics measurements. Our studies show that primary isomerization dynamics occur on an ∼10 ps timescale, yet remarkably, the red-shifted primary Lumi-R_f photoproduct found in all photoactive canonical R/G CBCRs examined to date is extremely short-lived in NpR3784. These results demonstrate that differences in reaction pathways reflect the evolutionary history of R/G CBCRs despite the convergent evolution of their photocycle end products.

Influence of Heterogeneity on the Ultrafast Photoisomerization Dynamics of Pfr in Cph1 Phytochrome

Photoisomerization of a protein-bound chromophore is the basis of light sensing and signaling in many photoreceptors. Phytochrome photoreceptors can be photoconverted reversibly between the Pr and Pfr states through photoisomerization of the methine bridge between rings C and D. Ground-state heterogeneity of the chromophore has been reported for both Pr and Pfr. Here, we report ultrafast visible (Vis) pump-probe and femtosecond polarization-resolved Vis pump-infrared (IR) probe studies of the Pfr photoreaction in native and ¹³ C/¹⁵ N-labeled Cph1 phytochrome with unlabeled PCB chromophore, demonstrating different S₀ substates, Pfr-I and Pfr-II, with distinct IR absorptions, orientations and dynamics of the carbonyl vibration of ring D. We derived time constants of 0.24 ps, 0.7 ps and 6 ps, describing the complete initial photoreaction. We identified an isomerizing pathway with 0.7 ps for Pfr-I, and silent dynamics with 6 ps for Pfr-II. We discuss different origins of the Pfr substates, and favor different facial orientations of ring D. The model provides a quantum yield for Pfr-I of 38%, in line with ~35% ring D rotation in the electronic excited state. We tentatively assign the silent form Pfr-II to a dark-adapted state that can convert to Pfr-I upon light absorption.

Protonation Heterogeneity Modulates the Ultrafast Photocycle Initiation Dynamics of Phytochrome Cph1

Phytochrome proteins utilize ultrafast photoisomerization of a linear tetrapyrrole chromophore to detect the ratio of red to far-red light. Femtosecond photodynamics in the PAS-GAF-PHY photosensory core of the Cph1 phytochrome from Synechocystis sp. PCC6803 (Cph1Δ) were resolved with a dual-excitation-wavelength-interleaved pump-probe (DEWI) approach with two excitation wavelengths (600 and 660 nm) at three pH values (6.5, 8.0, and 9.0). Observed spectral and kinetic heterogeneity in the excited-state dynamics were described with a self-consistent model comprised of three spectrally distinct populations with different protonation states (P_r-I, P_r-II, and P_r-III), each composed of multiple kinetically distinct subpopulations. Apparent partitioning among these populations is dictated by pH, temperature, and excitation wavelength. Our studies provide insight into photocycle initiation dynamics at physiological temperatures, implicate the low-pH/low-temperature P_r-I state as the photoactive state in vitro, and implicate an internal hydrogen-bonding network in regulating the photochemical quantum yield.

Photoreceptors Take Charge: Emerging Principles for Light Sensing

The first stage in biological signaling is based on changes in the functional state of a receptor protein triggered by interaction of the receptor with its ligand(s). The light-triggered nature of photoreceptors allows studies on the mechanism of such changes in receptor proteins using a wide range of biophysical methods and with superb time resolution. Here, we critically evaluate current understanding of proton and electron transfer in photosensory proteins and their involvement both in primary photochemistry and subsequent processes that lead to the formation of the signaling state. An insight emerging from multiple families of photoreceptors is that ultrafast primary photochemistry is followed by slower proton transfer steps that contribute to triggering large protein conformational changes during signaling state formation. We discuss themes and principles for light sensing shared by the six photoreceptor families: rhodopsins, phytochromes, photoactive yellow proteins, light-oxygen-voltage proteins, blue-light sensors using flavin, and cryptochromes.

Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila

Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump-probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results.

Conformational Homogeneity in the Pr Isomer of Phytochrome Cph1

Numerous time-resolved studies of the P_r to P_fr photoisomerization in phytochrome Cph1 have revealed multiphasic excited-state decay kinetics. It remains unclear whether these kinetics arise from multiple ground-state conformational subpopulations or from a single ground-state conformation that undergoes an excited-state photoisomerization process-either branching on the excited state or relaxing through multiple sequential intermediates. Many studies have attempted to resolve this debate by fitting the measured dynamics to proposed kinetic models, arriving at different conclusions. Here we probe spectral signatures of ground-state heterogeneity of P_r. Two-dimensional electronic spectra display negligible inhomogeneous line broadening, and vibrational coherence spectra extracted from transient absorption measurements do not contain nodes and phase shifts at the fluorescence maximum. These spectroscopic results support the homogeneous model, in which the primary photochemical transformation of P_r to Lumi-R occurs adiabatically on the excited-state potential energy surface.

Bright blue-shifted fluorescent proteins with Cys in the GAF domain engineered from bacterial phytochromes: fluorescence mechanisms and excited-state dynamics

Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes (BphPs) are of great interest for in vivo imaging. They utilize biliverdin (BV) as a chromophore, which is a heme degradation product, and therefore they are straightforward to use in mammalian tissues. Here, we report on fluorescence properties of NIR FPs with key alterations in their BV binding sites. BphP1-FP, iRFP670 and iRFP682 have Cys residues in both PAS and GAF domains, rather than in the PAS domain alone as in wild-type BphPs. We found that NIR FP variants with Cys in the GAF or with Cys in both PAS and GAF show blue-shifted emission with long fluorescence lifetimes. In contrast, mutants with Cys in the PAS only or no Cys residues at all exhibit red-shifted emission with shorter lifetimes. Combining these results with previous biochemical and BphP1-FP structural data, we conclude that BV adducts bound to Cys in the GAF are the origin of bright blue-shifted fluorescence. We propose that the long fluorescence lifetime follows from (i) a sterically more constrained thioether linkage, leaving less mobility for ring A than in canonical BphPs, and (ii) that π-electron conjugation does not extend on ring A, making excited-state deactivation less sensitive to ring A mobility.

Bacteriophytochrome Photoisomerization Proceeds Homogeneously Despite Heterogeneity in Ground State

Phytochromes are red/far-red photoreceptors that are widely distributed in plants and prokaryotes. Ultrafast photoisomerization of a double bond in a biliverdin cofactor or other linear tetrapyrrole drives their photoactivity, but their photodynamics are only partially understood. Multiexponential dynamics were observed in previous ultrafast spectroscopic studies and were attributed to heterogeneous populations of the pigment-protein complex. In this work, two-dimensional photon echo spectroscopy was applied to study dynamics of the bacteriophytochromes RpBphP2 and PaBphP. Two-dimensional photon echo spectroscopy can simultaneously resolve inhomogeneity in ensembles and fast dynamics by correlating pump wavelength with the emitted signal wavelength. The distribution of absorption and emission energies within the same state indicates an ensemble of heterogeneous protein environments that are spectroscopically distinct. However, the lifetimes of the dynamics are uniform across the ensemble, suggesting a homogeneous model involving sequential intermediates for the initial photodynamics of isomerization.

Ultrafast deactivation of bilirubin: dark intermediates and two-photon isomerization

The Franck-Condon state A couples to the dark intermediate B, which shows tight molecular skeleton and distorted hydrogen bonding. B deactivates with nearly 100% efficiency. 2-Photon excitation at 400 nm triggers Z,E isomerization efficiently.

Fast Photochemistry of Prototypical Phytochromes-A Species vs. Subunit Specific Comparison

Phytochromes are multi-domain red light photosensor proteins, which convert red light photons to biological activity utilizing the multitude of structural and chemical reactions. The steady increase in structural information obtained from various bacteriophytochromes has increased understanding about the functional mechanism of the photochemical processes of the phytochromes. Furthermore, a number of spectroscopic studies have revealed kinetic information about the light-induced reactions. The spectroscopic changes are, however, challenging to connect with the structural changes of the chromophore and the protein environment, as the excited state properties of the chromophores are very sensitive to the small structural and chemical changes of their environment. In this article, we concentrate on the results of ultra-fast spectroscopic experiments which reveal information about the important initial steps of the photoreactions of the phytochromes. We survey the excited state properties obtained during the last few decades. The differences in kinetics between different research laboratories are traditionally related to the differences of the studied species. However, we notice that the variation in the excited state properties depends on the subunit composition of the protein as well. This observation illustrates a feedback mechanism from the other domains to the chromophore. We propose that two feedback routes exist in phytochromes between the chromophore and the remotely located effector domain. The well-known connection between the subunits is the so-called tongue region, which changes its secondary structure while changing the light-activated state of the system. The other feedback route which we suggest is less obvious, it is made up of several water molecules ranging from the dimer interface to the vicinity of the chromophore, allowing even proton transfer reactions nearby the chromophore.

Non-Bonded Interactions Drive the Sub-Picosecond Bilin Photoisomerization in the P(fr) State of Phytochrome Cph1

Phytochromes are protein-based photoreceptors harboring a bilin-based photoswitch in the active site. The timescale of photosignaling via C15 =C16 E-to-Z photoisomerization has been ambiguous in the far-red-absorbing Pfr state. Here we present a unified view of the structural events in phytochrome Cph1 post excitation with femtosecond precision, obtained via stimulated Raman and polarization-resolved transient IR spectroscopy. We demonstrate that photoproduct formation occurs within 700 fs, determined by a two-step partitioning process initiated by a planarization on the electronic excited state with a 300 fs time scale. The ultrafast isomerization timescale for Pfr -to-Pr conversion highlights the active role of the nonbonding methyl-methyl clash initiating the reaction in the excited state. We envision that our results will motivate the synthesis of new artificial photoswitches with precisely tuned non-bonded interactions for ultrafast response.

Ultrafast excited-state dynamics and fluorescence deactivation of near-infrared fluorescent proteins engineered from bacteriophytochromes

Near-infrared fluorescent proteins, iRFPs, are recently developed genetically encoded fluorescent probes for deep-tissue in vivo imaging. Their functions depend on the corresponding fluorescence efficiencies and electronic excited state properties. Here we report the electronic excited state deactivation dynamics of the most red-shifted iRFPs: iRFP702, iRFP713 and iRFP720. Complementary measurements by ultrafast broadband fluorescence and absorption spectroscopy show that single exponential decays of the excited state with 600~700 ps dominate in all three iRFPs, while photoinduced isomerization was completely inhibited. Significant kinetic isotope effects (KIE) were observed with a factor of ~1.8 in D2O, and are interpreted in terms of an excited-state proton transfer (ESPT) process that deactivates the excited state in competition with fluorescence and chromophore mobility. On this basis, new approaches for rational molecular engineering may be applied to iRFPs to improve their fluorescence.

Comprehensive analysis of the green-to-blue photoconversion of full-length Cyanobacteriochrome Tlr0924

Cyanobacteriochromes are members of the phytochrome superfamily of photoreceptors and are of central importance in biological light-activated signaling mechanisms. These photoreceptors are known to reversibly convert between two states in a photoinitiated process that involves a basic E/Z isomerization of the bilin chromophore and, in certain cases, the breakage of a thioether linkage to a conserved cysteine residue in the bulk protein structure. The exact details and timescales of the reactions involved in these photoconversions have not been conclusively shown. The cyanobacteriochrome Tlr0924 contains phycocyanobilin and phycoviolobilin chromophores, both of which photoconvert between two species: blue-absorbing and green-absorbing, and blue-absorbing and red-absorbing, respectively. Here, we followed the complete green-to-blue photoconversion process of the phycoviolobilin chromophore in the full-length form of Tlr0924 over timescales ranging from femtoseconds to seconds. Using a combination of time-resolved visible and mid-infrared transient absorption spectroscopy and cryotrapping techniques, we showed that after photoisomerization, which occurs with a lifetime of 3.6 ps, the phycoviolobilin twists or distorts slightly with a lifetime of 5.3 μs. The final step, the formation of the thioether linkage with the protein, occurs with a lifetime of 23.6 ms.

Photoisomerization among ring-open merocyanines. I. Reaction dynamics and wave-packet oscillations induced by tunable femtosecond pulses

Upon ultraviolet excitation, photochromic spiropyran compounds can be converted by a ring-opening reaction into merocyanine molecules, which in turn can form several isomers differing by cis and trans configurations in the methine bridge. Whereas the spiropyran-merocyanine conversion reaction of the nitro-substituted indolinobenzopyran 6-nitro-1',3',3'-trimethylspiro[2H-1-benzopyran-2,2'-indoline] (6-nitro BIPS) has been studied extensively in theory and experiments, little is known about photoisomerization among the merocyanine isomers. In this article, we employ femtosecond transient absorption spectroscopy with variable excitation wavelengths to investigate the excited-state dynamics of the merocyanine in acetonitrile at room temperature, where exclusively the trans-trans-cis (TTC) and trans-trans-trans (TTT) isomers contribute. No photochemical ring-closure pathways exist for the two isomers. Instead, we found that (18±4)% of excited TTC isomers undergo an ultrafast excited-state cis→trans photoisomerization to TTT within 200 fs, while the excited-state lifetime of TTC molecules that do not isomerize is 35 ps. No photoisomerization was detected for the TTT isomer, which relaxes to the ground state with a lifetime of roughly 160 ps. Moreover, signal oscillations at 170 cm(-1) and 360 cm(-1) were observed, which can be ascribed to excited-state wave-packet dynamics occurring in the course of the TTC→TTT isomerization. The results of high-level time-dependent density functional theory in conjunction with polarizable continuum models are presented in the subsequent article [C. Walter, S. Ruetzel, M. Diekmann, P. Nuernberger, T. Brixner, and B. Engels, J. Chem. Phys. 140, 224311 (2014)].

Femto- to Microsecond Photodynamics of an Unusual Bacteriophytochrome

A bacteriophytochrome from Stigmatella aurantiaca is an unusual member of the bacteriophytochrome family that is devoid of hydrogen bonding to the carbonyl group of ring D of the biliverdin (BV) chromophore. The photodynamics of BV in SaBphP1 wild type and the single mutant T289H reintroducing hydrogen bonding to ring D show that the strength of this particular weak interaction determines excited-state lifetime, Lumi-R quantum yield, and spectral heterogeneity. In particular, excited-state decay is faster in the absence of hydrogen-bonding to ring D, with excited-state half-lives of 30 and 80 ps for wild type and the T289H mutant, respectively. Concomitantly, the Lumi-R quantum yield is two times higher in wild type as compared with the T289H mutant. Furthermore, the spectral heterogeneity in the wild type is significantly higher than that in the T289H mutant. By extending the observable time domain to 25 μs, we observe a new deactivation pathway from the Lumi-R intermediate in the 100 ns time domain that corresponds to a backflip of ring D to the original Pr 15Za isomeric state.

Single-molecule spectroscopy and femtosecond transient absorption studies on the excitation energy transfer process in ApcE(1–240) dimers

The red-shifted absorption of ApcE dimers results from extending chromophore conformation, which does not depend on strong exction coupling.

Phototransformation of the red light sensor cyanobacterial phytochrome 2 from Synechocystis species depends on its tongue motifs

Phytochromes are photoreceptors using a bilin tetrapyrrole as chromophore, which switch in canonical phytochromes between red (Pr) and far red (Pfr) light-absorbing states. Cph2 from Synechocystis sp., a noncanonical phytochrome, harbors besides a cyanobacteriochrome domain a second photosensory module, a Pr/Pfr-interconverting GAF-GAF bidomain (SynCph2(1-2)). As in the canonical phytochromes, a unique motif of the second GAF domain, the tongue region, seals the bilin-binding site in the GAF1 domain from solvent access. Time-resolved spectroscopy of the SynCph2(1-2) module shows four intermediates during Pr → Pfr phototransformation and three intermediates during Pfr → Pr back-conversion. A mutation in the tongue's conserved PRXSF motif, S385A, affects the formation of late intermediate R3 and of a Pfr-like state but not the back-conversion to Pr via a lumi-F-like state. In contrast, a mutation in the likewise conserved WXE motif, W389A, changes the photocycle at intermediate R2 and causes an alternative red light-adapted state. Here, back-conversion to Pr proceeds via intermediates differing from SynCph2(1-2). Replacement of this tryptophan that is ∼15 Å distant from the chromophore by another aromatic amino acid, W389F, restores native Pr → Pfr phototransformation. These results indicate large scale conformational changes within the tongue region of GAF2 during the final processes of phototransformation. We propose that in early intermediates only the chromophore and its nearest surroundings are altered, whereas late changes during R2 formation depend on the distant WXE motifs of the tongue region. Ser-385 within the PRXSF motif affects only late intermediate R3, when refolding of the tongue and docking to the GAF1 domain are almost completed.

Heterogeneous photodynamics of the pfr state in the cyanobacterial phytochrome Cph1

Femtosecond photodynamics of the P_fr form of the red/far-red phytochrome N-terminal PAS-GAF-PHY photosensory core module of the cyanobacterial phytochrome Cph1 (termed Cph1Δ) from Synechocystis were resolved with visible broadband transient absorption spectroscopy. Multiphasic generation dynamics via global target analysis revealed parallel evolution of two pathways with distinct excited- and ground-state kinetics. These measurements resolved two subpopulations: a majority subpopulation with fast excited-state decay and slower ground-state dynamics, corresponding to previous descriptions of P_fr dynamics, and a minority subpopulation with slower excited-state decay and faster ground-state primary dynamics. Both excited-state subpopulations generated the isomerized, red-shifted Lumi-F_f photoproduct (715 nm); subsequent ground-state evolution to a blue-shifted Meta-F_r population (635 nm) proceeded on 3 ps and 1.5 ns time scales for the two subpopulations. Meta-F_r was spectrally similar to a recently described photoinactive fluorescent subpopulation of P_r (^FluorP_r). Thus, the reverse P_fr to P_r photoconversion of Cph1Δ involves minor structural deformation of Meta-F_r to generate the fluorescent, photochemically refractory form of P_r, with slower subsequent equilibration with the photoactive P_r subpopulation (^PhotoP_r).

Tyrosine 263 in Cyanobacterial Phytochrome Cph1 Optimizes Photochemistry at the prelumi‐R→lumi‐R Step

We report a low‐temperature fluorescence spectroscopy study of the PAS‐GAF‐PHY sensory module of Cph1 phytochrome, its Y263F mutant (both with known 3D structures) as well as Y263H and Y263S to connect their photochemical parameters with intramolecular interactions. None of the holoproteins showed photochemical activity at low temperature, and the activation barriers for the Pr→lumi‐R photoreaction (2.5–3.1 kJ mol−1) and fluorescence quantum yields (0.29–0.42) were similar. The effect of the mutations on Pr→Pfr photoconversion efficiency (ΦPr→Pfr) was observed primarily at the prelumi‐R S0 bifurcation point corresponding to the conical intersection of the energy surfaces at which the molecule relaxes to form lumi‐R or Pr, lowering ΦPr→Pfr from 0.13 in the wild type to 0.05–0.07 in the mutants. We suggest that the Ea activation barrier in the Pr* S1 excited state might correspond to the D‐ring (C19) carbonyl – H290 hydrogen bond or possibly to the hindrance caused by the C131/C171 methyl groups of the C and D rings. The critical role of the tyrosine hydroxyl group can be at the prelumi‐R bifurcation point to optimize the yield of the photoprocess and energy storage in the form of lumi‐R for subsequent rearrangement processes culminating in Pfr formation.

Electronic transitions and heterogeneity of the bacteriophytochrome Pr absorption band: An angle balanced polarization resolved femtosecond VIS pump-IR probe study

Photoisomerization of biliverdin (BV) chromophore triggers the photoresponse in native Agp1 bacteriophytochrome. We discuss heterogeneity in phytochrome Pr form to account for the shape of the absorption profile. We investigated different regions of the absorption profile by angle balanced polarization resolved femtosecond VIS pump-IR probe spectroscopy. We studied the Pr form of Agp1 with its natural chromophore and with a sterically locked 18Et-BV (locked Agp1). We followed the dynamics and orientations of the carbonyl stretching vibrations of ring D and ring A in their ground and electronically excited states. Photoisomerization of ring D is reflected by strong signals of the ring D carbonyl vibration. In contrast, orientational data on ring A show no rotation of ring A upon photoexcitation. Orientational data allow excluding a ZZZasa geometry and corroborates a nontwisted ZZZssa geometry of the chromophore. We found no proof for heterogeneity but identified a new, to our knowledge, electronic transition in the absorption profile at 644 nm (S0→S2). Excitation of the S0→S2 transition will introduce a more complex photodynamics compared with S0→S1 transition. Our approach provides fundamental information on disentanglement of absorption profiles, identification of chromophore structures, and determination of molecular groups involved in the photoisomerization process of photoreceptors.

The photoinitiated reaction pathway of full-length cyanobacteriochrome Tlr0924 monitored over 12 orders of magnitude

The coupling of photochemistry to protein chemical and structural change is crucial to biological light-activated signaling mechanisms. This is typified by cyanobacteriochromes (CBCRs), members of the phytochrome superfamily of photoreceptors that exhibit a high degree of spectral diversity, collectively spanning the entire visible spectrum. CBCRs utilize a basic E/Z isomerization of the bilin chromophore as the primary step in their photocycle, which consists of reversible photoconversion between two photostates. Despite intense interest in these photoreceptors as signal transduction modules a complete description of light-activated chemical and structural changes has not been reported. The CBCR Tlr0924 contains both phycocyanobilin and phycoviolobilin chromophores, and these two species photoisomerize in parallel via spectrally and kinetically equivalent intermediates before the second step of the photoreaction where the reaction pathways diverge, the loss of a thioether linkage to a conserved cysteine residue occurs, and the phycocyanobilin reaction terminates in a red-absorbing state, whereas the phycoviolobilin reaction proceeds more rapidly to a final green-absorbing state. Here time-resolved visible transient absorption spectroscopy (femtosecond to second) has been used, in conjunction with time-resolved IR spectroscopy (femtosecond to nanosecond) and cryotrapping techniques, to follow the entire photoconversion of the blue-absorbing states to the green- and red-absorbing states of the full-length form of Tlr0924 CBCR. Our analysis shows that Tlr0924 undergoes an unprecedented long photoreaction that spans from picoseconds to seconds. We show that the thermally driven, long timescale changes are less complex than those reported for the red/far-red photocycles of the related phytochrome photoreceptors.

Dynamic inhomogeneity in the photodynamics of cyanobacterial phytochrome Cph1

Phytochromes are widespread red/far-red photosensory proteins well known as critical regulators of photomorphogenesis in plants. It is often assumed that natural selection would have optimized the light sensing efficiency of phytochromes to minimize nonproductive photochemical deexcitation pathways. Surprisingly, the quantum efficiency for the forward P_r-to-P_fr photoconversion of phytochromes seldom exceeds 15%, a value very much lower than that of animal rhodopsins. Exploiting ultrafast excitation wavelength- and temperature-dependent transient absorption spectroscopy, we resolve multiple pathways within the ultrafast photodynamics of the N-terminal PAS-GAF-PHY photosensory core module of cyanobacterial phytochrome Cph1 (termed Cph1Δ) that are primarily responsible for the overall low quantum efficiency. This inhomogeneity primarily reflects a long-lived fluorescent subpopulation that exists in equilibrium with a spectrally distinct, photoactive subpopulation. The fluorescent subpopulation is favored at elevated temperatures, resulting in anomalous excited-state dynamics (slower kinetics at higher temperatures). The spectral and kinetic behavior of the fluorescent subpopulation strongly resembles that of the photochemically compromised and highly fluorescent Y₁₇₆H variant of Cph1Δ. We present an integrated, heterogeneous model for Cph1Δ that is based on the observed transient and static spectroscopic signals. Understanding the molecular basis for this dynamic inhomogeneity holds potential for rational design of efficient phytochrome-based fluorescent and photoswitchable probes.

Tyrosine 263 in cyanobacterial phytochrome Cph1 optimizes photochemistry at the prelumi-R→lumi-R step

We report a low-temperature fluorescence spectroscopy study of the PAS-GAF-PHY sensory module of Cph1 phytochrome, its Y263F mutant (both with known 3D structures) as well as Y263H and Y263S to connect their photochemical parameters with intramolecular interactions. None of the holoproteins showed photochemical activity at low temperature, and the activation barriers for the Pr→lumi-R photoreaction (2.5-3.1 kJ mol(-1)) and fluorescence quantum yields (0.29-0.42) were similar. The effect of the mutations on Pr→Pfr photoconversion efficiency (ΦPr→Pfr) was observed primarily at the prelumi-R S0 bifurcation point corresponding to the conical intersection of the energy surfaces at which the molecule relaxes to form lumi-R or Pr, lowering ΦPr→Pfr from 0.13 in the wild type to 0.05-0.07 in the mutants. We suggest that the Ea activation barrier in the Pr* S1 excited state might correspond to the D-ring (C19) carbonyl - H290 hydrogen bond or possibly to the hindrance caused by the C13(1) /C17(1) methyl groups of the C and D rings. The critical role of the tyrosine hydroxyl group can be at the prelumi-R bifurcation point to optimize the yield of the photoprocess and energy storage in the form of lumi-R for subsequent rearrangement processes culminating in Pfr formation.

Active and silent chromophore isoforms for phytochrome Pr photoisomerization: An alternative evolutionary strategy to optimize photoreaction quantum yields

Photoisomerization of a protein bound chromophore is the basis of light sensing of many photoreceptors. We tracked Z-to-E photoisomerization of Cph1 phytochrome chromophore PCB in the Pr form in real-time. Two different phycocyanobilin (PCB) ground state geometries with different ring D orientations have been identified. The pre-twisted and hydrogen bonded PCB(a) geometry exhibits a time constant of 30 ps and a quantum yield of photoproduct formation of 29%, about six times slower and ten times higher than that for the non-hydrogen bonded PCB(b) geometry. This new mechanism of pre-twisting the chromophore by protein-cofactor interaction optimizes yields of slow photoreactions and provides a scaffold for photoreceptor engineering.