13-cis Configuration Research Articles

How to Choose the Best Optogenetic Tool for Your Research

All-optical methods that provide deeper understanding of neural activity are currently being developed. Optogenetics is a biological technique useful to control neuronal activity or life phenomena using light. Microbial rhodopsins are light-activated membrane proteins used as optogenetic tools. Microbial rhodopsins such as channelrhodopsin2 (ChR2) consist of seven-pass transmembrane proteins with a covalently bound retinal. Light absorption is followed by photoisomerization of the all-trans retinal to a 13-cis configuration and subsequent conformational changes in the molecule, with consequent permeability of the channel structure to ions. Recent studies have reported the discovery of microbial rhodopsins with novel functions. Microbial rhodopsin diversity has also increased. We describe the characteristics of microbial rhodopsins used as optogenetic tools and the latest research in this domain.

How Do Xanthophylls Protect Lipid Membranes from Oxidative Damage?

Here, we address the problem of the antioxidant activity of carotenoids in biomembranes. The activity of lutein and zeaxanthin in the quenching of singlet oxygen generated by photosensitization was monitored in lipid vesicles using a singlet oxygen-sensitive fluorescent probe and with the application of fluorescence lifetime imaging microscopy. The antioxidant activity of xanthophylls was interpreted on the basis of electron paramagnetic resonance oximetry results showing that xanthophylls constitute a barrier to the penetration of molecular oxygen into lipid membranes: to a greater extent in the 13-cis configuration than in all-trans. These results are discussed in relation to the trans-cis photoisomerization of xanthophylls observed in the human retina. It can be concluded that photoisomerization of xanthophylls is a regulatory mechanism that is important for both the modulation of light filtration through the macula and photoprotection by quenching singlet oxygen and creating a barrier to oxygen permeation to membranes.

Covalent Bond between the Lys-255 Residue and the Main Chain Is Responsible for Stable Retinal Chromophore Binding and Sodium-Pumping Activity of Krokinobacter Rhodopsin 2.

Microbial rhodopsins are light-receptive proteins with various functions triggered by the photoisomerization of the retinal chromophore from the all-trans to 13-cis configuration. A retinal chromophore is covalently bound to a lysine residue in the middle of the seventh transmembrane helix via a protonated Schiff base. Bacteriorhodopsin (BR) variants lacking a covalent bond between the side chain of Lys-216 and the main chain formed purple pigments and exhibited a proton-pumping function. Therefore, the covalent bond linking the lysine residue and the protein backbone is not considered a prerequisite for microbial rhodopsin function. To further examine this hypothesis regarding the role of the covalent bond at the lysine side chain for rhodopsin functions, we investigated K255G and K255A variants of sodium-pumping rhodopsin, Krokinobacter rhodopsin 2 (KR2), with an alkylamine retinal Schiff base (prepared by mixing ethyl- or n-propylamine and retinal (EtSB or nPrSB)). The KR2 K255G variant incorporated nPrSB and EtSB as similarly to the BR variants, whereas the K255A variant did not incorporate these alkylamine Schiff bases. The absorption maximum of K255G + nPrSB was 524-516 nm, which was close to the 526 nm absorption maximum of the wild-type + all-trans retinal (ATR). However, the K255G + nPrSB did not exhibit any ion transport activity. Since the KR2 K255G variant easily released nPrSB during light illumination and did not form an O intermediate, we concluded that a covalent bond at Lys-255 is important for the stable binding of the retinal chromophore and formation of an O intermediate to achieve light-driven Na+ pump function in KR2.

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.

Existence of two substates in the O intermediate of the bacteriorhodopsin photocycle

The proton pumping cycle of bacteriorhodopsin (bR) is initiated when the retinal chromophore with the 13-trans configuration is photo-isomerized into the 13-cis configuration. To understand the recovery processes of the initial retinal configuration that occur in the late stage of the photocycle, we have performed a comprehensive analysis of absorption kinetics data collected at various pH levels and at different salt concentrations. The result of analysis revealed the following features of the late stages of the trans photocycle. i) Two substates occur in the O intermediate. ii) The visible absorption band of the first substate (O1) appears at a much shorter wavelength than that of the late substate (O2). iii) O1 is in rapid equilibrium with the preceding state (N), but O1 becomes less stable than N when an ionizable residue (X1) with a pKa value of 6.5 (in 2 M KCl) is deprotonated. iv) At a low pH and at a low salt concentration, the decay time constant of O2 is longer than those of the preceding states, but the relationship between these time constants is altered when the medium pH or the salt concentration is increased. On the basis of the present observations and previous studies on the structure of the chromophore in O, we suspect that the retinal chromophore in O1 takes on a distorted 13-cis configuration and the O1-to-O2 transition is accompanied by cis-to-trans isomerization about C13C14 bond.

Analog Retinal Redshifts Visible Absorption of QuasAr Transmembrane Voltage Sensors into Near-infrared.

Opsin‐based transmembrane voltage sensors (OTVSs) are increasingly important tools for neuroscience enabling neural function in complex brain circuits to be explored in live, behaving animals. However, the visible wavelengths required for fluorescence excitation of the current generation of OTVSs limit optogenetic imaging in the brain to depths of only a few mm due to the strong absorption and scattering of visible light by biological tissues. We report that substitution of the native A1 retinal chromophore of the widely used QuasAr1/2 OTVSs with the retinal analog MMAR containing a methylamino‐modified dimethylphenyl ring results in over a 100‐nm redshift of the maxima of the absorption and fluorescence emission bands to near 700 and 840 nm, respectively. FT‐Raman spectroscopy reveals that at pH 7 QuasAr1 with both the A1 and MMAR chromophores possess predominantly an all‐trans protonated Schiff base configuration with the MMAR chromophore exhibiting increased torsion of the polyene single‐/double‐bond system similar to the O‐intermediate of the BR photocycle. In contrast, the A1 and the MMAR chromophores of QuasAr2 exist partially in a 13‐cis PSB configuration. These results demonstrate that QuasArs containing the MMAR chromophore are attractive candidates for use as NIR‐OTVSs, especially for applications such as deep brain imaging.

Retinal Configuration of ppR Intermediates Revealed by Photoirradiation Solid-State NMR and DFT

Pharanois phoborhodopsin (ppR) from Natronomonas pharaonis is a transmembrane photoreceptor protein involved in negative phototaxis. Structural changes in ppR triggered by photoisomerization of the retinal chromophore are transmitted to its cognate transducer protein (pHtrII) through a cyclic photoreaction pathway involving several photointermediates. This pathway is called the photocycle. It is important to understand the detailed configurational changes of retinal during the photocycle. We previously observed one of the photointermediates (M-intermediates) by in situ photoirradiation solid-state NMR experiments. In this study, we further observed the 13C cross-polarization magic-angle-spinning NMR signals of late photointermediates such as O- and N′-intermediates by illumination with green light (520 nm). Under blue-light (365 nm) irradiation of the M-intermediates, 13C cross-polarization magic-angle-spinning NMR signals of 14- and 20-13C-labeled retinal in the O-intermediate appeared at 115.4 and 16.4 ppm and were assigned to the 13-trans, 15-syn configuration. The signals caused by the N′-intermediate appeared at 115.4 and 23.9 ppm and were assigned to the 13-cis configuration, and they were in an equilibrium state with the O-intermediate during thermal decay of the M-intermediates at −60°C. Thus, photoirradiation NMR studies revealed the photoreaction pathways from the M- to O-intermediates and the equilibrium state between the N′- and O-intermediate. Further, we evaluated the detailed retinal configurations in the O- and N′-intermediates by performing a density functional theory chemical shift calculation. The results showed that the N′-intermediate has a 63° twisted retinal state due to the 13-cis configuration. The retinal configurations of the O- and N′-intermediates were determined to be 13-trans, 15-syn, and 13-cis, respectively, based on the chemical shift values of [20-13C] and [14-13C] retinal obtained by photoirradiation solid-state NMR and density functional theory calculation.

Function of Tyr185 in Stabilizing the Isomerization Equilibrium of the Retinal Chromophore in the Bacteriorhodopsin Ground State

Bacteriorhodopsin (bR), a member of the microbial rhodopsin family's seven trans-membrane receptors, functions as a light-driven proton pump for light energy capture and conversion in Halobacterium Salinarum. In the dark-adapted (DA) state, bR contains two thermally interconvertible retinal isomers: 13-cis, 15-syn retinal (bRcis), and all-trans, 15-anti retinal (bRtrans) with a molar ratio of 6:4 in the purple membrane. Absorption of a photon causes photoisomerization of the chromophore from the all-trans to the 13-cis, 15-anti configuration and triggers a series of structural rearrangements of the protein that initiates a vectorial translocation of a proton out of the cell.The function of Tyrosine 185 (Tyr185) in bR photoreaction mechanism has long been a topic of discussion, and been suggested to play an important role in stabilizing the pentagonal hydrogen-bonded network on the extracellular side of the protonated Schiff base during the photoreaction. However, little is to know on coupling of Tyr185 with the protonated Schiff base with respect to the thermal isomerization of the retinal chromophore at the bR ground state. Heteronuclear single molecular manipulation, combined with homonuclear correlation experiments, UV spectroscopy, light-induced transient absorption change measurements, molecular dynamic simulations and mutagenesis, has been established as a powerful tool for providing insight into the conformation and coupling of Tyr185 with the retinal chromophore at the bR ground state in the purple membrane. Our results show that the retinal chromophore in 13-cis and 15-syn configurations has more accumulated charge and, is more twisted and rigid than that in the all-trans configuration. Moreover, the cis-trans thermal isomerization equilibrium with the molar ratio of 6:4 at the ground state is stabilized by coupling with Tyr185.

Asymmetric Toggling of a Natural Photoswitch: Ultrafast Spectroscopy of Anabaena Sensory Rhodopsin

Photochemistry in retinal proteins (RPs) is determined both by the properties of the retinal chromophore and by its interactions with the surrounding protein. The initial retinal configuration, and the isomerization coordinates active in any specific protein, must be important factors influencing the course of photochemistry. This is illustrated by the vast differences between the photoisomerization dynamics in visual pigments which start 11-cis and end all-trans, and those observed in microbial ion pumps and sensory rhodopsins which start all-trans and end in a 13-cis configuration. However, isolating these factors is difficult since most RPs accommodate only one active stable ground-state configuration. Anabaena sensory rhodopsin, allegedly functioning in cyanobacteria as a wavelength sensor, exists in two stable photoswitchable forms, containing all-trans and 13-cis retinal isomers, at a wavelength-dependent ratio. Using femtosecond spectroscopy, and aided by extraction of coherent vibrational signatures, we show that cis-to-trans photoisomerization, as in visual pigments, is ballistic and over in a fraction of a picosecond, while the reverse is nearly 10 times slower and kinetically reminiscent of other microbial rhodopsins. This provides a new test case for appreciating medium effects on primary events in RPs.

Femtosecond Time-Resolved Stimulated Raman Reveals the Birth of Bacteriorhodopsin’s J and K Intermediates

Light-activated proton translocation in halobacteria is driven by photoisomerization of the retinal chromophore within the membrane-bound protein bacteriorhodopsin. The molecular mechanism of this process has been widely debated due to the absence of structural information on the time scale of the reactive dynamics (the initial 0.1-1 ps). Here we use tunable femtosecond stimulated Raman spectroscopy to obtain time-resolved resonance Raman vibrational spectra of bacteriorhodopsin's key J and K photoisomerization intermediates. The appearance of the J state is delayed by approximately 150 fs relative to the zero of time and rises after this dwell with a 450 fs time constant. The J state is characterized by a 16 cm(-1) red-shifted C=C stretch, which blue shifts by 5 cm(-1) coincident with the rise of the K state. The delayed 3 ps rise of the C(15)-H HOOP mode with enhanced intensity in K reveals the appearance of strain near the Schiff's base once the 13-cis configuration is fully formed. The delay in the initial appearance of J is assigned to nuclear dynamics on the excited state that precede the formation of the proper geometry for reactive internal conversion.

Pressure-induced Isomerization of Retinal on Bacteriorhodopsin as Disclosed by Fast Magic Angle Spinning NMR†

Bacteriorhodopsin (bR) is a retinal protein in purple membrane of Halobacterium salinarum, which functions as a light-driven proton pump. We have detected pressure-induced isomerization of retinal in bR by analyzing 15N cross polarization-magic angle spinning (CP-MAS) NMR spectra of [zeta-15N]Lys-labeled bR. In the 15N-NMR spectra, both all-trans and 13-cis retinal configurations have been observed in the Lys N(zeta) in protonated Schiff base at 148.0 and 155.0 ppm, respectively, at the MAS frequency of 4 kHz in the dark. When the MAS frequency was increased up to 12 kHz corresponding to the sample pressure of 63 bar, the 15N-NMR signals of [zeta-15N]Lys in Schiff base of retinal were broadened. On the other hand, other [zeta-15N]Lys did not show broadening. Subsequently, the increased signal intensity of [zeta-15N]Lys in Schiff base of 13-cis retinal at 155.0 ppm was observed when the MAS frequency was decreased from 12 to 4 kHz. These results showed that the equilibrium constant of [all-trans-bR]/[13-cis-bR] in retinal decreased by the pressure of 63 bar. It was also revealed that the structural changes induced by the pressure occurred in the vicinity of retinal. Therefore, microscopically, hydrogen-bond network around retinal would be disrupted or distorted by a constantly applied pressure. It is, therefore, clearly demonstrated that increased pressure induced by fast MAS frequencies generated isomerization of retinal from all-trans to 13-cis state in the membrane protein bR.

Solid-State NMR Studies of Two Backbone Conformations at Tyr185 as a Function of Retinal Configurations in the Dark, Light, and Pressure Adapted Bacteriorhodopsins

Backbone conformations near tyrosine in bacteriorhodopsin (bR) corresponding to all-trans and 13-cis retinal configurations in the dark, light, and pressure adapted states were investigated for Tyr-X peptide bonds by using double amino acid labeling with [1-13C]Tyr, [15N]X-bR by means of rotational echo double resonance (REDOR) technique. The NMR signals obtained from the difference spectra between REDOR and full echo experiments allowed selectively detect on a tyrosine signals for Tyr185-Pro186, Tyr26-Phe27, and Tyr64-Gly65. Two 13C NMR peaks were observed for REDOR-filtered spectrum of Tyr185 in the dark at ambient temperature. These two signals are attributed to the bR with all-trans and 13-cis retinals. REDOR-filtered spectra for Tyr26 and 64 show singlet lines because they are located far from the retinal. All-trans peak intensity was increased in the light adapted state, while the 13-cis state increased for the pressure-adapted state. These results indicate that REDOR-filtered experiments provide us with valuable information of protein-retinal interaction.

Femtosecond infrared spectroscopy of bacteriorhodopsin chromophore isomerization.

The vibrational dynamics of the retinal chromophore all-trans-to-13-cis photoisomerization in bacteriorhodopsin has been studied with mid-infrared absorption spectroscopy at high time resolution (about 200 femtoseconds). After photoexcitation of light-adapted bacteriorhodopsin, the transient infrared absorption was probed in a broad spectral region, including vibrations with dominant C-C, C=C, and C=NH stretching mode amplitude. All photoproduct modes, especially those around 1190 reciprocal-centimeters that are indicative for a 13-cis configuration of the chromophore, rise with a time constant of approximately 0.5 picosecond. The results presented give direct vibrational-spectroscopic evidence for the isomerization taking place within 0.5 picosecond, as has been suggested by previous optical femtosecond time-resolved experiments but questioned recently by picosecond time-resolved vibrational spectroscopy experiments.

High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle.

Bacteriorhodopsin is the simplest known photon-driven proton pump and as such provides a model for the study of a basic function in bioenergetics. Its seven transmembrane helices encompass a proton translocation pathway containing the chromophore, a retinal molecule covalently bound to lysine 216 through a protonated Schiff base, and a series of proton donors and acceptors. Photoisomerization of the all-trans retinal to the 13-cis configuration initiates the vectorial translocation of a proton from the Schiff base, the primary proton donor, to the extracellular side, followed by reprotonation of the Schiff base from the cytoplasm. Here we describe the high-resolution X-ray structure of an early intermediate in the photocycle of bacteriorhodopsin, which is formed directly after photoexcitation. A key water molecule is dislocated, allowing the primary proton acceptor, Asp 85, to move. Movement of the main-chain Lys 216 locally disrupts the hydrogen-bonding network of helix G, facilitating structural changes later in the photocycle.

On the Nature of the Primary Light-Induced Events in Bacteriorhodopsin: Ultrafast Spectroscopy of Native and C13=C14 Locked Pigments

The primary light-induced events in the photosynthetic retinal protein bacteriorhodopsin (bR) are investigated by ultrafast optical spectroscopy over the 440−1000 nm spectral range. The study compares the early dynamics of the native all-trans pigment bR570 with those of two synthetic analogues, bR5.12 and bR5.13, in which isomerization around the critical C13C14 bond is blocked by a five-membered ring into all-trans and 13-cis configurations, respectively. Nearly identical spectral evolution is observed in both native and artificial systems over the first 100−200 fs of probe delay. During this period stimulated near-IR (∼900 nm) emission, and intense ∼460 nm absorption bands, due to analogous fluorescent I states (denoted as I460, I5.12 and I5.13, respectively), appear concurrently within 30 fs. In all systems continuous spectral shifting over tens of femtoseconds is observed in the 500−700 nm range. Native bR goes on to produce the J625 absorption band within ∼1 ps, which is accompanied by disappearance...

Semiconductor Photocatalysis: Photodegradation and Trans−Cis Photoisomerization of Carotenoids

In the presence of semiconductor CdS or ZnO particles, irradiation (>350 nm) of all-trans-β-carotene (II) in dichloromethane leads to rapid degradation of the carotenoid, which is relatively stable in the absence of the semiconductors. Canthaxanthin (I), however, undergoes significant photocatalyzed degradation only on ZnO, not on CdS. High-performance liquid chromatographic studies indicate that CdS catalyzes trans−cis photoisomerization of both I and II. As in the photoisomerization in the absence of semiconductor, the major cis isomers have the 9-cis and 13-cis configuration, but, under otherwise the same condition, the ratio of cis/trans isomers has doubled. In contrast to CdS, ZnO does not catalyze the photoisomerization of either I or II, although it enhances their rate of degradation. A photoisomerization mechanism involving carotenoid radicals formed by reaction with interstitial sulfur on the CdS surface is proposed.

Evidence for a Long-Lived 13-cis-Containing Intermediate in the Photocycle of the Leu 93 → Ala Bacteriorhodopsin Mutant

Previous studies have shown that replacement of Leu 93 by amino acids such as Ala or Thr dramatically slows the rate of completion of the bacteriorhodopsin photocycle through the formation of a long-lived intermediate assigned to the O intermediate on the basis of its red-shifted absorption spectrum. Spectroscopic and biochemical studies have implicated this kinetic defect with a slowing of the reisomerization of retinal from the 13-cis to the initial all-trans state in the Leu 93 mutants. These results have suggested that the van der Waals interaction of Leu 93 with retinal is essential for the rapid thermal reisomerization of retinal in the photocycle. Here, this hypothesis is independently tested by carrying out time-resolved resonance Raman spectroscopic studies of the long-lived intermediate in the photocycle of the Leu 93 → Ala mutant. Raman difference spectra obtained with a 631 nm probe show a single band in the fingerprint region at 1192 cm-1, confirming the previous observation of a 13-cis configuration for retinal during the lifetime of the long-lived intermediate. We conclude that a 13-cis-containing intermediate is accumulated in the late stages of the photocycle of the Leu 93 → Ala mutant, supporting our hypothesis that the interaction of Leu 93 with retinal is critical for the rapid thermal reisomerization of retinal in the bacteriorhodopsin photocycle.

Molecular mechanism of protein-retinal coupling in bacteriorhodopsin.

Bacteriorhodopsin is a membrane protein that functions as a light-driven proton pump. Each cycle of proton transport is initiated by the light-induced isomerization of retinal from the all-trans to 13-cis configuration and is completed by the protein-driven reisomerization of retinal to the all-trans configuration. Previous studies have shown that replacement of Leu-93, a residue in close proximity to the 13-methyl group of retinal, by alanine, resulted in a 250-fold increase in the time required to complete each photocycle. Here, we show that the kinetic defect in the photocycle of the Leu-93-->Ala mutant occurs at a stage after the completion of proton transport and can be overcome in the presence of strong background illumination. Time-resolved retinal-extraction experiments demonstrate the continued presence of a 13-cis intermediate in the photocycle of the Leu-93-->Ala mutant well after the completion of proton release and uptake. These results indicate that retinal reisomerization is kinetically the rate-limiting step in the photocycle of this mutant and that the slow thermal reisomerization can be bypassed by the absorption of a second photon. The effects observed for the Leu-93-->Ala mutant are not observed upon replacement of any other residue in van der Waals contact with retinal or upon replacement of Leu-93 by valine. We conclude that the contact between Leu-93 and the 13-methyl group of retinal plays a key role in controlling the rate of protein conformational changes associated with retinal reisomerization and return of the protein to the initial state.

Repeated topical administration of all- trans-retinoic acid and plasma levels of retinoic acids in humans

Vitamin A ingestion raises plasma levels of several potentially teratogenic retinoic acids (RAs) with all-trans and 13-cis configuration, but definitive data concerning the consequences of topical administration of all-trans-RA are lacking. The study objective was to investigate the potential for inducing systemic activity after topical administration of 0.025% all-trans-RA by measuring plasma retinoid levels. Plasma levels of all-trans-RA, 13-cis-RA, and 4-oxo-13-cis-RA were measured in four healthy subjects before, during, and after 14 daily topical applications of all-trans-RA. Topical administration of all-trans-RA did not significantly increase plasma levels of all-trans-RA, 13-cis-RA, and 4-oxo-13-cis-RA. Significant decreases in levels of these RAs observed during the night may reflect diurnal variations of retinoid metabolism or lowered absorption of dietary vitamin A. Diurnal and nutritional factors influence plasma levels of endogenous retinoids to a greater extent than topical administration of all-trans-RA at doses used for acne therapy, which on the basis of these results appears unlikely to induce systemic effects.

Light-driven proton or chloride pumping by halorhodopsin.

Halorhodopsin from Halobacterium halobium was purified and reconstituted with lipids from purple membranes. The resulting protein-containing membrane sheets were adsorbed to a planar lipid membrane and photoelectric properties were analyzed. Depending on light conditions, halorhodopsin acted either as a light-driven chloride pump or as a proton pump: green light caused chloride transport and additional blue light induced proton pumping. In the living cell, both to these vectorial processes would be directed toward the cytoplasm and, compared to ion transport by bacteriorhodopsin, this is an inversed proton flow. Azide, a catalyst for reversible deprotonation of halorhodopsin, enhanced proton transport, and the deprotonated Schiff base in the 13-cis configuration (H410) was identified as the key intermediate of this alternative catalytic cycle in halorhodopsin. While chloride transport in halorhodopsin is mediated by a one-photon process, proton transport requires the absorption of two photons: one photon for formation of H410 and release of a proton, and one photon for photoisomerization of H410 and re-formation of H578 with concomitant uptake of a proton by the Schiff base.