Conformation Of Chromophore Research Articles

Selective incorporation of one of the isomers of a photoswitchable molecule in wormlike micelles

Understanding the physical and chemical mechanisms underlying the interactions between giant micelles and photoswitchable molecules is essential because it is not evident why some photoswitchable chromophores with apparently good potential to modify micellar systems' macroscopic properties have a poor performance on UV-irradiation. We report a mechanism that describes the trans-isomer's expulsion embedded in the wormlike micelles when it is transformed into the cis-isomer on UV-irradiation. Consequently, a small change in the rheological properties of the micellar solution is observed on UV-irradiation. As a model system, 4-(phenylazo)benzoate ion as the photoresponsive chromophore and giant cylindrical micelles made of N-Tetradecyl-N,N-Dimethyl-3-ammonio-1-PropaneSulfonate, and Sodium Dodecyl Sulfate, in saline water, are used. The trans-isomer chromophore incorporates into the micelles modifying the solution viscosity and viscoelastic spectra, which follows the Maxwell model at low and intermediate frequencies. However, the effect of UV-irradiation on rheological properties is not significant. Micro-rheological experiments are performed with diffusive wave spectroscopy to obtain high-frequency viscoelastic spectra to estimate the characteristic length scales of the wormlike micellar network with the embedded chromophore to understand its rheological behavior better. Detailed interaction between the chromophore and the micelles is obtained with 1H-NMR and 1H DOSY NMR experiments to determine the chromophore conformation into the micelles and diffusivity of the isomers.

Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance.

For many species, vision is one of the most important sensory modalities for mediating essential tasks that include navigation, predation and foraging, predator avoidance, and numerous social behaviors. The vertebrate visual process begins when photons of the light interact with rod and cone photoreceptors that are present in the neural retina. Vertebrate visual photopigments are housed within these photoreceptor cells and are sensitive to a wide range of wavelengths that peak within the light spectrum, the latter of which is a function of the type of chromophore used and how it interacts with specific amino acid residues found within the opsin protein sequence. Minor differences in the amino acid sequences of the opsins are known to lead to large differences in the spectral peak of absorbance (i.e. the λmax value). In our prior studies, we developed a new approach that combined homology modeling and molecular dynamics simulations to gather structural information associated with chromophore conformation, then used it to generate statistical models for the accurate prediction of λmax values for photopigments derived from Rh1 and Rh2 amino acid sequences. In the present study, we test our novel approach to predict the λmax of phylogenetically distant Sws2 cone opsins. To build a model that can predict the λmax using our approach presented in our prior studies, we selected a spectrally-diverse set of 11 teleost Sws2 photopigments for which both amino acid sequence information and experimentally measured λmax values are known. The final first-order regression model, consisting of three terms associated with chromophore conformation, was sufficient to predict the λmax of Sws2 photopigments with high accuracy. This study further highlights the breadth of our approach in reliably predicting λmax values of Sws2 cone photopigments, evolutionary-more distant from template bovine RH1, and provided mechanistic insights into the role of known spectral tuning sites.

Active Rhodopsin Chromophore Conformation Revealed by Solid-state 2H NMR and QM/MM Simulations

Active Rhodopsin Chromophore Conformation Revealed by Solid-state 2H NMR and QM/MM Simulations

Structural elements regulating the photochromicity in a cyanobacteriochrome

The three-dimensional (3D) crystal structures of the GAF3 domain of cyanobacteriochrome Slr1393 (Synechocystis PCC6803) carrying a phycocyanobilin chromophore could be solved in both 15-Z dark-adapted state, Pr, λmax = 649 nm, and 15-E photoproduct, Pg, λmax = 536 nm (resolution, 1.6 and 1.86 Å, respectively). The structural data allowed identifying the large spectral shift of the Pr-to-Pg conversion as resulting from an out-of-plane rotation of the chromophore's peripheral rings and an outward movement of a short helix formed from a formerly unstructured loop. In addition, a third structure (2.1-Å resolution) starting from the photoproduct crystals allowed identification of elements that regulate the absorption maxima. In this peculiar form, generated during X-ray exposition, protein and chromophore conformation still resemble the photoproduct state, except for the D-ring already in 15-Z configuration and tilted out of plane akin the dark state. Due to its formation from the photoproduct, it might be considered an early conformational change initiating the parental state-recovering photocycle. The high quality and the distinct features of the three forms allowed for applying quantum-chemical calculations in the framework of multiscale modeling to rationalize the absorption maxima changes. A systematic analysis of the PCB chromophore in the presence and absence of the protein environment showed that the direct electrostatic effect is negligible on the spectral tuning. However, the protein forces the outer pyrrole rings of the chromophore to deviate from coplanarity, which is identified as the dominating factor for the color regulation.

Expression and Characterization of a Bright Far-red Fluorescent Protein from the Pink-Pigmented Tissues of Porites lobata.

Members of the anthozoan green fluorescent protein (GFP) family display a diversity of photo-physical properties that can be associated with normal and damaged coral tissues. Poritid coral species often exhibit localized pink pigmentation in diseased or damaged tissues. Our spectral and histological analyses of pink-pigmented Porites lobata lesions show co-localization of bright red fluorescence with putative amoebocytes concentrating in the epidermis, suggesting an activated innate immune response. Here we report the cloning, expression, and characterization of a novel red fluorescent protein (plobRFP) from the pink-pigmented tissues associated with lesions on Porites lobata. In vitro, the recombinant plobRFP exhibits a distinct red emission signal of 614 nm (excitation maximum: 578 nm), making plobRFP the furthest red-shifted natural fluorescent protein isolated from a scleractinian coral. The recombinant protein has a high molar extinction coefficient (84,000 M-1 cm-1) and quantum yield (0.74), conferring a notable brightness to plobRFP. Sequence analysis suggests the distinct brightness and marked red shift may be inherent features of plobRFP's chromophore conformation. While plobRFP displays a tendency to aggregate, its high pH stability, photostability, and spectral properties make it a candidate for cell imaging applications and a potential template for engineering optimized RFPs. The association of plobRFP with a possible immune response furthers its potential use as a visual diagnostic and molecular biomarker for monitoring coral health.

Phylogenetic and crystallographic analysis of Nostoc phycocyanin having blue-shifted spectral properties

The distinct sequence feature and spectral blue-shift (~10 nm) of phycocyanin, isolated from Nostoc sp. R76DM (N-PC), were investigated by phylogenetic and crystallographic analyses. Twelve conserved substitutions in N-PC sequence were found distributed unequally among α- and β-subunit (3 in α- and 9 in β-subunit). The phylogenetic analysis suggested that molecular evolution of α- and β-subunit of Nostoc-phycocyanin is faster than evolution of Nostoc-species. The divergence events seem to have occurred more frequently in β-subunit, compared to α-subunit (relative divergence, 7.38 for α-subunit and 9.66 for β-subunit). Crystal structure of N-PC was solved at 2.35 Å resolution to reasonable R-factors (Rwork/RFree = 0.199/0.248). Substitutions congregate near interface of two αβ-monomer in N-PC trimer and are of compensatory nature. Six of the substitutions in β-subunit may be involved in maintaining topology of β-subunit, one in inter-monomer interaction and one in interaction with linker-protein. The β153Cys-attached chromophore adopts high-energy conformational state resulting due to reduced coplanarity of B- and C-pyrrole rings. Distortion in chromophore conformation can result in blue-shift in N-PC spectral properties. N-PC showed significant in-vitro and in-vivo antioxidant activity comparable with other phycocyanin. Since Nostoc-species constitute a distinct phylogenetic clade, the present structure would provide a better template to build a model for phycocyanins of these species.

Crystal structure of the blue fluorescent protein with a Leu-Leu-Gly tri-peptide chromophore derived from the purple chromoprotein of Stichodactyla haddoni.

Chromoproteins are a good source of engineered biological tools. We previously reported the development of a blue fluorescent protein, termed shBFP, which was derived from a purple chromoprotein shCP found in the sea anemone Stichodacyla haddoni. shBFP contains a Leu63-Leu64-Gly65 tri-peptide chromophore, and shows maximum excitation and emission wavelengths at 401 nm and 458 nm, along with a high quantum yield. How this chromophore endows shBFP with the unique fluorescence property in the absence of a hydroxyphenyl ring remained unclear. Here, we present the crystal structures of shCP and shBFP at 1.9- and 2.05-Å resolution, respectively. Both proteins crystallized as similar tetramers, but they are more likely to function as dimers in solution. The chromophore in shCP shows a trans-conformation and its non-planarity is similar to most other homologues. The shBFP chromophore also contains an imidazolidone moiety in its structure, but there are a smaller number of conjugated double bonds compared to shCP. Consequently, the chromophore may prefer absorbing shorter wavelength lights in the UV region, followed by the emission of blue fluorescence. These observations provide new insights into the molecular basis that correlates chromophore conformation with light absorption and fluorescence emission for the development of improved biomarkers.

Influence of the Protein Environment on the Electronic Excitation of Chromophores in the Phycoerythrin 545 Light-Harvesting Complex: A Combined MD-QM/MM Method with Polarized Protein-Specific Charge Scheme.

To gain better insight into how the fluctuating protein environment influences the site energy ordering of the chromophores in PE545 light-harvesting antenna system, we carried out quantum mechanics/molecular mechanics (QM/MM) calculations along the molecular dynamics (MD) trajectory. The Polarized Protein-Specific Charge (PPC) scheme was adopted in both the MD simulation and the QM/MM calculations for a more realistic description of the protein environment. The deduced site energy ladder calculated using ZINDO/S-CIS agrees well with the best model extracted from experiments by a simultaneous fit of the steady-state spectra and transient absorption spectra. Three combinations of charge schemes were compared to elucidate how the protein environment modulates the site energy of chromophores. The result indicates that the multiroles that the protein environment is playing, for instance, by fine-tuning of the conformation of chromophores or by specific pigment-protein interactions, are both crucial for site energy arrangement. Furthermore, we investigated the effects of individual environments and found that the polar residues and water molecules contribute most to the energy shifts.

Side Methyl Groups Control the Conformation and Contribute to Symmetry Breaking of Isoprenoid Chromophores.

Ab initio DFT computations reveal that the essential structural and photophysical features of the conjugated π-electron system of retinal and carotenoids are dictated by "innocent" methyl substituents. These methyl groups shape the conformation and symmetry of the isoprenoid chromophores by causing a sigmoidal distortion of the polyene skeleton and increasing its flexibility, which facilitates fitting to their binding pockets in proteins. Comparison of in vacuo conformations of the chromophores with their native (protein-bound) conformations showed, surprisingly, that the peripheral groups and interactions with the protein environment are much less significant than the methyl side groups in tuning their structural features. The methyl side groups also contribute to a loss of symmetry elements specific to linear polyenes. In effect, the symmetry-imposed restrictions on the chromophore electronic properties are disabled, which is of tremendous relevance to their photophysics. This is evidenced by their non-negligible permanent dipole moments and by the simulated and experimentally measured circular dichroism spectra, which necessarily reflect the chirality of the conjugated π-electron system.

Side Methyl Groups Control the Conformation and Contribute to Symmetry Breaking of Isoprenoid Chromophores

AbstractAb initio DFT computations reveal that the essential structural and photophysical features of the conjugated π‐electron system of retinal and carotenoids are dictated by “innocent” methyl substituents. These methyl groups shape the conformation and symmetry of the isoprenoid chromophores by causing a sigmoidal distortion of the polyene skeleton and increasing its flexibility, which facilitates fitting to their binding pockets in proteins. Comparison of in vacuo conformations of the chromophores with their native (protein‐bound) conformations showed, surprisingly, that the peripheral groups and interactions with the protein environment are much less significant than the methyl side groups in tuning their structural features. The methyl side groups also contribute to a loss of symmetry elements specific to linear polyenes. In effect, the symmetry‐imposed restrictions on the chromophore electronic properties are disabled, which is of tremendous relevance to their photophysics. This is evidenced by their non‐negligible permanent dipole moments and by the simulated and experimentally measured circular dichroism spectra, which necessarily reflect the chirality of the conjugated π‐electron system.

X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature.

The photochromic fluorescent protein Skylan-NS (Nonlinear Structured illumination variant mEos3.1H62L) is a reversibly photoswitchable fluorescent protein which has an unilluminated/ground state with an anionic and cis chromophore conformation and high fluorescence quantum yield. Photo-conversion with illumination at 515 nm generates a meta-stable intermediate with neutral trans-chromophore structure that has a 4 h lifetime. We present X-ray crystal structures of the cis (on) state at 1.9 Angstrom resolution and the trans (off) state at a limiting resolution of 1.55 Angstrom from serial femtosecond crystallography experiments conducted at SPring-8 Angstrom Compact Free Electron Laser (SACLA) at 7.0 keV and 10.5 keV, and at Linac Coherent Light Source (LCLS) at 9.5 keV. We present a comparison of the data reduction and structure determination statistics for the two facilities which differ in flux, beam characteristics and detector technologies. Furthermore, a comparison of droplet on demand, grease injection and Gas Dynamic Virtual Nozzle (GDVN) injection shows no significant differences in limiting resolution. The photoconversion of the on- to the off-state includes both internal and surface exposed protein structural changes, occurring in regions that lack crystal contacts in the orthorhombic crystal form.

Chiral dialkyl ditellurides: Conformation of chiral chromophore by circular dichroism and DFT calculation.

The twisted structure of ditellurides, in a similar way as in other dichalcogenes, leads to different absorption of circularly polarized light by quasi-enantiomeric chiral orbitals. Chiral optically active ditellurides are not common compounds and this phenomenon is not widely reported. As chiral ditellurides found an application in asymmetric synthesis, their molecular structure, understood as their conformation, became an important factor for understanding their reactivity. Until now there are few examples of chiral ditellurides known and their structure was not analyzed in details. This article presents the results of our most recent research on the structure of chiral ditellurides investigated by electronic circular spectroscopy (ECD) supported by quantum-chemical calculation. This enables us to suggest a relationship between chirality of alkyl substituent and chirality (conformation) of ditelluride.

Raman Optical Activity Reveals Carotenoid Photoactivation Events in the Orange Carotenoid Protein in Solution.

The orange carotenoid protein (OCP) plays an important role in photoprotection in cyanobacteria, which is achieved by the photoconversion from the orange dark state (OCPO) to the red active state (OCPR). Using Raman optical activity (ROA), we studied the conformations of the carotenoid chromophore in the active sites of OCPO and OCPR. This ROA measurement directly observed the chromophore conformation of native OCP in solution, and the measurement of OCPR first demonstrated the ROA spectroscopy for the transient species. For OCPO, the spectral features of ROA were mostly reproduced by the quantum chemical calculation based on the crystal structure of the OCP. Within the spatial resolution (∼2 Å), a slight modification of the polyene-chain distortion improved the agreement between the observed and calculated ROA spectra. While the crystal structure of OCPR is not available, the ROA spectrum of OCPR was reproduced by using the crystal structure of red carotenoid protein (RCP), an OCPR proxy. The present results showed that the chromophore conformations in the crystal structures of OCP and RCP hold true for OCPO and OCPR in solution. Particularly, ROA spectroscopy of the native OCPR provides a direct support for the 12 Å translocation of chromophore in the photoactivation, which was proposed by X-ray crystallography using RCP [R. L. Leverenz, M. Sutter, et al. Science 2015, 348, 1463-1466].

Structural and functional investigation of allophycocyanin trimer

Nature has been developing and optimizing photosynthesis billions years, including green plants, algae, photosynthetic bacteria and cyanobacteria. Phycobiliproteins system, as the phycobilisomes, in cyanobacteria and red algae is the one of two major light-harvesting systems, after evolution in billions years. Allophycocyanin (APC) trimer is a primary composition of phycobilisomes core for efficient lower-energy photons funneling pathway. In 2009, Liu et al. have firstly assembled the highly soluble self-assembled recombinant APC trimer with N-terminus polyhistidine, which the entire biosynthesis pathway of APC trimer was reconstituted in Escherichia coli strain with the full-length genes of apoprotein α subunit and β subunit from Synechocystis sp. PCC 6803. The recombinant APC trimer was used to be the subject in this research. An optimum protocol with immobilized metal-ion affinity chromatography with chelating transition metal ion (Ni2+) was used to purify the recombinant protein. Then, the second purification was performed to obtain APC trimer with a higher purity ( A 650/ A 620=1.346), using density gradient centrifugation. Single molecules of recombinant APC trimers were investigated with atomic force microscopy. Three-dimensional images with resolution at nanoscale indicated that the recombinant allophycocyanin trimers were approximately 1.5 nm in short axis, and 15 nm in long axis, which were in accordance with the sizes of natural allophycocyanin trimer measured by transmission electron microscopy or X-ray crystallography. Moreover, the correct conformation of recombinant allophycocyanin trimer was confirmed by fluorescence spectra (studied energy transfer ability), absorption spectra (studied the light-harvesting ability), and circular dichroism (CD) spectra (studied changes of secondary structure and aggregation state). The CD spectra of recombinant allophycocyanin induced by a wide range of pH were analyzed both at wavelengths in ultraviolet range (190–250 nm) and visible range (450–750 nm). The α -helices were the dominant secondary structure in recombinant allophycocyanin trimer by analysis of CD spectra in ultraviolet range, while the analysis of CD spectra in visible range suggested the existence of exciton-coupled pairs of phycocyanobilins, in which the energy transfer was mainly in the form of exciton splitting. By studying its spectra property variations in response to pH changes, we found that recombinant APC trimer showed good absorbance and fluorescence stability at varying pH. The conformation of chromophores in recombinant APC trimer was relatively stable, between the range of pH 4–9, which was revealed by the stable absorption and fluorescence spectra properties of recombinant APC trimer. The trimeric structure of recombinant APC was maintained while local variations of protein peptides were also shown in response to the environmental disturbance. Beyond this pH range, secondary structure as well as overall conformation of recombinant APC dramatically changed, and the energy absorption and transfer ability were also disrupted. This work demonstrated that correct function in energy transfer was retained in the recombinant allophycocyanin trimer compared with nature allophycocyanin trimer.

An Experimental and Molecular Dynamics Study of Red Fluorescent Protein mCherry in Novel Aqueous Amino Acid Ionic Liquids.

The search for biocompatible ionic liquids (ILs) with novel biochemical and biomedical applications has recently gained greater attention. In this report, we characterize the effects of two novel amino acid-based aqueous ILs composed of tetramethylguanidinium (TMG) and amino acids on the structure and stability of a widely used red fluorescent protein (mCherry). Our experimental data shows that while the aspartic acid-based IL (TMGAsp) has effects similar to previously studied conventional ILs (BMIBF4, EMIAc, and TMGAc), the alanine-based IL (TMGAla) has a much stronger destabilization effect on the protein structure. Addition of 0.30 M TMGAla to mCherry decreases the unfolding temperature from 83 to 60 °C. Even at 25 °C, TMGAla results in a blue shift of the mCherry absorbance and fluorescence peaks and an increased Stokes shift. Molecular dynamics simulations show that the chromophore conformation and its interaction with mCherry with TMGAla are changed relative to those with TMGAsp or in the absence of ILs. Protein-ILs contact analysis indicates that the mCherry-Asp interactions are hydrophilic but the (fewer) mCherry-Ala interactions are more hydrophobic and may modulate the TMG interaction with the protein. Hence, the anion hydrophobicity may explain the special TMGAla destabilization of mCherry.

Activation of GPCR Rhodopsin Investigated by Solid-State NMR Spectroscopy

Rhodopsin is the G-protein-coupled receptor (GPCR) responsible for scotopic vision in vertebrates. Although published X-ray structures are similar, the conformation and orientation of the retinal chromophore of active rhodopsin are not established unambiguously. Under debate is a proposed flip of all-trans retinal in the active state, due to a change of the roll angle of the β-ionone ring, as well as the central part of the polyene chain that includes the C9-Me group [1]. Here we applied solid-state 2H NMR spectroscopy to study the structure and orientation of the retinylidene ligand in the active state of rhodopsin in aligned membranes [2].

Resolving Electronic Transitions in Synthetic Fluorescent Protein Chromophores by Magnetic Circular Dichroism.

The detailed electronic structures of fluorescent chromophores are important for their use in imaging of living cells. A series of green fluorescent protein chromophore derivatives is examined by magnetic circular dichroism (MCD) spectroscopy, which allows the resolution of more bands than plain absorption and fluorescence. Observed spectral patterns are rationalized with the aid of time-dependent density functional theory (TDDFT) computations and the sum-over-state (SOS) formalism, which also reveals a significant dependence of MCD intensities on chromophore conformation. The combination of organic and theoretical chemistry with spectroscopic techniques also appears useful in the rational design of fluorescence labels and understanding of the chromophore's properties. For example, the absorption threshold can be heavily affected by substitution on the phenyl ring but not much on the five-member ring, and methoxy groups can be used to further tune the electronic levels.

Crystal structure analysis of phycocyanin from chromatically adapted Phormidium rubidum A09DM

Structural and sequence analyses ofPhormidium phycocyaninrevealed three co-evolving residues that determine the conformation of a phycocyanobilin chromophore believed to play role in alternate pathways for intra and inter-rod energy transfer.

Spectroscopic studies of different poly3hexylthiophene chain environments in a polyfluorene matrix

Optical properties of blends made of poly(9,9-dioctyl-fluorene-2,7-diyl) (PFO) and poly(3-hexylthiophene-2,5-diyl) (P3HT) were investigated and compared to those of poly(9,9-dioctylfluorene-alt-bithiophene) (F8T2) by steady state optical spectroscopy. In addition to the individual emissions of PFO and P3HT chromophores, the blends composed by these two polymers show a new peak emission around 590nm. The new peak is attributed to well dissolved, “isolated”, P3HT chains dispersed into the PFO matrix. It was observed that the well dissolved P3HT chains are activated by Förster energy transfer, where PFO and P3HT molecules act as a donor and an acceptor, respectively. Further, emission from ordered aggregates of P3HT is clearly observed and the interplay between aggregate and isolate P3HT chains was studied. In contrast to the PFO:P3HT blends, the emission spectra from F8T2 co-polymer show clear interaction in the ground state between the dioctylfluorene and bithiophene monomer-units, giving rise to a wholly new chromophore conformation on the backbone.

The primary photoreaction of channelrhodopsin-1: wavelength dependent photoreactions induced by ground-state heterogeneity.

The primary photodynamics of channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) was investigated by VIS-pump supercontinuum probe experiments from femtoseconds to 100 picoseconds. In contrast to reported experiments on channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2), we found a clear dependence of the photoreaction dynamics on varying the excitation wavelength. Upon excitation at 500 and at 550 nm we detected different bleaching bands, and spectrally distinct photoproduct absorptions in the first picoseconds. We assign the former to the ground-state heterogeneity of a mixture of 13-cis and all-trans retinal maximally absorbing around 480 and 540 nm, respectively. At 550 nm, all-trans retinal of the ground state is almost exclusively excited. Here, we found a fast all-trans to 13-cis isomerization process to a hot and spectrally broad P1 photoproduct with a time constant of (100 ± 50) fs, followed by photoproduct relaxation with time constants of (500 ± 100) fs and (5 ± 1) ps. The remaining fraction relaxes back to the parent ground state with time constants of (500 ± 100) fs and (5 ± 1) ps. Upon excitation at 500 nm a mixture of both chromophore conformations is excited, resulting in overlapping reaction dynamics with additional time constants of <300 fs, (1.8 ± 0.3) ps and (90 ± 25) ps. A new photoproduct Q is formed absorbing at around 600 nm. Strong coherent oscillatory signals were found pertaining up to several picoseconds. We determined low frequency modes around 200 cm−1, similar to those reported for bacteriorhodopsin.