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Yellow Protein (yellow + protein)
Kinds of Yellow Protein Selected AbstractsTransient Vibronic Structure in Ultrafast Fluorescence Spectra of Photoactive Yellow Protein,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Ryosuke Nakamura The ultrafast photo-induced dynamics of wild-type photoactive yellow protein and its site-directed mutant of E46Q in aqueous solution was studied at room temperature by femtosecond fluorescence spectroscopy using the optical Kerr-gate method. The vibronic structure appears, depending on the excitation photon energy, in the time-resolved fluorescence spectra just after photoexcitation, which winds with time and disappears on a time scale of sub-picoseconds. This result indicates that the wavepacket is localized in the electronic excited state followed by dumped oscillations and broadening, and also that the initial condition of the wavepacket prepared depending on the excitation photon energy affects much the following ultrafast dynamics in the electronic excited state. [source] Low-temperature Spectroscopy of Met100Ala Mutant of Photoactive Yellow Protein,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Yasushi Imamoto The trans -to- cis photoisomerization of the p -coumaroyl chromophore of photoactive yellow protein (PYP) triggers the photocycle. Met100, which is located in the vicinity of the chromophore, is a key residue for the cis -to- trans back-isomerization of the chromophore, which is a rate-determining reaction of the PYP photocycle. Here 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 (M100ABL), while the corresponding intermediate of wild type (WT; PYPBL) is formed above 90 K. The amounts of redshifted intermediates produced from M100A (M100AB, and M100AL) were substantially less than those from WT. While the near-UV intermediate (PYPM) is not formed from WT in glycerol samples at low temperature, M100AM was clearly observed above 190 K. These alterations of the photocycle of M100A were explained by the shift in the equilibrium between the intermediates. The carbonyl oxygen of the thioester linkage of the cis -chromophore in the photocycle intermediates is close to the phenyl ring of Phe96 (<3.5 Å), which would be displaced by the mutation of Met100. These findings imply that the interaction between chromophore and amino acid residues near Met100 is altered during the early stage of the PYP photocycle. [source] Interaction Between N-terminal Loop and , -Scaffold of Photoactive Yellow Protein,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Miki Harigai During the photoreaction cycle of photoactive yellow protein (PYP), a physiologically active intermediate (PYPM) 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 located across the central , -sheet from the p -coumaric acid chromophore. In this paper, the hydrophobic interaction between N-terminal loop and , -sheet was studied by characterizing PYP mutants of the hydrophobic residues. The rate constants and structural changes of the photocycle of L15A and L23A possibly participating in such an interaction were more similar to wild-type than F6A, showing that the CH/, interaction between Phe6 and Lys123 is the most essential as reported previously. To better understand the interactions between N-terminal tail and , -sheet of PYP, Phe6 and Phe121 were replaced by Cys and linked by a disulfide bond. Since the photocycle kinetics, structural change and thermal stability of F6C/F121C were similar to F6A, the CH/, interaction between Phe6 and Lys123 is not substitutable. It is likely that the detachment of position 6 from position 123 substantially alters the nature of PYP. [source] Structure and Photoreaction of Photoactive Yellow Protein, a Structural Prototype of the PAS Domain Superfamily,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 1 2007Yasushi Imamoto Photoactive yellow protein (PYP) is a water-soluble photosensor protein found in purple photosynthetic bacteria. Unlike bacterial rhodopsins, photosensor proteins composed of seven transmembrane helices and a retinal chromophore in halophilic archaebacteria, PYP is a highly soluble globular protein. The ,/, fold structure of PYP is a structural prototype of the PAS domain superfamily, many members of which function as sensors for various kinds of stimuli. To absorb a photon in the visible region, PYP has a p -coumaric acid chromophore binding to the cysteine residue via a thioester bond. It exists in a deprotonated trans form in the dark. The primary photochemical event is photo-isomerization of the chromophore from trans to cis form. The twisted cis chromophore in early intermediates is relaxed and finally protonated. Consequently, the chromophore becomes electrostatically neutral and rearrangement of the hydrogen-bonding network triggers overall structural change of the protein moiety, in which local conformational change around the chromophore is propagated to the N-terminal region. Thus, it is an ideal model for protein conformational changes that result in functional change, responding to stimuli and expressing physiological activity. In this paper, recent progress in investigation of the photoresponse of PYP is reviewed. [source] Identification of Six New Photoactive Yellow Proteins,Diversity and Structure,Function Relationships in a Bacterial Blue Light Photoreceptor,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Masato Kumauchi Photoactive yellow proteins (PYP) are bacterial photoreceptors with a Per-Arnt-Sim (PAS) domain fold. 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 ruber from the phylum Bacteriodetes. The new PYPs greatly increase the sequence diversity of the PYP family, reducing the most prevalent pair-wise identity from 45% to 25%. Sequence alignments and analysis indicate that all 14 PYPs share a common structure with 13 highly conserved residues that form the chromophore binding pocket. Nevertheless, the functional properties of the PYPs vary greatly,the absorbance maximum extends from 432 to 465 nm, the pKa of the chromophore varies from pH 2.8 to 10.2, and the lifetime of the presumed PYP signaling state ranges from 1 ms to 1 h. Thus, the PYP family offers an excellent opportunity to investigate how functional properties are tuned over a wide range, while maintaining the same overall protein structural fold. We discuss the implications of these results for structure,function relationships in the PYP family. [source] Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2006Azuma Matsuura Abstract Here we improved our hybrid QM/MM methodology (Houjou et al. J Phys Chem B 2001, 105, 867) for evaluating the absorption maxima of photoreceptor proteins. The renewed method was applied to evaluation of the absorption maxima of several retinal proteins and photoactive yellow protein. The calculated absorption maxima were in good agreement with the corresponding experimental data with a computational error of <10 nm. In addition, our calculations reproduced the experimental gas-phase absorption maxima of model chromophores (protonated all-trans retinal Schiff base and deprotonated thiophenyl- p -coumarate) with the same accuracy. It is expected that our methodology allows for definitive interpretation of the spectral tuning mechanism of retinal proteins. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006 [source] Quantum Mechanical/Molecular Mechanical Studies on Spectral Tuning Mechanisms of Visual Pigments and Other Photoactive Proteins,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Ahmet Altun The protein environments surrounding the retinal tune electronic absorption maximum from 350 to 630 nm. Hybrid quantum mechanical/molecular mechanical (QM/MM) methods can be used in calculating excitation energies of retinal in its native protein environments and in studying the molecular basis of spectral tuning. We hereby review recent QM/MM results on the phototransduction of bovine rhodopsin, bacteriorhodopsin, sensory rhodopsin II, nonretinal photoactive yellow protein and their mutants. [source] The Photoreaction of the Photoactive Yellow Protein Domain in the Light Sensor Histidine Kinase Ppr is Influenced by the C-terminal Domains,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Hironari Kamikubo To study the role of the C-terminal domains in the photocycle of a light sensor histidine kinase (Ppr) having a photoactive yellow protein (PYP) domain as the photosensor domain, 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 ligase for biosynthesis in cells. The light/dark difference spectra of Ppr-PYP were pH sensitive. They were represented as a linear combination of two independent difference spectra analogous to the PYPL/dark and PYPM/dark difference spectra of PYP from Halorhodospira halophila, suggesting that the pH dependence of the difference spectra is explained by the equilibrium shift between the PYPL - and PYPM -like intermediates. The light/dark difference spectrum of Ppr showed the equilibrium shift toward PYPL compared with that of Ppr-PYP. Kinetic measurements of the photocycles of Ppr and Ppr-PYP revealed that the C-terminal domains accelerate the recovery of the dark state. These observations suggest an interaction between the C-terminal domains and the PYP domain during the photocycle, by which light signals captured by the PYP domain are transferred to the C-terminal domains. [source] Transient Vibronic Structure in Ultrafast Fluorescence Spectra of Photoactive Yellow Protein,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Ryosuke Nakamura The ultrafast photo-induced dynamics of wild-type photoactive yellow protein and its site-directed mutant of E46Q in aqueous solution was studied at room temperature by femtosecond fluorescence spectroscopy using the optical Kerr-gate method. The vibronic structure appears, depending on the excitation photon energy, in the time-resolved fluorescence spectra just after photoexcitation, which winds with time and disappears on a time scale of sub-picoseconds. This result indicates that the wavepacket is localized in the electronic excited state followed by dumped oscillations and broadening, and also that the initial condition of the wavepacket prepared depending on the excitation photon energy affects much the following ultrafast dynamics in the electronic excited state. [source] Low-temperature Spectroscopy of Met100Ala Mutant of Photoactive Yellow Protein,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Yasushi Imamoto The trans -to- cis photoisomerization of the p -coumaroyl chromophore of photoactive yellow protein (PYP) triggers the photocycle. Met100, which is located in the vicinity of the chromophore, is a key residue for the cis -to- trans back-isomerization of the chromophore, which is a rate-determining reaction of the PYP photocycle. Here 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 (M100ABL), while the corresponding intermediate of wild type (WT; PYPBL) is formed above 90 K. The amounts of redshifted intermediates produced from M100A (M100AB, and M100AL) were substantially less than those from WT. While the near-UV intermediate (PYPM) is not formed from WT in glycerol samples at low temperature, M100AM was clearly observed above 190 K. These alterations of the photocycle of M100A were explained by the shift in the equilibrium between the intermediates. The carbonyl oxygen of the thioester linkage of the cis -chromophore in the photocycle intermediates is close to the phenyl ring of Phe96 (<3.5 Å), which would be displaced by the mutation of Met100. These findings imply that the interaction between chromophore and amino acid residues near Met100 is altered during the early stage of the PYP photocycle. [source] Interaction Between N-terminal Loop and , -Scaffold of Photoactive Yellow Protein,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Miki Harigai During the photoreaction cycle of photoactive yellow protein (PYP), a physiologically active intermediate (PYPM) 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 located across the central , -sheet from the p -coumaric acid chromophore. In this paper, the hydrophobic interaction between N-terminal loop and , -sheet was studied by characterizing PYP mutants of the hydrophobic residues. The rate constants and structural changes of the photocycle of L15A and L23A possibly participating in such an interaction were more similar to wild-type than F6A, showing that the CH/, interaction between Phe6 and Lys123 is the most essential as reported previously. To better understand the interactions between N-terminal tail and , -sheet of PYP, Phe6 and Phe121 were replaced by Cys and linked by a disulfide bond. Since the photocycle kinetics, structural change and thermal stability of F6C/F121C were similar to F6A, the CH/, interaction between Phe6 and Lys123 is not substitutable. It is likely that the detachment of position 6 from position 123 substantially alters the nature of PYP. [source] Structure and Photoreaction of Photoactive Yellow Protein, a Structural Prototype of the PAS Domain Superfamily,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 1 2007Yasushi Imamoto Photoactive yellow protein (PYP) is a water-soluble photosensor protein found in purple photosynthetic bacteria. Unlike bacterial rhodopsins, photosensor proteins composed of seven transmembrane helices and a retinal chromophore in halophilic archaebacteria, PYP is a highly soluble globular protein. The ,/, fold structure of PYP is a structural prototype of the PAS domain superfamily, many members of which function as sensors for various kinds of stimuli. To absorb a photon in the visible region, PYP has a p -coumaric acid chromophore binding to the cysteine residue via a thioester bond. It exists in a deprotonated trans form in the dark. The primary photochemical event is photo-isomerization of the chromophore from trans to cis form. The twisted cis chromophore in early intermediates is relaxed and finally protonated. Consequently, the chromophore becomes electrostatically neutral and rearrangement of the hydrogen-bonding network triggers overall structural change of the protein moiety, in which local conformational change around the chromophore is propagated to the N-terminal region. Thus, it is an ideal model for protein conformational changes that result in functional change, responding to stimuli and expressing physiological activity. In this paper, recent progress in investigation of the photoresponse of PYP is reviewed. [source] Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromoleculesACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Paul D. Adams X-ray and neutron crystallographic techniques provide complementary information on the structure and function of biological macromolecules. X-ray and neutron (XN) crystallographic data have been combined in a joint structure-refinement procedure that has been developed using recent advances in modern computational methodologies, including cross-validated maximum-likelihood target functions with gradient-based optimization and simulated annealing. The XN approach for complete (including hydrogen) macromolecular structure analysis provides more accurate and complete structures, as demonstrated for diisopropyl fluorophosphatase, photoactive yellow protein and human aldose reductase. Furthermore, this method has several practical advantages, including the easier determination of the orientation of water molecules, hydroxyl groups and some amino-acid side chains. [source] Structure of photoactive yellow protein (PYP) E46Q mutant at 1.2,Å resolution suggests how Glu46 controls the spectroscopic and kinetic characteristics of PYPACTA CRYSTALLOGRAPHICA SECTION D, Issue 12-2 2004Masakazu Sugishima Photoactive yellow protein from Ectothiorhodospira halophila is a photoreceptor protein involved in the negative phototaxis of this bacterium. Its chromophore (p -coumaric acid) is deprotonated in the ground state, which is stabilized by a hydrogen-bond network between Tyr42, Glu46 and Thr50. Glu46 is a key residue as it has been suggested that the proton at Glu46 is transferred to the chromophore during its photoconversion from the dark state to the signalling state. The structure of E46Q mutant protein was determined at 1.2,Å resolution, revealing that the phenolic O atom of p -coumaric acid is hydrogen bonded to NH2 of Gln46 in E46Q with a longer distance (2.86 ± 0.02,Å) than its distance (2.51,Å) to Glu46,OH in the wild type. This and the decreased thermal stability of E46Q relative to the wild type show that this hydrogen bond is weakened in the E46Q mutant compared with the corresponding bond in the wild type. Several characteristic features of E46Q such as an alkali shift in the pKa and the rapid photocycle can be explained by this weakened hydrogen bond. Furthermore, the red shift in the absorption maximum in E46Q can be explained by the delocalization of the electron on the phenolic oxygen of p -coumaric acid owing to the weakening of this hydrogen bond. [source] Crystallization and X-ray diffraction studies of the fatty-acid responsive transcription factor FadR from Escherichia coliACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2000Daan M. F. Van Aalten FadR, an acylCoA-dependent Escherichia coli transcription factor controlling the expression of genes involved in fatty-acid degradation and synthesis, has been crystallized. Crystals of two binary complexes were obtained. The FadR,CoA complex crystallized in space group C2221, with unit-cell parameters a = 61.3, b = 102.0, c = 91.3,Å. The FadR,octanoyl-CoA complex crystallized in space group P6522, with unit-cell parameters a = b = 59.7, c = 296.2,Å. Both crystal forms diffracted to 3.5,Å on a rotating-anode generator. In both crystal forms, the asymmetric unit contains one subunit. The protein is known to be a homodimer; each subunit consists of two domains of unknown fold. For the acyl-CoA-binding domain, a previously undetected sequence homology to PAS domains, in particular the photoactive yellow protein, is reported. [source] Ultrafast Photoisomerization of Photoactive Yellow Protein Chromophore Analogues in Solution: Influence of the Protonation StateCHEMPHYSCHEM, Issue 8 2006Agathe Espagne Dr. Abstract We investigate solvent viscosity and polarity effects on the photoisomerization of the protonated and deprotonated forms of two analogues of the photoactive yellow protein (PYP) chromophore. These are trans- p -hydroxybenzylidene acetone and trans- p -hydroxyphenyl cinnamate, studied in solutions of different polarity and viscosity at room temperature, by means of femtosecond fluorescence up-conversion. The fluorescence lifetimes of the protonated forms are found to be barely sensitive to solvent viscosity, and to increase with increasing solvent polarity. In contrast, the fluorescence decays of the deprotonated forms are significantly slowed down in viscous media and accelerated in polar solvents. These results elucidate the dramatic influence of the protonation state of the PYP chromophore analogues on their photoinduced dynamics. The viscosity and polarity effects are, respectively, interpreted in terms of different isomerization coordinates and charge redistribution in S1. A trans-to-cis isomerization mechanism involving mainly the ethylenic double-bond torsion and/or solvation is proposed for the anionic forms, whereas "concerted" intramolecular motions are proposed for the neutral forms. [source] Identification of Six New Photoactive Yellow Proteins,Diversity and Structure,Function Relationships in a Bacterial Blue Light Photoreceptor,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Masato Kumauchi Photoactive yellow proteins (PYP) are bacterial photoreceptors with a Per-Arnt-Sim (PAS) domain fold. 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 ruber from the phylum Bacteriodetes. The new PYPs greatly increase the sequence diversity of the PYP family, reducing the most prevalent pair-wise identity from 45% to 25%. Sequence alignments and analysis indicate that all 14 PYPs share a common structure with 13 highly conserved residues that form the chromophore binding pocket. Nevertheless, the functional properties of the PYPs vary greatly,the absorbance maximum extends from 432 to 465 nm, the pKa of the chromophore varies from pH 2.8 to 10.2, and the lifetime of the presumed PYP signaling state ranges from 1 ms to 1 h. Thus, the PYP family offers an excellent opportunity to investigate how functional properties are tuned over a wide range, while maintaining the same overall protein structural fold. We discuss the implications of these results for structure,function relationships in the PYP family. [source] | ||||||||||