Direct observation of the femtosecond excited-state cis-trans isomerization in bacteriorhodopsin

Ultrafast terahertz Stark spectroscopy reveals the excited-state dipole moments of retinal in bacteriorhodopsin

The photoinduced all-trans to 13-cis isomerization of the retinal Schiff base represents the ultrafast first step in the reaction cycle of bacteriorhodopsin (BR). Extensive experimental and theoretical work has addressed excited-state dynamics and isomerization via a conical intersection with the ground state. In conflicting molecular pictures, the excited state potential energy surface has been modeled as a pure S[Formula: see text] state that intersects with the ground state, or in a 3-state picture involving the S[Formula: see text] and S[Formula: see text] states. Here, the photoexcited system passes two crossing regions to return to the ground state. The electric dipole moment of the Schiff base in the S[Formula: see text] and S[Formula: see text] state differs strongly and, thus, its measurement allows for assessing the character of the excited-state potential. We apply the method of ultrafast terahertz (THz) Stark spectroscopy to measure electric dipole changes of wild-type BR and a BR D85T mutant upon electronic excitation. A fully reversible transient broadening and spectral shift of electronic absorption is induced by a picosecond THz field of several megavolts/cm and mapped by a 120-fs optical probe pulse. For both BR variants, we derive a moderate electric dipole change of 5 [Formula: see text] 1 Debye, which is markedly smaller than predicted for a neat S[Formula: see text]-character of the excited state. In contrast, S[Formula: see text]-admixture and temporal averaging of excited-state dynamics over the probe pulse duration gives a dipole change in line with experiment. Our results support a picture of electronic and nuclear dynamics governed by the interaction of S[Formula: see text] and S[Formula: see text] states in a 3-state model.

A subgroup of light-driven sodium pumps with an additional Schiff base counterion

Light-driven sodium pumps (NaRs) are unique ion-transporting microbial rhodopsins. The major group of NaRs is characterized by an NDQ motif and has two aspartic acid residues in the central region essential for sodium transport. Here we identify a subgroup of the NDQ rhodopsins bearing an additional glutamic acid residue in the close vicinity to the retinal Schiff base. We thoroughly characterize a member of this subgroup, namely the protein ErNaR from Erythrobacter sp. HL-111 and show that the additional glutamic acid results in almost complete loss of pH sensitivity for sodium-pumping activity, which is in contrast to previously studied NaRs. ErNaR is capable of transporting sodium efficiently even at acidic pH levels. X-ray crystallography and single particle cryo-electron microscopy reveal that the additional glutamic acid residue mediates the connection between the other two Schiff base counterions and strongly interacts with the aspartic acid of the characteristic NDQ motif. Hence, it reduces its pKa. Our findings shed light on a subgroup of NaRs and might serve as a basis for their rational optimization for optogenetics.

Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct

Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as "K". We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.

The Functionality of the DC Pair in a Rhodopsin Guanylyl Cyclase from Catenaria anguillulae

Rhodopsin guanylyl cyclases (RGCs) belong to the class of enzymerhodopsins catalyzing the transition from GTP into the second messenger cGMP, whereas light-regulation of enzyme activity is mediated by a membrane-bound microbial rhodopsin domain, that holds the catalytic center inactive in the dark. Structural determinants for activation of the rhodopsin moiety eventually leading to catalytic activity are largely unknown. Here, we investigate the mechanistic role of the D283-C259 (DC) pair that is hydrogen bonded via a water molecule as a crucial functional motif in the homodimeric C. anguillulae RGC. Based on a structural model of the DC pair in the retinal binding pocket obtained by MD simulation, we analyzed formation and kinetics of early and late photocycle intermediates of the rhodopsin domain wild type and specific DC pair mutants by combined UV-Vis and FTIR spectroscopy at ambient and cryo-temperatures. By assigning specific infrared bands to S-H vibrations of C259 we are able to show that the DC pair residues are tightly coupled. We show that deprotonation of D283 occurs already in the inactive L state as a prerequisite for M state formation, whereas structural changes of C259 occur in the active M state and early cryo-trapped intermediates. We propose a comprehensive molecular model for formation of the M state that activates the catalytic moiety. It involves light induced changes in bond strength and hydrogen bonding of the DC pair residues from the early J state to the active M state and explains the retarding effect of C259 mutants.

Unique Vibrational Characteristics and Structures of the Photoexcited Retinal Chromophore in Ion-Pumping Rhodopsins

Photoisomerization of an all-trans-retinal chromophore triggers ion transport in microbial ion-pumping rhodopsins. Understanding chromophore structures in the electronically excited (S1) state provides insights into the structural evolution on the potential energy surface of the photoexcited state. In this study, we examined the structure of the S1-state chromophore in Natronomonas pharaonis halorhodopsin (NpHR), a chloride ion-pumping rhodopsin, using time-resolved resonance Raman spectroscopy. The spectral patterns of the S1-state chromophore were completely different from those of the ground-state chromophore, resulting from unique vibrational characteristics and the structure of the S1 state. Mode assignments were based on a combination of deuteration shifts of the Raman bands and hybrid quantum mechanics-molecular mechanics calculations. The present observations suggest a weakened bond alternation in the π conjugation system. A strong hydrogen-out-of-plane bending band was observed in the Raman spectra of the S1-state chromophore in NpHR, indicating a twisted polyene structure. Similar frequency shifts for the C═N/C═C and C-C stretching modes of the S1-state chromophore in NpHR were observed in the Raman spectra of sodium ion-pumping and proton-pumping rhodopsins, suggesting that these unique features are common to the S1 states of ion-pumping rhodopsins.

Quantifying Bacteriorhodopsin Activity as a Function of its Local Environment with a Raman-Based Assay

Bacteriorhodopsin (bR) is a transmembrane protein that functions as a light-driven proton pump in halophilic archaea. The bR photocycle has been well-characterized; however, these measurements almost exclusively measured purified bR, outside of its native membrane. To investigate what effect the cellular environment has on the bR photocycle, we have developed a Raman-based assay that can monitor the activity of the bR in a variety of conditions, including in its native membrane. The assay uses two continuous-wave lasers, one to initiate photochemistry and one to monitor bR activity. The excitation leads to the steady-state depletion of ground-state bR, which directly relates to the population of photocycle intermediate states. We have used this assay to monitor bR activity both in vitro and in vivo. Our in vitro measurements confirm that our assay is sensitive to bulk environmental changes reported in the literature. Our in vivo measurements show a decrease in bR activity with increasing extracellular pH for bR in its native membrane. The difference in activity with increasing pH indicates that the native membrane environment affects the function of bR. This assay opens the door to future measurements into understanding how the local environment of this transmembrane protein affects function.

Na+ Binding and Transport: Insights from Light-Driven Na+-Pumping Rhodopsin

Na+ plays a vital role in numerous physiological processes across humans and animals, necessitating a comprehensive understanding of Na+ transmembrane transport. Among the various Na+ pumps and channels, light-driven Na+-pumping rhodopsin (NaR) has emerged as a noteworthy model in this field. This review offers a concise overview of the structural and functional studies conducted on NaR, encompassing ground/intermediate-state structures and photocycle kinetics. The primary focus lies in addressing key inquiries: (1) unraveling the translocation pathway of Na+; (2) examining the role of structural changes within the photocycle, particularly in the O state, in facilitating Na+ transport; and (3) investigating the timing of Na+ uptake/release. By delving into these unresolved issues and existing debates, this review aims to shed light on the future direction of Na+ pump research.

Effects of the Unique Chromophore-Protein Interactions on the Primary Photoreaction of Schizorhodopsin

Schizorhodopsin (SzR) is a newly discovered microbial rhodopsin subfamily, functioning as an unusual inward-proton (H+) pump upon absorbing light. Two major protein structural differences around the chromophore have been found, resulting in unique chromophore-protein interactions that may be responsible for its unusual function. Therefore, it is important to elucidate how such a difference affects the primary photoreaction dynamics. We study the primary dynamics of SzR and its C75S mutant by femtosecond time-resolved absorption (TA) spectroscopy. The obtained TA data revealed that the photoisomerization in SzR proceeds more slowly and less efficiently than typical outward H+-pumping rhodopsins and that it further slows in the C75S mutant. We performed impulsive stimulated Raman measurements to clarify the effect of the cysteine residue on the retinal chromophore and found that interactions with Cys75 flatten the retinal chromophore of wild-type SzR. We discuss the effect of the unique chromophore-cysteine interaction on the retinal isomerization dynamics and structure of SzR.

Voltage Imaging with Engineered Proton-Pumping Rhodopsins: Insights from the Proton Transfer Pathway

Voltage imaging using genetically encoded voltage indicators (GEVIs) has taken the field of neuroscience by storm in the past decade. Its ability to create subcellular and network level readouts of electrical dynamics depends critically on the kinetics of the response to voltage of the indicator used. Engineered microbial rhodopsins form a GEVI subclass known for their high voltage sensitivity and fast response kinetics. Here we review the essential aspects of microbial rhodopsin photocycles that are critical to understanding the mechanisms of voltage sensitivity in these proteins and link them to insights from efforts to create faster, brighter and more sensitive microbial rhodopsin-based GEVIs.

Photoinduced isomerization sampling of retinal in bacteriorhodopsin

Photoisomerization of retinoids inside a confined protein pocket represents a critical chemical event in many important biological processes from animal vision, nonvisual light effects, to bacterial light sensing and harvesting. Light-driven proton pumping in bacteriorhodopsin entails exquisite electronic and conformational reconfigurations during its photocycle. However, it has been a major challenge to delineate transient molecular events preceding and following the photoisomerization of the retinal from noisy electron density maps when varying populations of intermediates coexist and evolve as a function of time. Here, I report several distinct early photoproducts deconvoluted from the recently observed mixtures in time-resolved serial crystallography. This deconvolution substantially improves the quality of the electron density maps, hence demonstrates that the all-trans retinal undergoes extensive isomerization sampling before it proceeds to the productive 13-cis configuration. Upon light absorption, the chromophore attempts to perform trans-to-cis isomerization at every double bond together with the stalled anti-to-syn rotations at multiple single bonds along its polyene chain. Such isomerization sampling pushes all seven transmembrane helices to bend outward, resulting in a transient expansion of the retinal binding pocket, and later, a contraction due to recoiling. These ultrafast responses observed at the atomic resolution support that the productive photoreaction in bacteriorhodopsin is initiated by light-induced charge separation in the prosthetic chromophore yet governed by stereoselectivity of its protein pocket. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable.

Characterizing Mode Anharmonicity and Huang-Rhys Factors Using Models of Femtosecond Coherence Spectra

Femtosecond laser pulses readily produce coherent quantum beats in transient-absorption spectra. These oscillatory signals often arise from molecular vibrations and therefore may contain information about the excited-state potential energy surface near the Franck-Condon region. Here, by fitting the measured spectra of two laser dyes to microscopic models of femtosecond coherence spectra (FCS) arising from molecular vibrations, we classify coherent quantum-beat signals as fundamentals or overtones and quantify their Huang-Rhys factors and anharmonicity values. We discuss the extracted Huang-Rhys factors in the context of quantum-chemical computations. This work solidifies the use of FCS for analysis of coherent quantum beats arising from molecular vibrations, which will aid studies of molecular aggregates and photosynthetic proteins.

Roles of functional lipids in bacteriorhodopsin photocycle in various delipidated purple membranes

Purple membrane (PM) is composed of several native lipids and the transmembrane protein bacteriorhodopsin (bR) in trimeric configuration. The delipidated PM (dPM) samples can be prepared by treating PM with CHAPS (3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate) to partially remove native lipids while maintaining bR in the trimeric configuration. By correlating the photocycle kinetics of bR and the exact lipid compositions of the various dPM samples, one can reveal the roles of native PM lipids. However, it is challenging to compare the lipid compositions of the various dPM samples quantitatively. Here, we utilized the absorbances of extracted retinal at 382 nm to normalize the concentrations of the remaining lipids in each dPM sample, which were then quantified by mass spectrometry, allowing us to compare the lipid compositions of different samples in a quantitative manner. The corresponding photocycle kinetics of bR were probed by transient difference absorption spectroscopy. We found that the removal rate of the polar lipids follows the order of BPG ≈ GlyC < S-TGD-1 ≈ PG < PGP-Me ≈ PGS. Since BPG and GlyC have more nonpolar phytanyl groups than other lipids at the hydrophobic tail, causing a higher affinity with the hydrophobic surface of bR, the corresponding removal rates are slowest. In addition, as the reaction period of PM and CHAPS increases, the residual amounts of PGS and PGP-Me significantly decrease, in concomitance with the decelerated rates of the recovery of ground state and the decay of intermediate M, and the reduced transient population of intermediate O. PGS and PGP-Me are the lipids with the highest correlation to the photocycle activity among the six polar lipids of PM. From a practical viewpoint, combining optical spectroscopy and mass spectrometry appears a promising approach to simultaneously track the functions and the concomitant active components in a given biological system.

Light Driven Ultrafast Bioinspired Molecular Motors: Steering and Accelerating Photoisomerization Dynamics of Retinal

Photoisomerization of retinal protonated Schiff base in microbial and animal rhodopsins are strikingly ultrafast and highly specific. Both protein environments provide conditions for fine-tuning the photochemistry of their chromophores. Here, by combining time-resolved action absorption spectroscopy and high-level electronic structure theory, we show that similar control can be gained in a synthetically engineered retinal chromophore. By locking the dimethylated retinal Schiff base at the C₁₁═C₁₂ double bond in its trans configuration (L-RSB), the excited-state decay is rendered from a slow picosecond to an ultrafast subpicosecond regime in the gas phase. Steric hindrance and pretwisting of L-RSB are found to be important for a significant reduction in the excited-state energy barriers, where isomerization of the locked chromophore proceeds along C₉═C₁₀ rather than the preferred C₁₁═C₁₂ isomerization path. Remarkably, the accelerated excited-state dynamics also becomes steered. We show that L-RSB is capable of unidirectional 360° rotation from all-trans to 9-cis and from 9-cis to all-trans in only two distinct steps induced by consecutive absorption of two 600 nm photons. This opens a way for the rational design of red-light-driven ultrafast molecular rotary motors based on locked retinal chromophores.

Spectroscopy and photoisomerization of protonated Schiff-base retinal derivatives in vacuo

The protonated Schiff-base retinal acts as the chromophore in bacteriorhodopsin as well as in rhodopsin. In both cases, photoexcitation initializes fast isomerization which eventually results in storage of chemical energy or signaling. The details of the photophysics for this important chromophore is still not fully understood. In this study, action-absorption spectra and photoisomerization dynamics of three retinal derivatives are measured in the gas phase and compared to that of the protonated Schiff-base retinal. The retinal derivatives include C₉C₁₀trans-locked, C₁₃C₁₄trans-locked and a retinal derivative without the β-ionone ring. The spectroscopy as well as the isomerization speed of the chromophores are altered significantly as a consequence of the steric constraints.

Trajectory surface hopping molecular dynamics simulations for retinal protonated Schiff-base photoisomerization

Global switching trajectory surface hopping molecular dynamics simulations are performed using accurate on-the-fly (TD)CAM-B3LYP/6-31G potential energy surfaces to study retinal protonated Schiff-base photoisomerization up to S₁ excitation. The simulations detected two-layer conical intersection networks: one is at an energy as high as 8 eV and the other is in the energy range around 3-4 eV. Six conical intersections within the low-layer energy region that correspond to active conical intersections under experimental conditions are found via the use of pairwise isomers, within which nonadiabatic molecular dynamics simulations are performed. Eight isomer products are populated with simulated sampling trajectories from which the simulated quantum yield in the gas phase is estimated to be 0.11 (0.08) moving from the all-trans isomer to the 11-cis (11-cis to all-trans) isomer in comparison with an experimental value of 0.09 (0.2) in the solution phase. Each conical intersection is related to one specific twist angle accompanying a related CC double bond motion during photoisomerization. Nonplanar distortion of the entire dynamic process has a significant role in the formation of the relevant photoisomerization products. The present simulation indicates that all hopping points show well-behaved potential energy surface topology, as calculated via the conventional TDDFT method, at conical intersections between S₁ and S₀ states. Therefore, the present nonadiabatic dynamics simulations with the TDDFT method are very encouraging for simulating various large systems related to retinal Schiff-base photoisomerization in the real world.

A Unified View on Varied Ultrafast Dynamics of the Primary Process in Microbial Rhodopsins

All-trans to 13-cis photoisomerization of the protonated retinal Schiff base (PRSB) chromophore is the primary step that triggers various biological functions of microbial rhodopsins. While this ultrafast primary process has been extensively studied, it has been recognized that the relevant excited-state relaxation dynamics differ significantly from one rhodopsin to another. To elucidate the origin of the complicated ultrafast dynamics of the primary process in microbial rhodopsins, we studied the excited-state dynamics of proteorhodopsin, its D97N mutant, and bacteriorhodopsin by femtosecond time-resolved absorption (TA) spectroscopy in a wide pH range. The TA data showed that their excited-state relaxation dynamics drastically change when pH approaches the pK_a of the counterion residue of the PRSB chromophore in the ground state. This result reveals that the varied excited-state relaxation dynamics in different rhodopsins mainly originate from the difference of the ground-state heterogeneity (i.e., protonation/deprotonation of the PRSB counterion).

Insights into the Early-Time Excited-State Dynamics of Structurally Inhomogeneous Rhodopsin KR2

The light-driven sodium-pump rhodopsin KR2 exhibits ultrafast photoisomerization dynamics of its all-trans protonated Schiff-base retinal (PSBR). However, the excited-state decay of KR2 also shows slow picosecond time constants, which are attributed to nonreactive states. The mechanism that produces long-lived states is unclear. Here, by using molecular dynamics simulations and large-scale XMCQDPT2-based QM/MM modeling, we explore the origin of reactive and nonreactive states in KR2. By calculating the S₀-S₁ vibronic band shapes, we gain insight into the early-time excited-state dynamics of PSBR and show that the protein environment can significantly alter vibrational modes that are active upon photoexcitation, thus facilitating photoisomerization from all-trans to 13-cis PSBR. Importantly, we reveal structural heterogeneity of the retinal-binding pocket of KR2, characterized by three distinct conformations, and conclude that the formation of a strong hydrogen bond between the retinal Schiff base and its counterion is essential for the ultrafast reaction dynamics.

The voltage dependent sidedness of the reprotonation of the retinal Schiff base determines the unique inward pumping of Xenorhodopsin

The new class of microbial rhodopsins, called xenorhodopsins (XeRs) (1), extends the versatility of this family by inward H + pumps (2-4). These pumps are an alternative optogenetic tool to the light-gated ion channels (e.g. ChR1,2), because the activation of electrically excitable cells by XeRs is independent from the surrounding physiological conditions. In this work we functionally and spectroscopically characterized XeR from Nanosalina ( Ns XeR) (1). The photodynamic behavior of Ns XeR was investigated on the ps to s time scale elucidating the formation of the J and K and a previously unknown long-lived intermediate. The pH dependent kinetics reveal that alkalization of the surrounding medium accelerates the photocycle and the pump turnover. In patch-clamp experiments the blue-light illumination of Ns XeR in the M state shows a potential-dependent vectoriality of the photocurrent transients, suggesting a variable accessibility of reprotonation of the retinal Schiff base. Insights on the kinetically independent switching mechanism could furthermore be obtained by mutational studies on the putative intracellular H + acceptor D220.

Signatures of Vibrational and Electronic Quantum Beats in Femtosecond Coherence Spectra

Femtosecond laser pulses can produce oscillatory signals in transient-absorption spectroscopy measurements. The quantum beats are often studied using femtosecond coherence spectra (FCS), the Fourier domain amplitude, and phase profiles at individual oscillation frequencies. In principle, one can identify the mechanism that gives rise to each quantum-beat signal by comparing its measured FCS to those arising from microscopic models. To date, however, most measured FCS deviate from the ubiquitous harmonic oscillator model. Here, we expand the inventory of models to which the measured spectra can be compared. We develop quantum-mechanical models of the fundamental, overtone, and combination-band FCS arising from harmonic potentials, the FCS of anharmonic potentials, and the FCS of a purely electronic dimer. This work solidifies the use of FCS for identifying electronic coherences that can arise in measurements of molecular aggregates including photosynthetic proteins. Furthermore, future studies can use the derived expressions to fit the measured FCS and thereby extract microscopic parameters of molecular potential-energy surfaces.

Floppy molecules—their internal dynamics, spectroscopy and applications

Floppy molecules can be defined as molecules performing large amplitude vibrations (LAVs). There are different types of LAVs among which the most common are inversion and internal rotation. Molecules with LAVs have been of great interest for a very long time since their dynamic, geometry and molecular spectra were very often considered as a challenge. In the review, we present an outline of the history and development of various theoretical approaches concerning molecules with LAVs. Different types of LAVs are described with the emphasis on inversion tunneling (wagging) and internal rotation (torsion). Furthermore, strategies for building explicit and effective Hamiltonians are given and explained in detail using a hydrazine molecule, which is an exemplary molecule performing three LAVs—two inversions and one internal rotation. Since floppy molecules play a significant role in numerous areas as chemistry, pharmacy, astrophysics, biology, agriculture etc., we also provide an overview of their applications.

Comparative Femtosecond Spectroscopy of Primary Photoreactions of Exiguobacterium sibiricum Rhodopsin and Halobacterium salinarum Bacteriorhodopsin

The primary stages of the Exiguobacterium sibiricum rhodopsin (ESR) photocycle were investigated by femtosecond absorption laser spectroscopy in the spectral range of 400-900 nm with a time resolution of 25 fs. The dynamics of the ESR photoreaction were compared with the reactions of bacteriorhodopsin (bR) in purple membranes (bR_PM) and in recombinant form (bR_rec). The primary intermediates of the ESR photocycle were similar to intermediates I, J, and K in bacteriorhodopsin photoconversion. The CONTIN program was applied to analyze the characteristic times of the observed processes and to clarify the reaction scheme. A similar photoreaction pattern was observed for all studied retinal proteins, including two consecutive dynamic Stokes shift phases lasting ∼0.05 and ∼0.15 ps. The excited state decays through a femtosecond reactive pathway, leading to retinal isomerization and formation of product J, and a picosecond nonreactive pathway that leads only to the initial state. Retinal photoisomerization in ESR takes 0.69 ps, compared with 0.48 ps in bR_PM and 0.74 ps in bR_rec. The nonreactive excited state decay takes 5 ps in ESR and ∼3 ps in bR. We discuss the similarity of the primary reactions of ESR and other retinal proteins.

Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins

Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H⁺, Na⁺, Cl^-, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.

Excited-State Vibronic Dynamics of Bacteriorhodopsin from Two-Dimensional Electronic Photon Echo Spectroscopy and Multiconfigurational Quantum Chemistry

Owing to the ultrafast time scale of the photoinduced reaction and high degree of spectral overlap among the reactant, product, and excited electronic states in bacteriorhodopsin (bR), it has been a challenge for traditional spectroscopies to resolve the interplay between vibrational dynamics and electronic processes occurring in the retinal chromophore of bR. Here, we employ ultrafast two-dimensional electronic photon echo spectroscopy to follow the early excited-state dynamics of bR preceding the isomerization. We detect an early periodic photoinduced absorptive signal that, employing a hybrid multiconfigurational quantum/molecular mechanical model of bR, we attribute to periodic mixing of the first and second electronic excited states (S₁ and S₂, respectively). This recurrent interaction between S₁ and S₂, induced by a bond length alternation of the retinal chromohore, supports the hypothesis that the ultrafast photoisomerization in bR is initiated by a process involving coupled nuclear and electronic motion on three different electronic states.

Acid-base equilibrium of the chromophore counterion results in distinct photoisomerization reactivity in the primary event of proteorhodopsin

Proteorhodopsin (PR) is a proton-pumping rhodopsin, and it is known to exhibit a multi-phasic decay of the excited-state population in the primary process. So far, this complex excited-state decay has been attributed to the branching of the relaxation pathway on the excited-state potential energy surface. However, a recent ultrafast spectroscopic study on a sodium-pumping rhodopsin suggested that such a complex decay may originate from the heterogeneity in the ground state due to the acid-base equilibrium of the counterion of the protonated retinal Schiff base (PRSB). In this study, we studied the excited-state dynamics of PR at pH 11 and 4, in which the counterion of the PRSB, Asp97, is completely deprotonated and protonated, respectively. The obtained time-resolved absorption data revealed that the excited-state lifetime is decisively governed by the protonation state of Asp97, and the photoisomerization of the PRSB chromophore proceeds faster and more efficiently when Asp97 is deprotonated. This conclusion was further supported by high similarity of the excited-state dynamics between PR at pH 4 and the D97N mutant in which Asp97 is replaced with neutral Asn. The results of this study suggest that the protonation state of the PRSB counterion plays a decisive role in determining the excited-state dynamics and the photoisomerization reactivity of rhodopsins in general, by making a significant influence on the exited-state potential energy surface of the PRSB chromophore.

Influence of Lipid Compositions in the Events of Retinal Schiff Base of Bacteriorhodopsin Embedded in Covalently Circularized Nanodiscs: Thermal Isomerization, Photoisomerization, and Deprotonation

Covalently circularized nanodiscs using circular membrane scaffold protein (MSP) serve as a suitable membrane mimetic for transmembrane proteins by providing stability and tunability in lipid compositions, providing controllable biological environments for targeted proteins. In this work, monomeric bacteriorhodopsin (mbR) was embedded in lipid nanodiscs of different lipid compositions using negatively charged lipid dioleoyl phosphatidylglycerol (DOPG) and the zwitterion lipid dioleoyl phosphatidylcholine (DOPC), and the events associated with the retinal Schiff base, including the thermal isomerization during the dark adaptation, photoisomerization, and deprotonation, were investigated. The retinal thermal isomerization from all-trans, 15-anti to the 13-cis, 15-syn configuration during the dark adaptation was accelerated in the DOPG bilayer, whereas the processes in the DOPC bilayer and in Triton X-100 micelles were similar. This observation indicated that the negatively charged lipid reduced the barrier for retinal thermal isomerization at C₁₃═C₁₄-C₁₅═N in the ground electronic state. Furthermore, the broader absorption contour of mbR in the DOPC nanodisc probably indicated various retinal isomers in the light-adapted state, consistent with the observed nontwo-state dark adaptation kinetics. Moreover, the kinetics of the photoisomerization of the retinal was slightly decelerated upon increasing the content of DOPC. However, the cascading deprotonation of the protonated Schiff base is not dependent on the types of the surrounding lipids in the nanodiscs. In summary, our research deepens the understanding of the coupling between lipid membrane and the photochemistry of bR retinal Schiff base. Combined with the results of our previous works (Lee, T.-Y.; Yeh, V.; Chuang, J.; Chan, J. C. C.; Chu, L.-K.; Yu, T.-Y. Biophys. J. 2015, 109, 1899-1906; Kao, Y.-M.; Cheng, C.-H.; Syue, M.-L.; Huang, H.-Y.; Chen, I-C.; Yu, T.-Y.; Chu, L.-K. J. Phys. Chem. B 2019, 123, 2032-2039), these outcomes extend our understanding of the control of photochemistry and biophysical events for other photosynthetic proteins via altering the lipid environments.

Protein Dynamics Preceding Photoisomerization of the Retinal Chromophore in Bacteriorhodopsin Revealed by Deep-UV Femtosecond Stimulated Raman Spectroscopy

Bacteriorhodopsin is a prototypical photoreceptor protein that functions as a light-driven proton pump. The retinal chromophore of bacteriorhodopsin undergoes C₁₃═C₁₄ trans-to-cis isomerization upon photoexcitation, and it has been believed to be the first event that triggers the cascaded structural changes in bacteriorhodopsin. We investigated the protein dynamics of bacteriorhodopsin using deep-ultraviolet resonance femtosecond stimulated Raman spectroscopy. It was found that the stimulated Raman signals of tryptophan and tyrosine residues exhibit significant changes within 0.2 ps after photoexcitation while they do not noticeably change during the isomerization process. This result implies that the protein environment changes first, and its change is small during isomerization. The obtained femtosecond stimulated Raman data indicate that ultrafast change is induced in the protein part by the sudden creation of the large dipole of the excited-state chromophore, providing an environment that realizes efficient and selective isomerization.

Control of Aromaticity and cis-/trans-Isomeric Structure of Non-Planar Hexaphyrin(2.1.2.1.2.1) and Metal Complexes

Vinylene-bridged hexaphyrin(2.1.2.1.2.1) was synthesized from dipyrrolyl diphenylethenes by acid-catalyzed condensation reactions. Freebase hexaphyrin(2.1.2.1.2.1) forms a distorted structure with non-aromatic characteristics. The aromaticity and molecular configuration of non-planar hexaphyrin(2.1.2.1.2.1) can be controlled by insertion of metal ions. Freebase and zinc complexes show a distorted structure without macrocyclic aromaticity, whereas copper complexes show a figure-of-eight structure with macrocyclic aromaticity. It is the first example of aromaticity conversion of a distorted expanded porphyrin involving vinylene bridges.

E to Z Photoisomerization of Phytochrome Cph1Δ Exceeds the Born-Oppenheimer Adiabatic Limit

The Born-Oppenheimer adiabatic limit applies broadly in chemistry because most reactions occur on the ground electronic state. Photochemical reactions involve two or more electronic states and need not be subject to this adiabatic limit. The spectroscopic signatures of nonadiabatic processes are subtle, and therefore, experimental investigations have been limited to the few systems dominated by single photochemical outcomes. Systems with branched excited-state pathways have been neglected, despite their potential to reveal insights into photochemical reactivity. Here we present experimental evidence from coherent three-dimensional electronic spectroscopy that the E to Z photoisomerization of phytochrome Cph1 is strongly nonadiabatic, and the simulations reproduce the measured features only when the photoisomerization proceeds nonadiabatically near, but not through, a conical intersection. The results broaden the general understanding of photoisomerization mechanisms and motivate future studies of nonadiabatic processes with multiple outcomes arising from branching on excited-state potential energy surfaces.

Effect of point mutations on the ultrafast photo-isomerization of Anabaena sensory rhodopsin

Anabaena sensory rhodopsin (ASR) is a particular microbial retinal protein for which light-adaptation leads to the ability to bind both the all-trans, 15-anti (AT) and the 13-cis, 15-syn (13C) isomers of the protonated Schiff base of retinal (PSBR). In the context of obtaining insight into the mechanisms by which retinal proteins catalyse the PSBR photo-isomerization reaction, ASR is a model system allowing to study, within the same protein, the protein-PSBR interactions for two different PSBR conformers at the same time. A detailed analysis of the vibrational spectra of AT and 13C, and their photo-products in wild-type ASR obtained through femtosecond (pump-) four-wave-mixing is reported for the first time, and compared to bacterio- and channelrhodopsin. As part of an extensive study of ASR mutants with blue-shifted absorption spectra, we present here a detailed computational analysis of the origin of the mutation-induced blue-shift of the absorption spectra, and identify electrostatic interactions as dominating steric effects that would entail a red-shift. The excited state lifetimes and isomerization reaction times (IRT) for the three mutants V112N, W76F, and L83Q are studied experimentally by femtosecond broadband transient absorption spectroscopy. Interestingly, in all three mutants, isomerization is accelerated for AT with respect to wild-type ASR, and this the more, the shorter the wavelength of maximum absorption. On the contrary, the 13C photo-reaction is slightly slowed down, leading to an inversion of the ESLs of AT and 13C, with respect to wt-ASR, in the blue-most absorbing mutant L83Q. Possible mechanisms for these mutation effects, and their steric and electrostatic origins are discussed.

Photoreaction Dynamics of Red-Shifting Retinal Analogues Reconstituted in Proteorhodopsin

Microbial rhodopsins constitute a key protein family in optobiotechnological applications such as optogenetics and voltage imaging. Spectral tuning of rhodopsins into the deep-red and near-infrared spectral regions is of great demand in such applications because more bathochromic light into the near-infrared range penetrates deeper in living tissue. Recently, retinal analogues have been successfully used in ion transporting and fluorescent rhodopsins to achieve red-shifted absorption, activity, and emission properties. Understanding their photochemical mechanism is essential for further design of appropriate retinal analogues but is yet only poorly understood for most retinal analogue pigments. Here, we report the photoreaction dynamics of red-shifted analogue pigments of the proton pump proteorhodopsin (PR) containing A2 (all-trans-3,4-dehydroretinal), MOA2 (all-trans-3-methoxy-3,4-dehydroretinal), or DMAR (all-trans-3-dimethylamino-16-nor-1,2,3,4-didehydroretinal), utilizing femto- to submillisecond transient absorption spectroscopy. We found that the A2 analogue photoisomerizes in 1.4, 3.0, and/or 13 ps upon 510 nm light illumination, which is comparable to the native retinal (A1) in PR. On the other hand, the deprotonation of the A2 pigment Schiff base was observed with a dominant time constant of 67 μs, which is significantly slower than the A1 pigment. In the MOA2 pigment, no isomerization or photoproduct formation was detected upon 520 nm excitation, implying that all the excited molecules returned to the initial ground state in 2.0 and 4.2 ps. The DMAR pigment showed very slow excited state dynamics similar to the previously studied MMAR pigment, but only very little photoproduct was formed. The low efficiency of the photoproduct formation likely is the reason why DMAR analogue pigments of PR showed very weak proton pumping activity.

Intrinsic photoisomerization dynamics of protonated Schiff-base retinal

The retinal protonated Schiff-base (RPSB) in its all-trans form is found in bacterial rhodopsins, whereas visual rhodopsin proteins host 11-cis RPSB. In both cases, photoexcitation initiates fast isomerization of the retinal chromophore, leading to proton transport, storage of chemical energy or signaling. It is an unsolved problem, to which degree this is due to protein interactions or intrinsic RPSB quantum properties. Here, we report on time-resolved action-spectroscopy studies, which show, that upon photoexcitation, cis isomers of RPSB have an almost barrierless fast 400 fs decay, whereas all-trans isomers exhibit a barrier-controlled slow 3 ps decay. Moreover, formation of the 11-cis isomer is greatly favored for all-trans RPSB when isolated. The very fast photoresponse of visual photoreceptors is thus directly related to intrinsic retinal properties, whereas bacterial rhodopsins tune the excited state potential-energy surface to lower the barrier for particular double-bond isomerization, thus changing both the timescale and specificity of the photoisomerization.

The primary photoresponse of protonated Schiff-base retinal in visual and bacterial rhodopsins is fast sub-ps isomerisation. Here, the authors show that the fast photoisomerization of rhodopsin is related to an intrinsic retinal property, whereas bacterial rhodopsins tune the excited-state potential-energy surface and improve the isomerization timescale and specificity.

Excited State Vibrational Spectra of All- trans Retinal Derivatives in Solution Revealed By Pump-DFWM Experiments

The ultrafast structural changes during the photoinduced isomerization of the retinal-protonated Schiff base (RPSB) is still a poorly understood aspect in the retinal's photochemistry. In this work, we apply pump-degenerate four-wave mixing (pump-DFWM) to all- trans retinal (ATR) and retinal Schiff bases (RSB) to resolve coherent high- and low-frequency vibrational signatures from excited electronic states. We show that the vibrational spectra of excited singlet states in these samples exhibit pronounced differences compared to the relaxed ground state. Pump-DFWM results indicate three major features for ATR and RSB. (i) Excited state vibrational spectra of ATR and RSB consist predominately of low-frequency modes in the energetic range 100-500 cm^-1. (ii) Excited state vibrational spectra show distinct differences for excitation in specific regions of electronic transitions of excited state absorption and emission. (iii) Low-frequency modes in ATR and RSB are inducible during the entire lifetime of the excited electronic states. This latter effect points to a transient molecular structure that, following initial relaxation between different excited electronic states, does not change anymore over the lifetime of the finally populated excited electronic state.

Mapping the ultrafast vibrational dynamics of all-trans and 13-cis retinal isomerization in Anabaena Sensory Rhodopsin

Discrepancies in the isomerization dynamics and quantum yields of the trans and cis retinal protonated Schiff base is a well-known issue in the context of retinal photochemistry. Anabaena Sensory Rhodopsin (ASR) is a microbial retinal protein that comprises a retinal chromophore in two ground state (GS) conformations: all-trans, 15-anti (AT) and 13-cis, 15-syn (13C). In this study, we applied impulsive vibrational spectroscopic techniques (DFWM, pump-DFWM and pump-IVS) to ASR to shed more light on how the structural changes take place in the excited state within the same protein environment. Our findings point to distinct features in the ground state structural conformations as well as to drastically different evolutions in the excited state manifold. The ground state vibrational spectra show stronger Raman activity of the C14-H out-of-plane wag (at about 805 cm-1) for the 13C isomer than that for the AT isomer, which hints at a pre-distortion of 13C in the ground state. Evolution of the Raman frequency after interaction with the actinic pulse shows a blue-shift for the C[double bond, length as m-dash]C stretching and CH3 rocking mode for both isomers. For AT, however, the blue-shift is not instantaneous as observed for the 13C isomer, rather it takes more than 200 fs to reach the maximum frequency shift. This frequency blue-shift is rationalized by a decrease in the effective conjugation length during the isomerization reaction, which further confirms a slower formation of the twisted state for the AT isomer and corroborates the presence of a barrier in the excited state trajectory previously predicted by quantum chemical calculations.

Strong pH-Dependent Near-Infrared Fluorescence in a Microbial Rhodopsin Reconstituted with a Red-Shifting Retinal Analogue

Near-infrared (NIR)-driven rhodopsins are of great interest in optogenetics and other optobiotechnological developments such as artificial photosynthesis and deep-tissue voltage imaging. Here we report that the proton pump proteorhodopsin (PR) containing a NIR-active retinal analogue (PR:MMAR) exhibits intense NIR fluorescence at a quantum yield of 3.3%. This is 130 times higher than native PR ( Lenz , M. O. ; Biophys J. 2006 , 91 , 255 - 262 ) and 3-8 times higher than the QuasAr and PROPS voltage sensors ( Kralj , J. ; Science 2011 , 333 , 345 - 348 ; Hochbaum , D. R. ; Nat. Methods 2014 , 11 , 825 - 833 ). The NIR fluorescence strongly depends on the pH in the range of 6-8.5, suggesting potential application of MMAR-binding proteins as ultrasensitive NIR-driven pH and/or voltage sensors. Femtosecond transient absorption spectroscopy showed that upon near-IR excitation, PR:MMAR features an unusually long fluorescence lifetime of 310 ps and the absence of isomerized photoproducts, consistent with the high fluorescence quantum yield. Stimulated Raman analysis indicates that the NIR-absorbing species develops upon protonation of a conserved aspartate, which promotes charge delocalization and bond length leveling due to an additional methylamino group in MMAR, in essence providing a secondary protonated Schiff base. This results in much smaller bond length alteration along the conjugated backbone, thereby conferring significant single-bond character to the C13═C14 bond and structural deformation of the chromophore, which interferes with photoinduced isomerization and extends the lifetime for fluorescence. Hence, our studies allow for a molecular understanding of the relation between absorption/emission wavelength, isomerization, and fluorescence in PR:MMAR. As acidification enhances the resonance state, this explains the strong pH dependence of the NIR emission.

Ultrafast Carotenoid to Retinal Energy Transfer in Xanthorhodopsin Revealed by the Combination of Transient Absorption and Two-Dimensional Electronic Spectroscopy

By comparing two-dimensional electronic spectroscopy (2DES) and Pump-Probe (PP) measurements on xanthorhodopsin (XR) and reduced-xanthorhodopsin (RXR) complexes, the ultrafast carotenoid-to-retinal energy transfer pathway is revealed, at very early times, by an excess of signal amplitude at the associated cross-peak and by the carotenoid bleaching reduction due to its ground state recovery. The combination of the measured 2DES and PP spectroscopic data with theoretical modelling allows a clear identification of the main experimental signals and a comprehensive interpretation of their origin and dynamics. The remarkable velocity of the energy transfer, despite the non-negligible energy separation between the two chromophores, and the analysis of the underlying transport mechanism, highlight the role played by the ground state carotenoid vibrations in assisting the process.

Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser

Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction.