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Photoreceptors, Microbial (2):
Recent article
Photoreceptors, Microbial
Abstract
The present work aims at characterizing the photophysical behavior of a first biomimetic cyclodextrin model (CD-PYP1) of the photoactive site of photoactive yellow protein (PYP). The hydrophobic cyclodextrin cavity in which the chromophore self-includes, mimics its local environment within the prote...
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PMID: 20856983
PDF is available here.
PDF is available here.
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Optics Express (18)20 2010
Abstract
Clean 7.5 fs pulses at 400 nm with less than 3% energy in tiny satellite pulses were obtained by spectral broadening in a hollow fiber and dispersive compensating using a prism pair together with a deformable mirror system. As an example, this stable and clean pulse was used to study the ultrafast p...
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PMID: 20940959
PDF is available here.
PDF is available here.
Abstract
Based on QM/MM calculations using a combination of time-dependent Hartree-Fock and coupled cluster response theory a mechanism is proposed for the photocycle of blue light using flavin (BLUF) domains in the signaling/light adapted conformation. In analogy to the dark-adapted form, a charge transfer...
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PMID: 20532291
PDF is available here.
PDF is available here.
Abstract
We used single particle cryoelectron microscopy to determine the quaternary arrangement of the phytochrome dimer as Pr, using the bacteriophytochrome (BphP) from Deinococcus radiodurans. Contrary to the long-standing view that the two monomers are held together solely via their C-terminal region, we...
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PMID: 20534495
PDF is available here.
PDF is available here.
Abstract
Abstract
We analyzed the role of the BLR photoreceptor complex (BLR1/BLR2) in photoconidiation and the regulation of gene expression. Both responses were dependent on both BLR proteins. Analyses of Deltablr1, Deltablr2 and Deltaenv1 mutants showed that the BLR proteins regulate growth under illumination. Ana...
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PMID: 20144726
PDF is available here.
PDF is available here.
Abstract
We use resonance Raman intensity analysis to calculate the vibronic absorption profile of cyanobacterial phytochrome Cph1 and show that this shoulder feature is due simply to vibronic transitions from a single species, thus reflecting a homogeneous ground-state population....
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PMID: 19739629
PDF is available here.
PDF is available here.
Abstract
We have performed excited-state dynamics simulations of a Photoactive Yellow Protein chromophore analogue in water. The results of the simulations demonstrate that in water the chromophore predominantly undergoes single-bond photoisomerization, rather than double-bond photoisomerization. Despite opp...
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PMID: 19728705
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (113)35 2009
Abstract
We used a 565 nm pump pulse to initiate the BR photocycle and two kinds of probe pulses with wavelengths of 225 and 238 nm to detect spectral changes in the tryptophan and tyrosine bands, respectively. The observed spectral changes of the Raman bands are most likely due to tryptophan and tyrosine re...
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PMID: 19678662
PDF is available here.
PDF is available here.
Abstract
Journal of Molecular Biology (386)5 2009
Abstract
These results demonstrated that only the decamer state is responsible for the conformational change. The results may suggest that the oligomeric state is functionally important in the signal transduction of this photosensory protein....
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PMID: 19452599
PDF is available here.
PDF is available here.
Current Genetics (55)1 2009
Abstract
Most flagellate green algae exhibiting phototaxis posses a singular specialized light sensitive organelle, the eyespot apparatus (EA). Its design principles are similar in all green algae and produce, in conjunction with the movement pattern of the cell, a highly directional optical device. It enabl...
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PMID: 19107486
PDF is available here.
PDF is available here.
Biochemistry (Washington) (47)52 2008
Abstract
We report high-throughput microscale methods for the purification and spectroscopic investigation of PYP and use these to examine the role of active site residue Glu46 in PYP, which is hydrogen bonded to the pCA anion. The functional and structural attributes of the 19 substitution mutants of PYP at...
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PMID: 19102703
PDF is available here.
PDF is available here.
Protein Science (17)12 2008
Abstract
We analyzed both fast and slow phases of the last-step photocycle in PYP. From the analysis of the denaturant dependence of the fast and slow phases, we found that the last-step photocycle proceeds through parallel channels of the folding pathway. The burial of the solvent-accessible area was respon...
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PMID: 18794212
PDF is available here.
PDF is available here.
Biophysical Journal (95)10 2008
Abstract
BLUF domains constitute a recently discovered class of photoreceptor proteins found in bacteria and eukaryotic algae. BLUF domains are blue-light sensitive through a FAD cofactor that is involved in an extensive hydrogen-bond network with nearby amino acid side chains, including a highly conserved t...
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PMID: 18708458
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)45 2008
Abstract
I calculated E(m) for Tyr-21, flavin, and redox-active Trp-104 and revealed the electron transfer (ET) driving energy. Rotation of the Gln-63 side chain that converts protein conformation from the dark state to the light state is responsible for the decrease of 150 mV in E(m) for Tyr-21, leading to...
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PMID: 18647748
PDF is available here.
PDF is available here.
Abstract
We reported that a benzoic acid derivative, 4-[(5-bromo-4-{[2,4-dioxo-3-(2-oxo-2-phenylethyl)-1,3-thiazolidin-5-ylidene]methyl}-2-ethoxyphenoxy)methyl]benzoic acid (D77) could potently inhibit the IN-LEDGF/p75 interaction and affect the HIV-1 IN nuclear distribution thus exhibiting antiretroviral ac...
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PMID: 18691555
PDF is available here.
PDF is available here.
Abstract
BLUF and LOV are blue-light sensor domains that possess flavin as a common chromophore but exhibit distinct photoreactions. Ile66 located in the BLUF domain of a cyanobacterial photosensor protein, TePixD, was replaced with Cys to mimic the LOV domain. Light-induced Fourier transform infrared spectr...
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PMID: 18774803
PDF is available here.
PDF is available here.
Plant and Cell Physiology (49)10 2008
Abstract
We show that in PixD, Met93, the residue conserved in all BLUF domains, is crucial for light-dependent signal transduction. Specifically, the light-insensitive M93A mutant of PixD revealed biochemical and physiological activities compatible with those of the light-adapted wild-type PixD. However, th...
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PMID: 18772185
PDF is available here.
PDF is available here.
Abstract
On the basis of extensive first-principle calculations within the framework of quantum mechanics/molecular mechanics (QM/MM), a conclusive mechanism for the formation of the signaling state of blue light using flavin (BLUF) domain proteins is proposed which is compatible with the experimental data p...
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PMID: 18722438
PDF is available here.
PDF is available here.
Abstract
The synthesis of novel ortho-coumaric acid derivatives, with an amide group linked with an olefin moiety, which introduced photoinduced switching of the intramolecular hydrogen bonds is presented. An intramolecular OH...O=C hydrogen bond formed in a Z-phenol compound was switched to an intramolecula...
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PMID: 18698471
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (112)30 2008
Abstract
We determined the fluorescence lifetimes of W119 in the I(1) and I (1') intermediates. Two coexisting distinct chromophore structures were proposed for the I(1) photointermediate from time-resolved X-ray diffraction ( Ihee, H., et al. Proc. Natl. Acad. Sci. U.S.A., 2005, 102, 7145 ): one with two hy...
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PMID: 18605685
PDF is available here.
PDF is available here.
Abstract
We isolated the chromophore-binding domain of CcaS from Synechocystis as well as from phycocyanobilin-producing Escherichia coli. Both preparations showed the same reversible photoconversion between a green-absorbing form (Pg, lambda(max) = 535 nm) and a red-absorbing form (Pr, lambda(max) = 672 nm)...
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PMID: 18621684
PDF is available here.
PDF is available here.
Journal of Molecular Biology (380)2 2008
Abstract
We identified singly methylated aspartate-glutamate and alanine-glutamate pairs and doubly methylated glutamate pairs. The largest methylatable regions detected in Htrs comprise six heptads along the coiled coil. One methylated glutamate residue was detected outside of such a region, in the signalin...
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PMID: 18514223
PDF is available here.
PDF is available here.
Abstract
We present atomistic Parallel Tempering (Replica Exchange Molecular Dynamics) simulations of conformational changes occurring during the photo-cycle of PYP. First, we study the signaling state formation of PYP in detail. Our previous simulations have shown that the formation of the signaling state i...
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PMID: 18214984
PDF is available here.
PDF is available here.
Abstract
Knockout mutants of Fusarium oxysporum lacking the putative photoreceptor Wc1 were impaired in aerial hyphae, surface hydrophobicity, light-induced carotenogenesis, photoreactivation after UV treatment, and upregulation of photolyase gene transcription. Infection experiments with tomato plants and i...
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PMID: 18503005
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (112)24 2008
Abstract
We discuss the role of the protein in controlling the absorption spectra of photoactive yellow protein (PYP), the archetype xanthopsin photoreceptor, using quantum mechanics/molecular mechanics (QM/MM) methods based on ab initio multireference perturbation theory, combined with molecular dynamics (M...
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PMID: 18507438
PDF is available here.
PDF is available here.
Abstract
We use the bacterial photoreceptor photoactive yellow protein (PYP) to test if subtle structural changes do, indeed, imply equally subtle functional effects. We flash froze crystals of PYP to trap the protein's conformational ensemble, and probed the molecules in this ensemble for their ability to f...
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PMID: 18547519
PDF is available here.
PDF is available here.
Genetika (Moskva) (44)5 2008
Abstract
The sll0886 gene, controlling light-activated heterotrophic growth (LAHG), was tested for the role in regulating phototaxis in cyanobacterium Synechocystis sp. PCC 6803. Insertional inactivation of the gene in the genome of a wildtype strain did not affect positive (toward light) or negative (away f...
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PMID: 18672807
PDF is available here.
PDF is available here.
Abstract
We cloned the only WC-1-like gene present in the available Fusarium genomes, that we called wcoA. The predicted WcoA polypeptide is highly similar to WC-1 and contains the relevant functional domains of this protein. In contrast to the Neurospora counterpart, wcoA expression is not affected by light...
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PMID: 18203635
PDF is available here.
PDF is available here.
Biophysical Journal (94)9 2008
Abstract
The role of glycine residues was studied by alanine-scanning mutagenesis using photoactive yellow protein, a structural prototype of PER ARNT SIM domain proteins, as a template. Mutation of glycine located close to the end of beta-strands with dihedral angles disallowed for alanine (Gly-37, Gly-59,...
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PMID: 18227128
PDF is available here.
PDF is available here.
Genetika (Moskva) (44)4 2008
Abstract
Phototaxis, positive (movement toward the light source) or negative (from the light source) mediates the adaptation of cyanobacteria to varying wave lengths and illumination intensity. The transcription regulator PrqR of the family TetR is known as a repressor of the prqRA operon controlling resista...
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PMID: 18666550
PDF is available here.
PDF is available here.
Abstract
I by Bogomolni and Spudich in 1982 provided a molecular link between the light environment and phototaxis in Halobacterium salinarum, and thus laid the foundation for the study of signal transducing photosensors in prokaryotes. In recent years, a number of new prokaryotic photosensory receptors have...
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PMID: 18400553
PDF is available here.
PDF is available here.
Microbiology (154)Pt 4 2008
Abstract
We present a new function of light, the enhancement of mycelial growth. The photostimulated mycelial growth of the soil fungus Hypocrea atroviridis was detected on 17 (out of 95 tested carbon sources) carbohydrates and polyols, which are metabolically related to cellulose and hemicelluloses, and whi...
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PMID: 18375815
PDF is available here.
PDF is available here.
Abstract
Journal of Physical Chemistry A: Molecules, Spectroscopy, Kinetics, Environment and General Theory (112)11 2008
Abstract
We give the parameters for the spectral densities for a wide range of chromophores, proteins, and solvents. Expressions for the spectral density are derived for continuum dielectric models of the chromophore environment. There are contributions to the spectral density from each component of the envi...
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PMID: 18293949
PDF is available here.
PDF is available here.
Abstract
We report a theoretical/computational study for the analysis of the intramolecular stress tensor for the dark state and three intermediate states, pR, pB1 and pB2, of PYP. As a result, we found that the magnitude of the stress released during the change from the pR to the pB1 state is significantly...
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PMID: 18309395
PDF is available here.
PDF is available here.
Biophysical Journal (94)6 2008
Abstract
The kinetics of conformational change in the N-terminal region of photoactive yellow protein (PYP) was studied by the time-resolved diffusion measurement. The transient grating signal that represented the protein diffusion of the ground state and pB state depended on the observation time range. An a...
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PMID: 18024503
PDF is available here.
PDF is available here.
Abstract
We cloned and expressed it in Escherichia coli, along with the genes for chromophore biosynthesis from Rhodobacter capsulatus. The Sr PYP has a 31-residue N-terminal extension as compared to other PYPs that appears to be important for dimerization; however, truncation of these extra residues did not...
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PMID: 18198898
PDF is available here.
PDF is available here.
Mikrobiologiia (77)2 2008
Abstract
These results indicate disrupted transduction in the WCC mutants of stress factor signals that promote ROS (reactive oxygen species) formation....
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PMID: 18522316
PDF is available here.
PDF is available here.
Abstract
We analyzed the photocycles of the PYP domain of Ppr (Ppr-PYP) and full-length Ppr. The gene fragment for Ppr-PYP was expressed in Escherichia coli, and it was chemically reconstituted with p-coumaric acid; the full-length gene of Ppr was coexpressed with tyrosine ammonia-lyase and p-coumaric acid l...
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PMID: 18346084
PDF is available here.
PDF is available here.
Abstract
We report the identification of six new PYPs, thus nearly doubling the size of this protein family. This extends the taxonomic diversity of PYP-containing bacteria from photosynthetic to nonphotosynthetic bacteria, from aquatic to soil-dwelling organisms, and from Proteobacteria to Salinibacter rube...
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PMID: 18399917
PDF is available here.
PDF is available here.
Abstract
During the photoreaction cycle of photoactive yellow protein (PYP), a physiologically active intermediate (PYP(M)) is formed as a consequence of global protein conformational change. Previous studies have demonstrated that the photocycle of PYP is regulated by the N-terminal loop region, which is lo...
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PMID: 18513230
PDF is available here.
PDF is available here.
Abstract
We characterized the photocycle of the Met100Ala mutant of PYP (M100A) by low temperature UV-visible spectroscopy. Irradiation of M100A at 80 K yielded a 380 nm species (M100A(BL)), while the corresponding intermediate of wild type (WT; PYP(BL)) is formed above 90 K. The amounts of redshifted interm...
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PMID: 18399916
PDF is available here.
PDF is available here.
The Journal of Chemical Physics (127)21 2007
Abstract
The ultrafast photoinduced dynamics of photoactive yellow protein in aqueous solution were studied at room temperature by femtosecond fluorescence spectroscopy using an optical Kerr-gate technique. Coherent oscillations of the wave packet were directly observed in the two-dimensional time-energy map...
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PMID: 18067379
PDF is available here.
PDF is available here.
Trends in Microbiology (15)12 2007
Abstract
We review the state of the art in this field. Because light signals can be manipulated accurately, these photoreceptors might help provide a systems-level understanding of the cytology of bacteria....
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PMID: 18024131
PDF is available here.
PDF is available here.
Acta Crystallographica Section D (63)Pt 11 2007
Abstract
Photoactive yellow protein (PYP) from Halorhodospira halophila is a soluble 14 kDa blue-light photoreceptor. It absorbs light via its para-coumaric acid chromophore (pCA), which is covalently attached to Cys69 and is believed to be involved in the negative phototactic response of the organism to blu...
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PMID: 18007033
PDF is available here.
PDF is available here.
Abstract
We review recent new insights on reaction dynamics of photoreceptors proteins gained from ultrafast spectroscopy. In Blue Light sensing Using FAD (BLUF) domains, a hydrogen-bond rearrangement around the flavin chromophore proceeds through a radical-pair mechanism, by which light-induced electron and...
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PMID: 17959372
PDF is available here.
PDF is available here.
Abstract
Advances in the adaptation of optical spectroscopy to monitor photo-induced or enzyme-catalyzed reactions in the crystalline state have enabled X-ray crystal structures to be accurately linked with spectroscopically defined intermediates. This, in turn, has led to a deeper understanding of the role...
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PMID: 17959373
PDF is available here.
PDF is available here.
Biochemistry (Washington) (46)35 2007
Abstract
The crystal structure of the cyan-fluorescent Cerulean green fluorescent protein (GFP), a variant of enhanced cyan fluorescent protein (ECFP), has been determined to 2.0 A. Cerulean bears an internal fluorophore composed of an indole moiety derived from Y66W, conjugated to the GFP-li...
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PMID: 17685554
PDF is available here.
PDF is available here.
Abstract
Abstract
We prepared TePixJ_GAF chromoprotein from heterologously expressed Synechocystis and performed spectral analysis after denaturation by comparing it with the cyanobacterial phytochrome Cph1 which harbors phycocyanobilin (PCB) as a chromophore. The results indicated that the chromophore of TePixJ is n...
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PMID: 17715149
PDF is available here.
PDF is available here.
Abstract
Our studies illustrate that relatively minor changes in the primary structure of an ammonia-lyase enzyme can significantly affect its substrate specificity....
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PMID: 17602252
PDF is available here.
PDF is available here.
Biophysical Journal (93)5 2007
Abstract
The effect of ionic strength on the conformational equilibrium between the I(2) intermediate and the signaling state I(2)' of the photoreceptor PYP and on the rate of recovery to the dark state were investigated by time-resolved absorption and fluorescence spectroscopy. With increasing salt concentr...
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PMID: 17496031
PDF is available here.
PDF is available here.
ChemPhysChem (8)12 2007
Abstract
Biochemistry (Washington) (46)28 2007
Abstract
We conclude that the photoactivated PYP domain in Ppr accelerates recovery of the activated Bph domain. Phytochromes can be reversibly switched between Pr and Pfr forms by red and far-red light, but the consequence of a bleaching phytochrome is that it cannot be photoreversed by far-red light. We th...
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PMID: 17590020
PDF is available here.
PDF is available here.
Abstract
Light regulates fungal development and behaviour and activates metabolic pathways. In addition, light is one of the many signals that fungi use to perceive and interact with the environment. In the ascomycete Neurospora crassa blue light is perceived by the white collar (WC) complex, a protein compl...
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PMID: 17609765
PDF is available here.
PDF is available here.
Abstract
We previously reported for the analogues bearing ketone and ester groups. The fluorescence decays of the full series are found to lie in the 1-10 ps range depending on the electron-acceptor character of the substituent, in good agreement with the excited-state relaxation kinetics extracted from tran...
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PMID: 17609772
PDF is available here.
PDF is available here.
Abstract
Three different families of blue-light receptors have been characterized from higher plants: three cryptochromes, two phototropins, and the three members of the ZTL/ADO family. Phototropins and the ZTL/ADO proteins have chromophore modules, designated LOV domains, that bind flavin mononucleotide and...
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PMID: 17380429
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (111)23 2007
Abstract
Picosecond time-resolved ultraviolet resonance Raman (UVRR) spectra of photoactive yellow protein (PYP) were measured. UVRR bands attributed to the vibration of tyrosine and tryptophan residues showed a spectral change upon photoreaction. It was found that the hydrogen-bond strength between the chro...
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PMID: 17523627
PDF is available here.
PDF is available here.