Modeling the syn-cycle in the light activated opening of the channelrhodopsin-2 ion channel

The ion channel of channelrhodopsin-2 (ChR2) is activated by absorbing light. The light stimulates retinal to isomerize to start the photocycle. There are two pathways for photocycles, which are caused by isomerization of the retinal from all-trans, 15-anti to 13-cis, 15-anti in the dark-adapted state (anti-cycle) and from 13-cis, 15-syn to all-trans, 15-syn in the light-adapted state (syn-cycle). In this work, the structure of the syn-cycle intermediate and mechanism of channel opening were studied by molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. Due to the lack of crystal structure of intermediates in the syn-cycle of ChR2, the intermediate models were constructed from the homologous intermediates in the anti-cycle. The isomerization of retinal was shown to cause the central gate (CG) hydrogen bond network to rearrange, cutting the link between TM2 and TM7. TM2 is moved by the intrahelical hydrogen bond of E90 and K93, and induced the intracellular gate (ICG) to expand. The ion penetration pathway between TM1, TM2, TM3 and TM7 in the P500* state was observed by MD simulations. However, this channel is not fully opened compared with the homologous P500 state in the anti-cycle. In addition, the protons on Schiff bases were found to be unable to form hydrogen bonds with the counter residues (E123 and D253) in the P500* state, preventing an evolution of the P500* state to a P390-like state in the syn-cycle.

Modelling the syn-cycle is a series of operations on the ChR2 crystal structure (PDB ID: 6EID). By replacement and isomerization, we obtained P500* and P480 intermediates. A feasible explanation that no P390* was observed in experiment was inferred.

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).

Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2

Channelrhodopsins are photosensitive proteins that trigger flagella motion in single-cell algae and have been successfully utilized in optogenetic applications. In optogenetics, light is used to activate neural cells in living organisms, which can be achieved by exploiting the ion channel signaling of channelrhodopsins. Tailoring channelrhodopsins for such applications includes the tuning of the absorption maximum. In order to establish rational design and to obtain a desired spectral shift, a basic understanding of the absorption spectrum is required. We have studied the chimera C1C2 as a representative of this protein family and the first member with an available crystal structure. For this purpose, we sampled the conformations of C1C2 using quantum mechanical/molecular mechanical molecular dynamics and subjected the resulting snapshots of the trajectory to excitation energy calculations using ADC(2) and simplified time-dependent density functional theory. In contrast to previous reports, we found that different hydrogen-bonding networks-involving the retinal protonated Schiff base, the putative counterions E162 and D292, and water molecules-had only a small impact on the absorption spectrum. However, in the case of deprotonated E162, increasing the distance to the Schiff base hydrogen-bonding partner led to a systematic blue shift. The β-ionone ring rotation was identified as another important contributor. Yet the most important factors were found to be the bond length alternation and bond order alternation that were linearly correlated to the absorption maximum by up to 62 and 82%, respectively. We ascribe this novel insight into the structural basis of the absorption spectrum to our enhanced protein setup that includes membrane embedding as well as long and extensive sampling.

The effect on ion channel of different protonation states of E90 in channelrhodopsin-2: a molecular dynamics simulation

Channelrhodopsin-2 (ChR2) is a cationic channel protein that has been extensively studied in optogenetics. The ion channel is opened via a series of proton transfers and H-bond changes during the photocycle but the detailed mechanism is still unknown. Molecular dynamics (MD) simulations with enhanced sampling were performed on the dark-adapted state (i.e., D470) and two photocycle intermediates (P₁⁵⁰⁰ and P₂³⁹⁰) to study the proton transfer path of the Schiff base and the subsequent conformational changes. The results suggest there are two possible proton transfer pathways from the Schiff base to proton acceptors (i.e., E123 or D253), depending on the protonation of E90. If E90 is protonated in the P₁⁵⁰⁰ state, the proton on the Schiff base will transfer to E123. The polyene chain of 13-cis retinal tilts and opens the channel that detours the blocking central gate (CG) and forms a narrow channel through the transmembrane helices (TM) 2, 3, 6 and 7. In contrast, if E90 deprotonates after retinal isomerization, the primary proton acceptor is D253, and an almost-open channel through TM1, 2, 3 and 7 is generated. The channel diameter is very close to the experimental value. The potential mean force (PMF) suggests that the free energy is extremely low for ions passing through this channel.

With E90 protonated, the proton acceptor of RSBH⁺ is E123 with a narrow channel along TM3; while with E90 deprotonated, proton transfer from RSBH⁺ to D253 generates an approximately open channel along TM2.

An assessment of water placement algorithms in quantum mechanics/molecular mechanics modeling: the case of rhodopsins' first spectral absorption band maxima

Quantum mechanics/molecular mechanics (QM/MM) models are a widely used tool to obtain detailed insight into the properties and functioning of proteins. The outcome of QM/MM studies heavily depends on the quality of the applied QM/MM model. Prediction and right placement of internal water molecules in protein cavities is one of the critical parts of any QM/MM model construction. Herein, we performed a systematic study of four protein hydration algorithms. We tested these algorithms for their ability to predict X-ray-resolved water molecules for a set of membrane photosensitive rhodopsin proteins, as well as the influence of the applied water placement algorithms on the QM/MM calculated absorption maxima (λ_max) of these proteins. We used 49 rhodopsins and their intermediates with available X-ray structures as the test set. We found that a proper choice of hydration algorithms and setups is needed to predict functionally important water molecules in the chromophore-binding cavity of rhodopsins, such as the water cluster in the N-H region of bacteriorhodopsin or two water molecules in the binding pocket of bovine visual rhodopsin. The QM/MM calculated λ_max of rhodopsins is also quite sensitive to the applied protein hydration protocols. The best methodology allows obtaining an 18.0 nm average value for the absolute deviation of the calculated λ_max from the experimental λ_max. Although the major effect of water molecules on λ_max originates from the water molecules located in the binding pocket, the water molecules outside the binding pocket also affect the calculated λ_max mainly by causing a reorganization of the protein structure. The results reported in this study can be used for the evaluation and further development of hydration methodologies, in general, and rhodopsin QM/MM models, in particular.

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.

Trans-to-cis photoisomerization of cyclocurcumin in different environments rationalized by computational photochemistry

Cyclocurcumin is a turmeric component that has attracted much less attention compared to the well-known curcumin. In spite of the less deep characterization of its properties, cyclocurcumin has shown promising anticancer effects when used in combination with curcumin. Especially, due to its peculiar molecular structure, cyclocurcumin can be regarded as an almost ideal photoswitch, whose capabilities can also be exploited for relevant biological applications. Here, by means of state-of-the-art computational methods for electronic excited-state calculations (TD-DFT, MS-CASPT2, and XMS-CASPT2), we analyze in detail the absorption and photoisomerization pathways leading from the more stable trans isomer to the cis one. The different molecular surroundings, taken into account by means of the electrostatic solvent effect and compared with available experimental data, have been found to be critical in describing the fate of irradiated cyclocurcumin: when in non-polar environments, an excited state barrier prevents photoisomerization and favours fluorescence, whereas in polar solvents, an almost barrierless path results in a striking decrease of fluorescence, opening the way toward a crossing region with the ground state and thus funneling the photoproduction of the cis isomer.

Far Red Fluorescent Proteins: Where Is the Limit of the Acylimine Chromophore?

The search for new near-infrared probes for fluorescence imaging applications is a rapidly growing field of research. Monomeric fluorescent proteins that autocatalyze their chromophore are the most versatile markers for in vivo applications, but the development of bright far-red fluorescent proteins (RFPs) has proven difficult. In this contribution, we search for the theoretical limit of the red shift and how it can be reached without sacrificing the fluorescence quantum yield. Through extensive excited-state pathway calculations, molecular dynamics sampling, and statistical modeling using QM/MM schemes, we provide a new understanding of the chromophore's photophysics including the role of its acylimine extension, which is the main difference from other families of fluorescent proteins. The excited-state dynamics of the mPlum RFP and its mutants provide an ideal basis due to mPlum's flexible binding pocket and extended dynamic Stokes shift. We found a large number of structural species with red-shifted emission that differ in rotamer states and H-bonds between key amino acid residues in the binding pocket. By analyzing their spectral and structural features, we derive guidelines for future rational genetic design strategies.

Nonadiabatic Photodynamics of Retinal Protonated Schiff Base in Channelrhodopsin 2

Channelrhodopsin 2 (ChR2) is a light-gated ion channel and an important tool in optogenetics. Photoisomerization of retinal protonated Schiff base (RPSB) in ChR2 triggers channel activation. Despite the importance of ChR2 in optogenetics, the detailed mechanism for photoisomerization and channel activation is still not fully understood. Here, we report on computer simulations to investigate the photoisomerization mechanism and its effect on the activation of ChR2. Nonadiabatic dynamics simulation of ChR2 was carried out using the ab initio multiple spawning (AIMS) method and quantum mechanics/molecular mechanics (QM/MM) with a restricted ensemble Kohn-Sham (REKS) treatment of the QM region. Our results agree well with spectroscopic measurements and reveal that the RPSB isomerization is highly specific around the C₁₃=C₁₄ bond and follows the "aborted bicycle-pedal" mechanism. In addition, RPSB photoisomerization facilitates its deprotonation and partially increases the hydration level in the channel, which could trigger subsequent channel opening and ion conduction.