Analyzing the red-shift characteristics of azulenic, naphthyl, other ring-fused and retinyl pigment analogs of bacteriorhodopsin

Merocyanines form bacteriorhodopsins with strongly bathochromic absorption maxima

There is a need to shift the absorbance of biomolecules to the optical transparency window of tissue for applications in optogenetics and photo-pharmacology. There are a few strategies to achieve the so-called red shift of the absorption maxima. Herein, a series of 11 merocyanine dyes were synthesized and employed as chromophores in place of retinal in bacteriorhodopsin (bR) to achieve a bathochromic shift of the absorption maxima relative to bR's [Formula: see text] of 568 nm. Assembly with the apoprotein bacterioopsin (bO) led to stable, covalently bound chromoproteins with strongly bathochromic absorbance bands, except for three compounds. Maximal red shifts were observed for molecules 9, 2, and 8 in bR where the [Formula: see text] was 766, 755, and 736 nm, respectively. While these three merocyanines have different end groups, they share a similar structural feature, namely, a methyl group which is located at the retinal equivalent position 13 of the polyene chain. The absorption and fluorescence data are also presented for the retinal derivatives in their aldehyde, Schiff base (SB), and protonated SB (PSB) forms in solution. According to their hemicyanine character, the PSBs and their analogue bRs exhibited fluorescence quantum yields (Φf) several orders of magnitude greater than native bR (Φf 0.02 to 0.18 versus 1.5 × 10-5 in bR) while also exhibiting much smaller Stokes shifts than bR (400 to 1000 cm-1 versus 4030 cm-1 in bR). The experimental results are complemented by quantum chemical calculations where excellent agreement between the experimental [Formula: see text] and the calculated [Formula: see text] was achieved with the second-order algebraic-diagrammatic construction [ADC(2)] method. In addition, quantum mechanics/molecular mechanics (QM/MM) calculations were employed to shed light on the origin of the bathochromic shift of merocyanine 2 in bR compared with native bR.

Automatic Rhodopsin Modeling with Multiple Protonation Microstates

Automatic Rhodopsin Modeling (ARM) is a simulation protocol providing QM/MM models of rhodopsins capable of reproducing experimental electronic absorption and emission trends. Currently, ARM is restricted to a single protonation microstate for each rhodopsin model. Herein, we incorporate an extension of the minimal electrostatic model (MEM) into the ARM protocol to account for all relevant protonation microstates at a given pH. The new ARM+MEM protocol determines the most important microstates contributing to the description of the absorption spectrum. As a test case, we have applied this methodology to simulate the pH-dependent absorption spectrum of a toy model, showing that the single-microstate picture breaks down at certain pH values. Subsequently, we applied ARM+MEM toAnabaenasensory rhodopsin, confirming an improved description of its absorption spectrum when the titration of several key residues is considered.

Redshifted and Near-infrared Active Analog Pigments Based upon Archaerhodopsin-3

Archaerhodopsin‐3 (AR3) is a member of the microbial rhodopsin family of hepta‐helical transmembrane proteins, containing a covalently bound molecule of all‐trans retinal as a chromophore. It displays an absorbance band in the visible region of the solar spectrum (λmax 556 nm) and functions as a light‐driven proton pump in the archaeon Halorubrum sodomense. AR3 and its mutants are widely used in neuroscience as optogenetic neural silencers and in particular as fluorescent indicators of transmembrane potential. In this study, we investigated the effect of analogs of the native ligand all‐trans retinal A1 on the spectral properties and proton‐pumping activity of AR3 and its single mutant AR3 (F229S). While, surprisingly, the 3‐methoxyretinal A2 analog did not redshift the absorbance maximum of AR3, the analogs retinal A2 and 3‐methylamino‐16‐nor‐1,2,3,4‐didehydroretinal (MMAR) did generate active redshifted AR3 pigments. The MMAR analog pigments could even be activated by near‐infrared light. Furthermore, the MMAR pigments showed strongly enhanced fluorescence with an emission band in the near‐infrared peaking around 815 nm. We anticipate that the AR3 pigments generated in this study have widespread potential for near‐infrared exploitation as fluorescent voltage‐gated sensors in optogenetics and artificial leafs and as proton pumps in bioenergy‐based applications.

Fluorinated retinoids and carotenoids

Methods of preparing fluorinated retinoids with labels located on odd-numbered carbons as well on even-numbered carbons and those containing trifluoromethyl groups are reviewed. The use of such retinoids in studies of protein-bound species is summarized, including the application of (19)F NMR spectroscopy for elucidating the mechanism of cis/trans isomerization, restricted rotation within the protein binding pocket, and identification of specific protein-substrate interactions. The fluorine label was also useful for wavelength attenuation of protein-bound species (including formation of NIR absorbing pigments) and for other unique applications. The more limited studies available on fluorinated carotenoids are also reviewed.

Synthesis of N-Heteroaryl Retinals and their Artificial Bacteriorhodopsins

N-Heteroaryl retinals derived from indole, 1-indolizine and 3-indolizine (10 a-c) have been synthesized after their UV/Vis red-shifted absorption properties had been predicted by time-dependent density functional theory (TD-DFT) computations. The three new analogues form artificial pigments upon recombination with bacterioopsin: indolyl retinal 10 a undergoes fast and efficient reconstitution to form a species with a UV/Vis absorbance maximum similar to that of wild-type bacteriorhodopsin, whilst the indolizinyl retinals 10 b and 10 c also reconstitute in significant proportion to give noticeably red-shifted, although unstable, pigments. Significant changes in the pK(a) values of these artificial bacteriorhodopsins are interpreted as arising from nonoptimal binding-site occupancy by the chromophore due to steric constraints.

Bacteriorhodopsin Analogs from Diphenylpolyene Chromophores¶

Chromophore-modified bacteriorhodopsin (bR) analogs are prepared, to study the nature of chromophore-protein interaction as well as to develop new bR analogs that can find applications as photoactive element in molecular electronic devices. This article describes the preparation and characterization of hitherto unknown bR analogs based on diphenylpolyene chromophores. Diphenylpolyene compounds, namely, 4-[(E)-2-phenylvinyl]benzaldehyde (1), 3-methyl-5-[4-[(E)-2-phenylvinyl]phenyl]penta-2E,4E-dienal (2), 4-[4-phenylbuta-1E,3E-dienyl]benzaldehyde (3) and 3-methyl-5-[4-[4-phenylbuta-lE,3E-dienyl]phenyl]penta-2E,4E-dienal (4), have been synthesized, and their interaction with bacterioopsin (bOP) has been studied. Whereas aldehydes 2 and 4 interact with bOP and yield bR analogs bR-2 and bR-4, aldehydes 1 and 3 do not yield any pigment. Analogs bR-2 and bR-4 have been characterized for their opsin shift, competitive binding, photochemical properties and fluorescence spectral behavior.

The nature of the delocalized cations in azulenic bacteriorhodopsin analogs

Depending on the size and shape of their azulenic chromophores, azulenic bacteriorhodopsin (bR) pigment analogs can exist as either an initial pigment P1, a more red-shifted final pigment P2 or an equilibrium mixture of both. The absorption spectra of red-shifted bR analogs exhibit characteristic narrow-band shapes similar to charge fully delocalized cyanine-like dyes. Therefore, all such red-shifted pigments are believed to be highly delocalized, bond-equalized carbocations. We have determined structural requirements that facilitate their formation. To describe fully the red-shift potentials of these retinal analogs, we have introduced a new parameter-percent red-shift (PRS). A large PRS value not only reflects the extent of red-shift, but is also suggestive of extensive delocalization of the positive charge. Relevance of these findings in consideration of the possibility of forming stable O-intermediates is presented. The postulated resonance hybrid-like structures for different cations of the positively charged protonated Schiff base chromophores are in fact structurally distinct species, equilibrating in response to local perturbations within the supramolecular protein environment.

Spectroscopic mimicry for the protonated retinal Schiff base in vivo with modified amphiphilic clay interlayers as a possible model of opsin environment

We have found that clay acts as a novel model matrix for the amphiphilic protein-opsin to mimic the visible absorption spectrum of a protonated retinal Schiff base (RSB) in vivo. Without strong acids at ambient temperature, a visible broad absorption spectrum with a lambda max at 530 nm covering the range from 400 to 680 nm was achieved for the protonated RSB with cationic surfactant-modified montmorillonite clay. The interlayers of the dimethyloctadecylamine (DOA) modified clay were found to provide amphiphilic space allowing the amphiphilic RSB to be intercalated easily and sequentially and protonated by the DOA. It is proposed that the visible absorption spectrum at lambda max 530 nm was attributable to electrostatic effects, permitting the appropriate distance between the nitrogen of the protonated RSB and the negatively charged clay interlayers and also to the anisotropic orientation of the RSB molecules in the interlayers.