The chromophore of pholasin: A highly luminescent protein

Pholasin is the photoprotein extracted from the marine bivalve Pholas dactylus. It undergoes an oxidative chemiluminescent reaction to oxypholasin with superoxide anion, hypochlorite, peroxidases and other oxidants. Since the observed absorbance and chemiluminescent emission spectra of pholasin solutions cannot be brought about solely by the amino acids composing the protein, there has to be a chemiluminescent chromophore. However, little is known about the chemical nature of this molecule. This work seeks to identify the chemical structure of the luminescent prosthetic group of pholasin. Pholasin could not be reactivated using chromophores from the hydroid Obelia geniculata (coelenterazine) and from the ostracod shrimp Vargula (formerly Cypridina) hilgendorfi. Furthermore, the reaction product of the Vargula chromophore could not be detected in solutions containing oxypholasin. Fluorescence analysis of such a solution revealed a compound with an emission spectrum (γ_max 480 nm; excitation at 320 nm), resembling the emission spectrum of the chemiluminescent reaction. This fluorescent substance was separated by gel filtration. It exhibited an apparent molecular mass of < 2000. Fluorescence masurements of extracts of partially purified pholasin suggested that a flavin moiety may be involved in pholasin luminescence.     

The structure of a far‐red fluorescent protein,AQ143, shows evidence in support of reported red‐shifting chromophore interactions

Engineering fluorescent proteins (FPs) to emit light at longer wavelengths is a significant focus in the development of the next generation of fluorescent biomarkers, as far‐red light penetrates tissue with minimal absorption, allowing better imaging inside of biological hosts. Structure‐guided design and directed evolution have led to the discovery of red FPs with significant bathochromic shifts to their emission. Here, we present the crystal structure of one of the most bathochromically shifted FPs reported to date, AQ143, a nine‐point mutant of aeCP597, a chromoprotein from Actinia equina. The 2.19 Å resolution structure reveals several important chromophore interactions that contribute to the protein's far‐red emission and shows dual occupancy of the green and red chromophores.     

Molecular docking of novel donor–π–acceptor dicyanomethylenedihydrofuran-based fluorescent chromophores

A series of donor–π–acceptor dicyanomethylenedihydrofuran (DCDHF)-based chromophores comprising different π-aryl bridges and different terminal groups was synthesized and characterized. The chromophores were synthesized via Knoevenagel condensation of the active methyl-bearing DCDHF (electron acceptor) with a tertiary amine-containing arylaldehyde (electron donor) in dry pyridine at room temperature in the presence of a few drops of acetic acid. The synthesis approach involved the development of phenyl(thienyl)vinyl-bridged dicyanomethylenedihydrofuran dyes with a tertiary amine terminal group. Both absorption and emission spectra were explored. The strong emission properties detected using the synthesized chromophores could be attributed to intramolecular charge transfer. The chemical structures of the synthesized chromophores were verified using ¹H/¹³C nuclear magnetic resonance and Fourier transform infrared spectroscopy. Both tertiary amine-containing and arylaldehyde groups were found to influence the biological properties of the synthesized chromophores. The synthesized (DCDHF)-based hybrids were tested to examine antibacterial effectiveness. Derivatives 1 and 2 demonstrated activity towards Gram-positive bacteria rather than Gram-negative bacteria when compared with an amoxicillin antibiotic reference. Finally, molecular docking inspiration was undertaken to determine their binding relationships (PDB code: 1LNZ).     

Some optical properties of carrier ampholytes for isoelectric focusing.

Some optical properties of carrier ampholytes are herewith described. Newly synthesized Ampholines do not possess asymmetric carbon atoms. pH 3–5 and pH 8–10 ranges, synthesized before 1970, rotate the plane of polarized light since they were “reinforced” with glutamic and aspartic acid, in the acidic side, and lysine in the basic region.The various pH ranges possess characteristic chromophores, whose absorbance is strongly pH dependent. These chromophores, when excited at appropriate wavelengths, exhibit a fluorescence emission spectrum, typically reproducing the pH dependence of the corresponding uv spectra.The optical properties here described can be useful in studying Ampholinesmacromolecules interactions. Due to the widespread use of optical scanning in situ of focusing systems, care has to be taken not to mistake Ampholine peaks at 285, 310, 315, 340, and 365 nm for the substance under study.     

Structure and function of the photosynthetic reaction center fromRhodobacter sphaeroides

The three-dimensional structure of the photosynthetic reaction center fromRhodobacter sphaeroides is described. The reaction center is a transmembrane protein that converts light into chemical energy. The protein has three subunits: L, M, and H. The mostly helical L and M subunits provide the scaffolding and the finely tuned environment in which the chromophores carry out electron transfer. The details of the protein-chromophore interactions are from studies of a trigonal crystal form that diffracted to 2.65-Å resolution. Functional studies of the multi-subunit complex by site-specific replacement of key amino acid residues are summarized in the context of the molecular structure.This work was supported in part by the U.S. Department of Energy, Office of Health and Environmental Research, under Contract No. W-31-109-ENG-38 and by Public Health Service Grant GM36598.     

Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation

Protein photoreceptors use small-molecule cofactors called chromophores to detect light. Only under the influence of the receptors' active sites do these chromophores adopt spectral and photochemical properties that suit the receptors' functional requirements. This protein-induced change in chromophore properties is called photochemical tuning and is a prime example for the general--but poorly understood--process of chemical tuning through which proteins shape the reactivity of their active-site groups. Here we report the 0.82-A resolution X-ray structure of the bacterial light receptor photoactive yellow protein (PYP). The unusually precise structure reveals deviations from expected molecular geometries and anisotropic atomic displacements in the PYP active site. Our analysis of these deviations points directly to the intramolecular forces and active-site dynamics that tune the properties of PYP's chromophore to absorb blue light, suppress fluorescence, and favor the required light-driven double-bond isomerization.     

Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy

Cryptophyte algae differ from cyanobacteria and red algae in the architecture of their photosynthetic light harvesting systems, even though all three are evolutionarily related. Central to cryptophyte light harvesting is the soluble antenna protein phycoerythrin 545 (PE545). The ultrahigh resolution crystal structure of PE545, isolated from a unicellular cryptophyte Rhodomonas CS24, is reported at both 1.1A and 0.97A resolution, revealing details of the conformation and environments of the chromophores. Absorption, emission and polarized steady state spectroscopy (298K, 77K), as well as ultrafast (20fs time resolution) measurements of population dynamics are reported. Coupled with complementary quantum chemical calculations of electronic transitions of the bilins, these enable assignment of spectral absorption characteristics to each chromophore in the structure. Spectral differences between the tetrapyrrole pigments due to chemical differences between bilins, as well as their binding and interaction with the local protein environment are described. Based on these assignments, and considering customized optical properties such as strong coupling, a model for light harvesting by PE545 is developed which explains the fast, directional harvesting of excitation energy. The excitation energy is funnelled from four peripheral pigments (beta158,beta82) into a central chromophore dimer (beta50/beta61) in approximately 1ps. Those chromophores, in turn, transfer the excitation energy to the red absorbing molecules located at the periphery of the complex in approximately 4ps. A final resonance energy transfer step sensitizes just one of the alpha19 bilins on a time scale of 22ps. Furthermore, it is concluded that binding of PE545 to the thylakoid membrane is not essential for efficient energy transfer to the integral membrane chlorophyll a-containing complexes associated with PS-II.     

Aspects of Light Production by Photobacterium fischeri

Studies of luminescence in growing cultures of Photobacterium fischeri revealed the characteristic kinetics of light emission, including a minimal phase of bacterial light output. A dialyzable substance present in the nutrient broth medium caused this transient inhibition in light production, although this substance did not affect culture growth. Experiments were carried out to determine the mechanism of action and the chemical properties of the inhibitor. The results suggest that the inhibitor may be binding directly to the luciferase molecules.     

Expansion of bilin-based red light sensors in the subaerial desert cyanobacterium Nostoc flagelliforme

Light is the crucial environmental signal for desiccation-tolerant cyanobacteria to activate photosynthesis and prepare for desiccation at dawn. However, the photobiological characteristics of desert cyanobacteria adaptation to one of the harshest habitats on Earth remain unresolved. In this study, we surveyed the genome of a subaerial desert cyanobacterium Nostoc flagelliforme and identified two phytochromes and seven cyanobacteriochromes (CBCRs) with one or more bilin-binding GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) domains. Biochemical and spectroscopic analyses of 69 purified GAF-containing proteins from recombinant phycocyanobilin (PCB), biliverdin or phycoerythrobilin-producing Escherichia coli indicated that nine of these proteins bind chromophores. Further investigation revealed that 11 GAFs form covalent adducts responsive to near-UV and visible light: eight GAFs contained PCB chromophores, three GAFs contained biliverdin chromophores and one contained the PCB isomer, phycoviolobilin. Interestingly, COO91_03972 is the first-ever reported GAF-only CBCR capable of sensing five wavelengths of light. Bioinformatics and biochemical analyses revealed that residue P132 of COO91_03972 is essential for chromophore binding to dual-cysteine CBCRs. Furthermore, the complement of N. flagelliforme CBCRs is enriched in red light sensors. We hypothesize that these sensors are critical for the acclimatization of N. flagelliforme to weak light environments at dawn.     

Chemistries and colors of bioluminescent reactions: a review

Many different organisms, ranging from bacteria and fungi to fireflies and fish, are endowed with the ability to emit light, but the bioluminescent systems are not evolutionarily conserved: genes coding for the luciferase proteins (Lase) are not homologous, and the luciferins are also different, falling into many unrelated chemical classes. Biochemically, all known Lase are oxygenases that utilize molecular oxygen to oxidize a substrate (a luciferin; literally the ‘light-bearing’ molecule), with formation of a product molecule in an electronically excited state. The color of the light may differ, even though the same luciferin/Lase system underlies the reaction. Filters or differences in Lase structure are responsible in some cases; in others a secondary emitter associated with a second protein is involved. In the coelenterates a green fluorescent protein, whose chromophore is derived from the primary amino-acid sequence, results in a red shift of the emission. In the bacteria accessory proteins causing either blue- or red-shifts have been isolated from different species; the chromophores are noncovalently bound. Although radiationless energy transfer has been implicated in the excitation of such accessory emitters, this may not be so in all cases.     

Presence of a class of chromophores as monitor of oxygen-linked conformational changes in hemocyanins

Summary Oxygenation of native hemocyanins fromHelix pomatia andPanulirus interruptus under conditions of cooperative binding, causes a change in the dynamic behaviour of the internal structure, leading to increased rotational mobility of a class of tryptophan residues emitting above 450 nm. This is associated with the complete depolarization of the emission on a time scale where the large hemocyanin is practically immobile. This class is thought to be very near the active site since it is strongly affected by the copper atoms. Moreover, fluorescence changes of the class of chromophores emitting above 450 nm is more marked in the molluscanHelix hemocyanin than in the arthropodanPanulirus hemocyanin, suggesting a possible difference in the structure of the active site or in the extent of the allosteric transition between the two species. This class of chromophores may by useful probes to monitor ligand-linked conformational change in hemocyanins.     

Photoinhibition and its wavelength dependence in the cyanobacterium Anabaena variabilis

In the cyanobacterium Anabaena variabilis the dependence of photoinhibition on fluence rate, duration and wavelength of irradiation were studied by measurements of oxygen production and fluorescence emission spectra. The analysis of the photosynthetic activity revealed that photoinhibition affects exclusively photosystem II (PS II), whereas photosystem I (PS I) remained largely unimpaired. Furthermore, PS II fluorescence emission decreased much faster in bleached than in unbleached controls.Studying the wavelength dependence of photoinhibition it was found that only radiation between 520 and 680 nm causes photoinhibition. This is about the same range of wavelengths which causes photobleaching. Fluorescence emission spectra of samples exposed to high fluence rates of 582 and 662 nm, respectively, essentially agree with those samples exposed to high fluence rates of white light, whereas the fluorescence emission spectra of samples exposed to blue light resemble those exposed to dim white light.NaN₃, a substance which prevents photobleaching, inhibits the photosynthetic O₂ production of Anabaena and, hence, enhances the photoinhibitory effect.     

Synthesis and properties of chromophores of fluorescent proteins

We describe the existing approaches to the synthesis of 5-arylidene-3,5-dihydro-4 H-imidazol-4-ones—model chromophores of fluorescent proteins and their nonnatural analogs. We discuss in detail the chemical (acid-base and redox reactions, cis-trans isomery, etc.) and spectral properties of the chromophores and the influence of substitutes and the environment. The study of synthetic chromophores allows for modeling of the photophysical characteristics of fluorescent proteins.     

Dyakia bioluminescence—1. Bioluminescence and fluorescence spectra of the land snail,D. striata

The luminescent land snail Dyakia striata displayed a bioluminescence spectrum with a maximum wavelength of 515 nm. A green fluorescent substance extracted from the photogenic organ of an adult snail had a similar wavelength maximum but its fluorescence spectrum differed from that of flavin chromophore substances involved in light emission in some other luminescent organisms.     

Fluorometric Characterization of Two Picocyanobacteria Strains from Lakes of Different Underwater Light Quality

Unicellular autofluorescent picoplankton ranging from 0.6 to 0.9 ym in diameter were isolated from Lake Maggiore and from Lake Balaton. The cyanobacterial isolates contain two accessory pigments: phycoerythrin (PE) and phycocyanin (PC) respectively. The in vivo spectral properties of the two clones were compared to identify characteristics of the pigments. In vivo fluorescence excitation and emission spectra revealed that clones with PE are composed only of phycoerythrobilin chromophores and lack phycourobilin. Glycerol treatment enhances the fluorescence yield up to 3 times and improves the detection sensitivity of PE particularly at 436 and 520 nm and of PC at 600 nm. The vertical profiles of the underwater irradiance at different wavelengths were measured in both lakes to study the light quality of the natural environment of the two strains. Growth rates of both clones growing at different light intensities and wavelengths, selected by the same filters used for vertical profiles, were estimated. The results showed a difference in growth rate of phycoerythrin and phycocyanin containing cells exposed to an equal quantum flux of preferential illumination. In particular the maximum growth rate was reached by PE cells exposed to green light and by PC cells exposed to red light.     

Time-resolved fluorescence studies of dityrosine in the outer layer of intact yeast ascospores.

The (time-resolved) fluorescence properties of dityrosine in the outermost layer of the spore wall of Saccharomyces cerevisiae were investigated. Steady-state spectra revealed an emission maximum at 404 nm and a corresponding excitation maximum at 326 nm. The relative fluorescence quantum yield decreased with increasing proton concentration. The fluorescence decay of yeast spores was found to be nonexponential and differed pronouncedly from that of unbound dityrosine in water. Analysis of the spore decay recorded at lambda ex = 323 nm and lambda em = 404 nm by an exponential series (ESM) algorithm revealed a bimodal lifetime distribution with maxima centered at tau 1C = 0.5 ns and tau 2C = 2.6 ns. The relative amplitudes of the two distributions are shown to depend on the emission wavelength, indicating contributions from spectrally different dityrosine chromophores. On quenching the spore fluorescence with acrylamide, a downward curvature of the Stern-Volmer plot was obtained. A multitude of chromophores more or less shielded from solvent in the spore wall is proposed to account for the nonlinear quenching of the total spore fluorescence. Analysis of the fluorescence anisotropy decay revealed two rotational correlation times (phi 1 = 0.9 ns and phi 2 = 30.6 ns) or a bimodal distribution of rotational correlation times (centers at 0.7 ns and 40 ns) when the data were analyzed by the maximum entropy method (MEM). We present a model that accounts for the differences between unbound (aqueous) and bound (incorporated in the spore wall) dityrosine fluorescence. The main feature of the photophysical model for yeast spores is the presence of at least two species of dityrosine chromophores differing in their chemical environments. A hypothetical photobiological role of these fluorophores in the spore wall is discussed: the protection of the spore genome from mutagenic UV light.     

Structural studies show energy transfer within stabilized phycobilisomes independent of the mode of rod–core assembly

The major light harvesting complex in cyanobacteria and red algae is the phycobilisome (PBS), comprised of hundreds of seemingly similar chromophores, which are protein bound and assembled in a fashion that enables highly efficient uni-directional energy transfer to reaction centers. The PBS is comprised of a core containing 2–5 cylinders surrounded by 6–8 rods, and a number of models have been proposed describing the PBS structure. One of the most critical steps in the functionality of the PBS is energy transfer from the rod substructures to the core substructure. In this study we compare the structural and functional characteristics of high-phosphate stabilized PBS (the standard fashion of stabilization of isolated complexes) with cross-linked PBS in low ionic strength buffer from two cyanobacterial species, Thermosynechococcus vulcanus and Acaryochloris marina. We show that chemical cross-linking preserves efficient energy transfer from the phycocyanin containing rods to the allophycocyanin containing cores with fluorescent emission from the terminal emitters. However, this energy transfer is shown to exist in PBS complexes of different structures as characterized by determination of a 2.4 Å structure by X-ray crystallography, single crystal confocal microscopy, mass spectrometry and transmission electron microscopy of negatively stained and cryogenically preserved complexes. We conclude that the PBS has intrinsic structural properties that enable efficient energy transfer from rod substructures to the core substructures without requiring a single unique structure. We discuss the significance of our observations on the functionality of the PBS in vivo.     

Ultrafast light harvesting dynamics in the cryptophyte phycocyanin 645.

Steady-state and femtosecond time-resolved optical methods have been used to study spectroscopic features and energy transfer dynamics in the soluble antenna protein phycocyanin 645 (PC645), isolated from a unicellular cryptophyte Chroomonas CCMP270. Absorption, emission and polarization measurements as well as one-colour pump-probe traces are reported in combination with complementary quantum chemical calculations of electronic transitions of the bilins. Estimation of bilin spectral positions and energy transfer rates aids in the development of a model for light harvesting by PC645. At higher photon energies light is absorbed by the centrally located dimer (DBV, beta50/beta61) and the excitation is subsequently funneled through a complex interference of pathways to four peripheral pigments (MBV alpha19, PCB beta158). Those chromophores transfer the excitation energy to the red-most bilins (PCB beta82). We suggest that the final resonance energy transfer step occurs between the PCB 82 bilins on a timescale estimated to be approximately 15 ps. Such a rapid final energy transfer step cannot be rationalized by calculations that combine experimental parameters and quantum chemical calculations, which predict the energy transfer time to be 40 ps.     

Functional organization and plasticity of the photosynthetic unit of the cyanobacterium Anacystis nidulans

Anacystis nidulans grown under high and low light, 100 and 10 μE m^?2 s^?1, respectively, was analyzed with respect to chlorophyll/P700, phycobiliproteins/P700, chlorophyll/cell, and oxygen evolution parameters. The photosynthetic unit sizes of this cyanobacterium, measured as the ratio of total chromophores (chlorophyll and bilin) to P700, were shown to be similar to those of higher plants and green algae. High light grown cells possessed a photosynthetic unit consisting of a core of 157 ± 6 chlorophyll a molecules per P700 associated with a light harvesting system of 95 ± 3.5 biliprotein chromophores. Low light grown cells had substantially more biliprotein chromophores per P700 (125 ± 3.1) than high light cells, but showed no significant difference in the numbers of chlorophyll a molecules per P700 (149 ± 4). Analyses of aqueous biliprotein extracts indicate that low light grown cells produce proportionately more phycocyanin relative to allophycocyanin than high light cells. Calculations of the molecular weight of biliproteins per P700 suggest that there is less than one phycobilisome per reaction center I under both growth conditions. Differences in chlorophyll/cell ratios and oxygen evolution characteristics were also observed. High light cells contain 6.3 × 10^?12 mg chlorophyll cell^?1, while low light grown cells contain 12.8 × 10^?12 mg chlorophyll cell^?1. Photosynthetic oxygen evolution rate vs. light intensity curves indicate that high light grown cells reach maximal levels of oxygen evolution at higher light intensity than low light grown cells. Maximal rates of oxygen evolution were 16.6 μmol oxygen min^?1 (mg chlorophyll)^?1 for high and 8.4 μmol oxygen min^?1 (mg chlorophyll)^?1 for low light cells. Maximal oxygen evolution rates per cell were equivalent for both cell types, although the amount of P700 per cell was lower in high light cells. High light grown cells are therefore capable of producing more oxygen per reaction center I than low light grown cells.