| early intermediates in the photocycle of the glu46gln mutant of photoactive yellow protein: femtosecond spectroscopy. | transient absorption spectroscopy in the time range from -1 ps to 4 ns, and over the wavelength range from 420 to 550 nm, was applied to the glu46gln mutant of the photoactive yellow protein (pyp) from ectothiorhodospira halophila. this has allowed us to elucidate the kinetic constants of excited state formation and decay and photochemical product formation, and the spectral characteristics of stimulated emission and the early photocycle intermediates. both the quantum efficiency ( approximately ... | 2000 | 11023916 |
| protonation states and ph titration in the photocycle of photoactive yellow protein. | photoactive yellow protein (pyp) undergoes a light-driven cycle of color and protonation states that is part of a mechanism of bacterial phototaxis. this article concerns functionally important protonation states of pyp and the interactions that stabilize them, and changes in the protonation state during the photocycle. in particular, the chromophore pk(a) is known to be shifted down so that the chromophore is negatively charged in the ground state (dark state) even though it is buried in the pr ... | 2000 | 10653656 |
| light-induced global conformational change of photoactive yellow protein in solution. | the light-induced global conformational change of photoactive yellow protein was directly observed by small-angle x-ray scattering (saxs). the n-terminal 6, 15, or 23 amino acid residues were enzymatically truncated (t6, t15, or t23, respectively), and their near-uv intermediates were accumulated under continuous illumination for saxs measurements. the kratky plot demonstrated that illumination induced partial loss of globularity. the change in globularity was marked in t6 but very small in t15 ... | 2002 | 12427020 |
| simultaneous interpretation of mössbauer, epr and 57fe endor spectra of the [fe4s4] cluster in the high-potential iron protein i from ectothiorhodospira halophila. | mössbauer spectra of the oxidized [fe4s4]3+ and the reduced [fe4s4]2+ clusters in the high-potential iron protein i from ectothiorhodospira halophila were measured in a temperature range from 5 k to 240 k. epr measurements and 57fe electron-nuclear double resonance (endor) experiments were carried out with the oxidized protein. in the oxidized state the cluster has a net spin s = 1/2 and is paramagnetic. as common in [fe4s4]3+ clusters, the mössbauer spectrum was simulated with two species contr ... | 1999 | 10631604 |
| dual photoactive species in glu46asp and glu46ala mutants of photoactive yellow protein: a ph-driven color transition. | photoactive yellow protein (pyp) is a blue light sensor present in the purple photosynthetic bacterium ectothiorhodospira halophila, which undergoes a cyclic series of absorbance changes upon illumination at its lambda(max) of 446 nm. the anionic p-hydroxycinnamoyl chromophore of pyp is covalently bound as a thiol ester to cys69, buried in a hydrophobic pocket, and hydrogen-bonded via its phenolate oxygen to glu46 and tyr42. the chromophore becomes protonated in the photobleached state (i(2)) af ... | 1999 | 10521284 |
| in situ analysis of sulfur in the sulfur globules of phototrophic sulfur bacteria by x-ray absorption near edge spectroscopy. | during the oxidation of sulfide and thiosulfate purple and green sulfur bacteria accumulate globules of 'elemental' sulfur. although essential for a thorough understanding of sulfur metabolism in these organisms, the exact chemical nature of the stored sulfur is still unclear. we applied sulfur k-edge x-ray absorption near edge spectroscopy (xanes) to probe the forms of sulfur in intact cells. comparing xanes spectra of allochromatium vinosum, thiocapsa roseopersicina, marichromatium purpuratum, ... | 1999 | 10434064 |
| porin from the halophilic species ectothiorhodospira vacuolata: cloning, structure of the gene and comparison with other porins. | the gene coding for the anion-specific porin of the halophilic eubacterium ectothiorhodospira (ect.) vacuolata was cloned and sequenced, the first such gene so analyzed from a purple sulfur bacterium. it encodes a precursor protein consisting of 374 amino acid (aa)-residues including a signal peptide of 22-aa residues. comparison with aa sequences of porins from several other members of the proteobacteria revealed little homology. only two regions showed local homology with the previously sequen ... | 1997 | 9218724 |
| stark spectroscopy on photoactive yellow protein, e46q, and a nonisomerizing derivative, probes photo-induced charge motion. | the change in the electrostatic properties on excitation of the cofactor of wild-type photoactive yellow protein (wt-pyp) have been directly determined using stark-effect spectroscopy. we find that, instantaneously on photon absorption, there is a large change in the permanent dipole moment, /delta(-->)mu/, (26 debye) and in the polarizability, (-)deltaalpha, (1000 a(3)). we expect such a large degree of charge motion to have a significant impact on the photocycle that is associated with the imp ... | 2003 | 12719252 |
| the phylogenetic relationship among ectothiorhodospiraceae: a reevaluation of their taxonomy on the basis of 16s rdna analyses. | sequences of the 16s rrna gene were determined from all type strains of the recognized ectothiorhodospira species and from a number of additional strains. for the first time, these data resolve the phylogenetic relationships of the ectothiorhodospiraceae in detail, confirm the established species, and improve the classification of strains of uncertain affiliation. two major groups that are recognized as separate genera were clearly established. the extremely halophilic species were removed from ... | 1996 | 8593098 |
| dynamics of wild-type hipips: a cys77ser mutant and a partially unfolded hipip. | the temperature dependence of the mean square displacement of the (57)fe nuclei due to motion faster than 100 ns are measured by temperature-dependent mössbauer spectroscopy for oxidized and reduced hipips from ectothiorhodospira halophila, chromatium vinosum wt and a cys77ser mutant. the behaviour is interpretable in the frame of the general model of protein dynamics distinguishing two temperature intervals. the character of harmonic and quasi-diffusional modes in hipips is discussed. dynamic i ... | 2002 | 12203006 |
| a role of methionine 100 in facilitating pyp(m)-decay process in the photocycle of photoactive yellow protein. | pyp (photoactive yellow protein) is a photoreceptor protein, which is activated upon photo-isomerization of the p-coumaric acid chromophore and is inactivated as the chromophore is thermally back-isomerized within a second (in pyp(m)-to-pyp(dark) conversion). here we have examined the mechanism of the rapid thermal isomerization by analyzing mutant pyps of met100, which was previously shown to play a major role in facilitating the reaction [devanathan, s. et al. (1998) biochemistry 37, 11563-115 ... | 2002 | 12153716 |
| resonance raman spectroscopy and quantum chemical calculations reveal structural changes in the active site of photoactive yellow protein. | photoactive yellow protein (pyp) is a bacterial photoreceptor containing a 4-hydroxycinnamyl chromophore. photoexcitation of pyp triggers a photocycle that involves at least two intermediate states: an early red-shifted pyp(l) intermediate and a long-lived blue-shifted pyp(m) intermediate. in this study, we have explored the active site structures of these intermediates by resonance raman spectroscopy. quantum chemical calculations based on a density functional theory are also performed to simul ... | 2002 | 11969428 |
| light-induced unfolding of photoactive yellow protein mutant m100l. | light-activation of the pas domain protein photoactive yellow protein (pyp) is believed to trigger a negative phototactic response in the phototropic bacterium halorhodospira halophila. to investigate transient conformational changes of the pyp photocycle, we utilized the pyp mutant m100l that displays an increased lifetime of the putative signaling-state photointermediate pyp(m) by 3 orders of magnitude, as previously reported for the m100a mutant [devanathan, s., genick, u. k., canestrelli, i. ... | 2002 | 11827538 |
| alcalilimnicola halodurans gen. nov., sp. nov., an alkaliphilic, moderately halophilic and extremely halotolerant bacterium, isolated from sediments of soda-depositing lake natron, east africa rift valley. | an alkaliphilic, halotolerant, gram-negative, heterotrophic, aerobic and rod-shaped organism was isolated from drying soda and at a water-covered site of lake natron, tanzania, by means of the most-probable-number technique developed for anoxygenic, phototrophic sulfur bacteria. it had an absolute requirement for alkalinity, but not for salinity; growth occurred at salt concentrations of 0-28% (w/v), with optimal growth at 3-8% (w/v) nacl. the bacterium preferentially metabolized volatile fatty ... | 2001 | 11760957 |
| a molecular movie at 1.8 a resolution displays the photocycle of photoactive yellow protein, a eubacterial blue-light receptor, from nanoseconds to seconds. | the photocycle of the bacterial blue-light photoreceptor, photoactive yellow protein, was stimulated by illumination of single crystals by a 7 ns laser pulse. the molecular events were recorded at high resolution by time-resolved x-ray laue diffraction as they evolved in real time, from 1 ns to seconds after the laser pulse. the complex structural changes during the photocycle at ambient temperature are displayed in a movie of difference electron density maps relative to the dark state. the step ... | 2001 | 11705368 |
| early photocycle kinetic behavior of the e46a and y42f mutants of photoactive yellow protein: femtosecond spectroscopy. | in the photoactive yellow protein, pyp, both glu46 and tyr42 form hydrogen bonds to the phenolic oh group of the p-hydroxycinnamoyl chromophore. previous work on replacement of the carboxyl group of glu46 by an amide group (glu46gln) has shown that changing the nature of this hydrogen bond has a minimal effect on the rate constant for the formation of the first intermediate (i(0)) and on the excited state lifetime, whereas the rate constants for the formation of the second (i(0)( not equal)) and ... | 2001 | 11566800 |
| low-temperature fourier transform infrared spectroscopy of photoactive yellow protein. | the photocycle intermediates of photoactive yellow protein (pyp) were characterized by low-temperature fourier transform infrared spectroscopy. the difference ftir spectra of pyp(b), pyp(h), pyp(l), and pyp(m) minus pyp were measured under the irradiation condition determined by uv-visible spectroscopy. although the chromophore bands of pyp(b) were weak, intense sharp bands complementary to the 1163-cm(-1) band of pyp, which show the chromophore is deprotonated, were observed at 1168-1169 cm(-1) ... | 2001 | 11467962 |
| amino acids in the n-terminal region regulate the photocycle of photoactive yellow protein. | the spectroscopic properties of photoactive yellow protein (pyp) partially digested by chymotrypsin were studied. chymotrypsin yielded three major products that were yellow but distinguishable by sds-page. they were readily separated by deae-sepharose column chromatography. protein sequencing and mass spectrometry demonstrated that chymotrypsin cleaved the n-terminal 6, 15, or 23 amino acids (t6, t15, and t23). the blue-shifts of the absorption maxima and the increases in the apparent pk(a) of t ... | 2001 | 11432779 |
| alkalispirillum mobile gen. nov., spec. nov., an alkaliphilic non-phototrophic member of the ectothiorhodospiraceae. | from cultures of the anoxygenic phototroph halorhodospira halophila sl-1, an aerobic, gram-negative spirillum was isolated. this moderately halophilic, alkaliphilic bacterium was motile by means of a single polar flagellum. it is described here as alkalispirillum mobile gen. nov., spec. nov. phylogenetic analysis of the alkalispirillum mobile 16s rrna gene led to its classification in the gamma-subclass of the proteobacteria, as it appears closely related to phototrophic purple sulfur bacteria o ... | 2001 | 11409547 |
| the role of the n-terminal domain of photoactive yellow protein in the transient partial unfolding during signalling state formation. | it is shown that the n-terminal domain of photoactive yellow protein (pyp), which appears relatively independently folded in the ground state of the protein, plays a key role in the transient unfolding during signalling state formation: genetic truncation of the n-terminal domain of pyp significantly decreases the extent of cooperativity of the titration curve that describes chromophore protonation in the ground state of pyp, which is in agreement with the notion that the n-terminal domain is li ... | 2001 | 11376657 |
| predicting the signaling state of photoactive yellow protein. | as a bacterial blue light sensor the photoactive yellow protein (pyp) undergoes conformational changes upon signal transduction. the absorption of a photon triggers a series of events that are initially localized around the protein chromophore, extends to encompass the whole protein within microseconds, and leads to the formation of the transient pb signaling state. we study the formation of this signaling state pb by molecular simulation and predict its solution structure. conventional straight ... | 2005 | 15722437 |
| dihydroxylycopene diglucoside diesters: a novel class of carotenoids from the phototrophic purple sulfur bacteria halorhodospira abdelmalekii and halorhodospira halochloris. | the carotenoids in halorhodospira abdelmalekii and halorhodospira halochloris were analyzed by spectroscopic methods. the carotenoid composition of the two species was almost the same. both species contained substantial amounts of unusual carotenoid glycoside fatty acid esters, which have been found for the first time in phototrophic purple bacteria. methoxy-hydroxylycopene glucoside was a major component, and dihydroxylycopene diglucoside and dihydroxylycopene diglucoside diester were also foun ... | 2001 | 11357508 |
| primary photoreaction of photoactive yellow protein studied by subpicosecond-nanosecond spectroscopy. | the primary photochemical event of photoactive yellow protein (pyp) was studied by laser flash photolysis experiments on a subpicosecond-nanosecond time scale. pyp was excited by a 390-nm pulse, and the transient difference absorption spectra were recorded by a multichannel spectrometer for a more reliable spectral analysis than previously possible. just after excitation, an absorbance decrease due to the stimulated emission at 500 nm and photoconversion of pyp at 450 nm were observed. the stimu ... | 2001 | 11352740 |
| improved osmotolerance of recombinant escherichia coli by de novo glycine betaine biosynthesis. | the genes from the extreme halophile ecto-thiorhodospira halochloris encoding the biosynthesis of glycine betaine from glycine were cloned into escherichia coli. the accumulation of glycine betaine and its effect on osmotolerance of the cells were studied. in mineral medium with nacl concentrations from 0.15 to 0.5 m, the accumulation of both endogenously synthesized and exogenously provided glycine betaine stimulated the growth of e. coli. the intracellular levels of glycine betaine and the cel ... | 2001 | 11330717 |
| characterization of glycine sarcosine n-methyltransferase and sarcosine dimethylglycine n-methyltransferase. | glycine betaine is accumulated in cells living in high salt concentrations to balance the osmotic pressure. glycine sarcosine n-methyltransferase (gsmt) and sarcosine dimethylglycine n-methyltransferase (sdmt) of ectothiorhodospira halochloris catalyze the threefold methylation of glycine to betaine, with s-adenosylmethionine acting as the methyl group donor. these methyltransferases were expressed in escherichia coli and purified, and some of their enzymatic properties were characterized. both ... | 2001 | 11319079 |
| roles of amino acid residues near the chromophore of photoactive yellow protein. | to investigate the roles of amino acid residues around the chromophore in photoactive yellow protein (pyp), new mutants, y42a, e46a, and t50a were prepared. their spectroscopic properties were compared with those of wild-type, y42f, e46q, t50v, r52q, and e46q/t50v, which were previously prepared and specified. the absorption maxima of y42a, e46a, and t50a were observed at 438, 469, and 454 nm, respectively. the results of ph titration for the chromophore demonstrated that the chromophore of pyp ... | 2001 | 11294635 |
| structure of the i1 early intermediate of photoactive yellow protein by ftir spectroscopy. | to understand how proteins translate the energy of sunlight into defined conformational changes, we have measured the photocycle reactions of photoactive yellow protein (pyp) using time-resolved step scan fourier transform infrared (ftir) spectroscopy. global fit analysis yielded the same apparent time constants for the reactions of the chromophore, the protonation changes of protein side chains and the protein backbone motions, indicating that the light cycle reactions are synchronized. changes ... | 2001 | 11224574 |
| when ft-ir spectroscopy meets x-ray crystallography. | | 2001 | 11224557 |
| probing the nature of the blue-shifted intermediate of photoactive yellow protein in solution by nmr: hydrogen-deuterium exchange data and ph studies. | the nature of the pb intermediate of photoactive yellow protein (pyp) from ectothiorhodospira halophila has been probed by nmr. ph-dependent changes in the nmr spectrum of the dark state of pyp are shown to closely mimic exchange broadening effects observed previously in the nmr spectrum of the pb intermediate in solution. amide h-d exchange data show that while pb retains a solid protected core, two regions become significantly less protected than the dark state. the amide exchange data help to ... | 2000 | 11087391 |
| deuterium isotope effects in the photocycle transitions of the photoactive yellow protein. | the photoactive yellow protein (pyp) from halorhodospira halophila (formerly ectothiorhodospira halophila) is increasingly used as a model system. as such, a thorough understanding of the photocycle of pyp is essential. in this study we have combined information from poh- (or ph-) dependence and (kinetic) deuterium isotope effects to elaborate on existing photocycle models. for several characteristics of pyp we were able to make a distinction between ph- and poh-dependence, a nontrivial distinct ... | 2003 | 12547797 |
| heterologous production of halorhodospira halophila holo-photoactive yellow protein through tandem expression of the postulated biosynthetic genes. | the photoactive yellow protein (pyp) is a bacterial photoreceptor which is the structural prototype for the pas domain superfamily of regulators and receptors. pyp is known to have a unique p-hydroxycinnamic acid chromophore, covalently attached to a cysteine. to date, it has not been shown how holo-pyp is formed in vivo. two genes, nearby pyp, were postulated to encode the biosynthetic enzymes, but only one was previously isolated and shown to have the requisite activity. by using a dual plasmi ... | 2003 | 12549916 |
| site-specific mutations provide new insights into the origin of ph effects and alternative spectral forms in the photoactive yellow protein from halorhodospira halophila. | acid/base titrations of wild-type pyp and mutants, either in buffer or in the presence of chaotropes such as thiocyanate, establish the presence of four spectral forms including the following: a neutral form (446-476 nm), an acidic form (350-355 nm), an alkaline form (430-440 nm), and an intermediate wavelength form (355-400 nm). the acidic species is formed by protonation of the oxyanion of the para-hydroxy-cinnamyl cysteine chromophore as a secondary result of acid denaturation (with pk(a) val ... | 2003 | 12641464 |
| isolation and characterization of spirilloid purple phototrophic bacteria forming red layers in microbial mats of mediterranean salterns: description of halorhodospira neutriphila sp. nov. and emendation of the genus halorhodospira. | microbial mats developing in the hypersaline lagoons of a commercial saltern in the salin-de-giraud (rhône delta) were found to contain a red layer fully dominated by spirilloid phototrophic purple bacteria underlying a cyanobacterial layer. from this layer four strains of spirilloid purple bacteria were isolated, all of which were extremely halophilic. all strains were isolated by using the same medium under halophilic photolithoheterotrophic conditions. one of them, strain sg 3105 was a purple ... | 2003 | 12656167 |
| initial steps of signal generation in photoactive yellow protein revealed with femtosecond mid-infrared spectroscopy. | photoactive yellow protein (pyp) is a bacterial blue light sensor that induces halorhodospira halophila to swim away from intense blue light. light absorption by pyp's intrinsic chromophore, p-coumaric acid, leads to the initiation of a photocycle that comprises several distinct intermediates. here we describe the initial structural changes of the chromophore and its nearby amino acids, using visible pump/mid-infrared probe spectroscopy. upon photoexcitation, the trans bands of the chromophore a ... | 2003 | 12939133 |
| characterization of photocycle intermediates in crystalline photoactive yellow protein. | the photocycle in photoactive yellow protein (pyp) crystals was studied by single-crystal absorption spectroscopy with experimental setups for low-temperature and time-resolved measurements. thin and flat pyp crystals, suitable for light absorption studies, were obtained using special crystallization conditions. illumination of pyp crystals at 100 k led to the formation of a photostationary state, which includes at least one hypsochromic and one bathochromic photoproduct that resemble pyp(h) and ... | 2003 | 12945580 |
| role of an n-terminal loop in the secondary structural change of photoactive yellow protein. | photoactive yellow protein (pyp) is photoconverted to its putative active form (pyp(m)) with global conformational change(s). the changes in the secondary structure were studied by far-uv circular dichroism (cd) and fourier transform infrared (ftir) spectroscopy using pyp, which lacks n-terminal 6, 15, or 23 amino acid residues (t6, t15, and t23, respectively). irradiation of truncated pyps induced the loss of the cd signal, where the maximal difference was located at 222 nm. the reduction of th ... | 2003 | 14636057 |
| lack of negative charge in the e46q mutant of photoactive yellow protein prevents partial unfolding of the blue-shifted intermediate. | the long-lived light-induced intermediate (pb) of the e46q mutant (glutamic acid is replaced by glutamine at position 46) of photoactive yellow protein (pyp) has been investigated by nmr spectroscopy. the ground state of this mutant is very similar to that of wild-type pyp (wt), whereas the pb state, formed upon illumination, appears to be much more structured in e46q than in wt. the differences are most striking in the n-terminal domain of the protein. in wt, the side-chain carboxylic group of ... | 2003 | 14661962 |
| rhodobacter capsulatus photoactive yellow protein: genetic context, spectral and kinetics characterization, and mutagenesis. | a gene for photoactive yellow protein (pyp) was previously cloned from rhodobacter capsulatus (rc), and we have now found it to be associated with genes for gas vesicle formation in the recently completed genome sequence. however, the pyp had not been characterized as a protein. we have now produced the recombinant rcpyp in escherichia coli as a glutathione-s-transferase (gst) fusion protein, along with the biosynthetic enzymes, resulting in the formation of holo-rcpyp following cleavage of the ... | 2004 | 14967022 |
| the transient accumulation of the signaling state of photoactive yellow protein is controlled by the external ph. | the signaling state of the photoreceptor photoactive yellow protein is the long-lived intermediate i(2)'. the ph dependence of the equilibrium between the transient photocycle intermediates i(2) and i(2)' was investigated. the formation of i(2)' from i(2) is accompanied by a major conformational change. the kinetics and intermediates of the photocycle and of the photoreversal were measured by transient absorption spectroscopy from ph 4.6 to 8.4. singular value decomposition (svd) analysis of the ... | 2006 | 16829563 |
| initial events in the photocycle of photoactive yellow protein. | the light-induced isomerization of a double bond is the key event that allows the conversion of light energy into a structural change in photoactive proteins for many light-mediated biological processes, such as vision, photosynthesis, photomorphogenesis, and photo movement. cofactors such as retinals, linear tetrapyrroles, and 4-hydroxy-cinnamic acid have been selected by nature that provide the essential double bond to transduce the light signal into a conformational change and eventually, a p ... | 2004 | 15026418 |
| resonance raman evidence for two conformations involved in the l intermediate of photoactive yellow protein. | the blue light receptor photoactive yellow protein (pyp) displays a photocycle that involves several intermediate states. here we report resonance raman spectroscopic investigations of the short-lived red-shifted intermediate denoted pyp(l). we have found that the raman bands of the carbonyl c=o stretching mode nu(11) as well as the c=c stretching mode nu(13) for the chromophore can be resolved into two peaks, and the ratio of the two components varies as a function of ph with pk(a) approximatel ... | 2004 | 15096497 |
| short hydrogen bonds in photoactive yellow protein. | eight high-resolution crystal structures of the ground state of photoactive yellow protein (pyp) solved under a variety of conditions reveal that its chromophore is stabilized by two unusually short hydrogen bonds. both tyr42 oeta and glu46 oepsilon are separated from the chromophore phenolate oxygen by less than the sum of their atomic van der waals radii, 2.6 angstroms. this is characteristic of strong hydrogen bonding, in which hydrogen bonds acquire significant covalent character. the hydrog ... | 2004 | 15159559 |
| photoactive yellow protein, bacteriophytochrome, and sensory rhodopsin in purple phototrophic bacteria. | the purple photosynthetic bacteria contain a large variety of sensory and regulatory proteins, and those responding to light are among the most interesting. these currently include bacteriophytochrome (bph), sensory rhodopsin (sr), and photoactive yellow protein (pyp), which all appear to function as light sensors. we herein interpret new findings within the context of current knowledge. for greater detail, the reader is referred to comprehensive reviews on these topics. of the three proteins, o ... | 2004 | 15170480 |
| tryptophan fluorescence monitors structural changes accompanying signalling state formation in the photocycle of photoactive yellow protein. | photoactive yellow protein, a small, water-soluble blue-light absorbing photoreceptor protein from ectothiorhodospira(halorhodospira)[space]halophila has a structure with two hydrophobic cores, of which the main one houses its light-sensitive chromophore (p-coumaric acid), separated by a central [small beta]-sheet. this photoreceptor protein contains a single tryptophan residue (w119) that is situated at the interface between the central beta-sheet and its n-terminal cap. the fluorescence proper ... | 2004 | 15170481 |
| structural role of tyrosine 98 in photoactive yellow protein: effects on fluorescence, gateway, and photocycle recovery. | we have recently shown that the y98q mutant of pyp has a major effect on the photocycle kinetics ( approximately 40 times slower recovery). we have now determined the crystal structure of y98q at 2.2 a resolution to reveal the role of residue y98 in the pyp photocycle. although the overall structure is very similar to that of wt, we observed two major effects of the mutation. one obvious consequence is a conformational change of the beta4-beta5 loop, which includes a repositioning of residue m10 ... | 2007 | 17198379 |
| vibrational assignment of the 4-hydroxycinnamyl chromophore in photoactive yellow protein. | photoactive yellow protein (pyp) is a bacterial photoreceptor containing a 4-hydroxycinnamyl chromophore. we report the raman spectra for the dark state of pyp whose chromophore is isotopically labeled with 13c at the carbonyl carbon atom or at the ring carbon atoms. spectra have been also measured with pyp in d2o where the exchangeable protons are deuterated. most of the observed raman bands are assigned on the basis of the observed isotope shifts and normal mode calculations using a density fu ... | 2007 | 17311445 |
| incoherent manipulation of the photoactive yellow protein photocycle with dispersed pump-dump-probe spectroscopy. | photoactive yellow protein is the protein responsible for initiating the "blue-light vision" of halorhodospira halophila. the dynamical processes responsible for triggering the photoactive yellow protein photocycle have been disentangled with the use of a novel application of dispersed ultrafast pump-dump-probe spectroscopy, where the photocycle can be started and interrupted with appropriately tuned and timed laser pulses. this "incoherent" manipulation of the photocycle allows for the detailed ... | 2004 | 15345564 |
| photoreversal kinetics of the i1 and i2 intermediates in the photocycle of photoactive yellow protein by double flash experiments with variable time delay. | we investigated the kinetics of photoreversal from the i(1) and i(2) intermediates of photoactive yellow protein (pyp) by time-resolved optical absorption spectroscopy with double flash excitation. a first flash, at 430 nm, initiated the photocycle. after a variable time delay, the i(1) intermediate was photoreversed by a second flash, at 500 nm, or a mixture of i(2) and i(2)' intermediates was photoreversed by a second flash, at 355 nm. by varying the delay from 1 micros to 3 s, we were able to ... | 2005 | 15641791 |
| study of the high-potential iron sulfur protein in halorhodospira halophila confirms that it is distinct from cytochrome c as electron carrier. | the role of high-potential iron sulfur protein (hipip) in donating electrons to the photosynthetic reaction center in the halophilic gamma-proteobacterium halorhodospira halophila was studied by epr and time-resolved optical spectroscopy. a tight complex between hipip and the reaction center was observed. the epr spectrum of hipip in this complex was drastically different from that of the purified protein and provides an analytical tool for the detection and characterization of the complexed for ... | 2005 | 15728382 |
| thermochromatium tepidum photoactive yellow protein/bacteriophytochrome/diguanylate cyclase: characterization of the pyp domain. | the purple phototrophic bacterium, thermochromatium tepidum, contains a gene for a chimeric photoactive yellow protein/bacteriophytochrome/diguanylate cyclase (ppd). we produced the tc. tepidum pyp domain (tt pyp) in escherichia coli, and found that it has a wavelength maximum at 358 nm due to a leu46 substitution of the color-tuning glu46 found in the prototypic halorhodospira halophila pyp (hh pyp). however, the 358 nm dark-adapted state is in a ph-dependent equilibrium with a yellow species a ... | 2005 | 15779902 |
| diverse roles of glycine residues conserved in photoactive yellow proteins. | 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, gly-86, and gly-115) induces destabilization of the protein structure. on the other hand, substitution for gly-77 and gly-82, incorporated into the fifth alpha-helix, slows the photocycle by 15-20 tim ... | 2008 | 18227128 |
| visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds. | determining 3d intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. here we use time-resolved laue crystallography to extract short-lived intermediate structures and thereby unveil signal transduction in the blue light photoreceptor photoactive yellow protein (pyp) from halorhodospira halophila. by analyzing a comprehensive set of laue data during the pyp photocycle (forty-seven time points fr ... | 2005 | 15870207 |
| initial photoinduced dynamics of the photoactive yellow protein. | the photoactive yellow protein (pyp) is the photoreceptor protein responsible for initiating the blue-light repellent response of the halorhodospira halophila bacterium. optical excitation of the intrinsic chromophore in pyp, p-coumaric acid, leads to the initiation of a photocycle that comprises several distinct intermediates. the dynamical processes responsible for the initiation of the pyp photocycle have been explored with several time-resolved techniques, which include ultrafast electronic ... | 2005 | 15884065 |
| the solution structure of a transient photoreceptor intermediate: delta25 photoactive yellow protein. | the n-terminally truncated variant of photoactive yellow protein (delta25-pyp) undergoes a very similar photocycle as the corresponding wild-type protein (wt-pyp), although the lifetime of its light-illuminated (pb) state is much longer. this has allowed determination of the structure of both its dark- (pg) as well as its pb-state in solution by nuclear magnetic resonance (nmr) spectroscopy. the pg structure shows a well-defined fold, similar to wt-pyp and the x-ray structure of the pg state of ... | 2005 | 16004868 |
| from primary photochemistry to biological function in the blue-light photoreceptors pyp and appa. | to properly respond to changes in fluency conditions, nature has developed a variety of photosensors that modulate gene expression, enzyme activity and/or motility. dedicated types have evolved, which can be classified in six families: rhodopsins, phytochromes, xanthopsins, cryptochromes, phototropins and bluf-proteins. the photochemistry of the first three families is based on cis/trans isomerization of an ethylene bond. surprisingly, the latter three all use flavin as their chromophore, but ea ... | 2005 | 16121278 |
| discovery and characterization of electron transfer proteins in the photosynthetic bacteria. | research on photosynthetic electron transfer closely parallels that of other electron transfer pathways and in many cases they overlap. thus, the first bacterial cytochrome to be characterized, called cytochrome c (2), is commonly found in non-sulfur purple photosynthetic bacteria and is a close homolog of mitochondrial cytochrome c. the cytochrome bc (1) complex is an integral part of photosynthetic electron transfer yet, like cytochrome c (2), was first recognized as a respiratory component. c ... | 2003 | 16228571 |
| effect of salt and ph on the activation of photoactive yellow protein and gateway mutants y98q and y98f. | we investigated the photocycle of mutants y98q and y98f of the photoactive yellow protein (pyp) from halorhodospira halophila. y98 is located in the beta4-beta5 loop and is thought to interact with r52 in the alpha3-alpha4 loop thereby stabilizing this region. y98 is conserved in all known pyp species, except in ppr and ppd where it is replaced by f. we find that replacement of y98 by f has no significant effect on the photocycle kinetics. however, major changes were observed with the y98q mutan ... | 2005 | 16229455 |
| photodissociation pathways of gas-phase photoactive yellow protein chromophores. | the absorption dynamics of two model chromophores of the photoactive yellow protein were studied in gas-phase experiments. using different time-resolving techniques with an overall sensitivity ranging from seconds down to a few nanoseconds, complex dynamics were revealed for the p -coumaric acid anion, involving both fragmentation and electron detachment as possible photoresponse channels. for the trans-thiophenyl-p-coumarate model, despite its more complex molecular structure, simpler decay dyn ... | 2008 | 19113164 |
| diversity of anoxygenic phototrophic sulfur bacteria in the microbial mats of the ebro delta: a combined morphological and molecular approach. | the diversity of purple and green sulfur bacteria in the multilayered sediments of the ebro delta was investigated. specific oligonucleotide primers for these groups were used for the selective amplification of 16s rrna gene sequences. subsequently, amplification products were separated by denaturing gradient gel electrophoresis and sequenced, which yielded a total of 32 sequences. six of the sequences were related to different cultivated members of the green sulfur bacteria assemblage, whereas ... | 2005 | 16329919 |
| time-resolved single tryptophan fluorescence in photoactive yellow protein monitors changes in the chromophore structure during the photocycle via energy transfer. | we show from time-resolved fluorescence intensity and depolarization experiments that the fluorescence of the unique tryptophan w119 of pyp is quenched by energy transfer to the 4-hydroxycinnamoyl chromophore. whereas the intensity decay has a time constant of 0.18 ns in p, the decay in the absence of the cofactor (apo-pyp) has a single exponential lifetime of 4.8 ns. this difference in lifetime with and without acceptor can be explained quantitatively on the basis of energy transfer and the hig ... | 2005 | 16363794 |
| structural evolution of the chromophore in the primary stages of trans/cis isomerization in photoactive yellow protein. | we have studied the structural changes induced by optical excitation of the chromophore in wild-type photoactive yellow protein (pyp) in liquid solution with a combined approach of polarization-sensitive ultrafast infrared spectroscopy and density functional theory calculations. we identify the nuc8-c9 marker modes for solution phase pyp in the p and i0 states, from which we derive that the first intermediate state i0 that appears with a 3 ps time constant can be characterized to have a cis geom ... | 2005 | 16366562 |
| primary steps of the photoactive yellow protein: isolated chromophore dynamics and protein directed function. | the cycle of the photoactive yellow protein (pyp) has been extensively studied, but the dynamics of the isolated chromophore responsible for transduction is unknown. here, we present real-time observation of the dynamics of the negatively charged chromophore and detection of intermediates along the path of trans-to-cis isomerization using femtosecond mass selection/electron detachment techniques. the results show that the role of the protein environment is not in the first step of double-bond tw ... | 2006 | 16407155 |
| time-resolved thermodynamics: heat capacity change of transient species during photoreaction of pyp. | heat capacity changes of short-lived transient species in different time ranges were measured for the first time by using the thermal component of the transient grating and transient lens signals at various temperatures. this method was applied to the transient intermediates of photoactive yellow protein (pyp). the temperature dependence of the enthalpy change shows that the heat capacity of the short-lived intermediate pr2 (also called i1 or pyp(l)) species is the same as that of the ground sta ... | 2006 | 16417392 |
| maldi-tof/tof de novo sequence analysis of 2-d page-separated proteins from halorhodospira halophila, a bacterium with unsequenced genome. | because protein identifications rely on matches with sequence databases, high-throughput proteomics is currently largely restricted to those species for which comprehensive sequence databases are available. the identification of proteins derived from organisms with unsequenced genomes mainly depends on homology searching. here, we report the use of a simplified, gel-based, chemical derivatization strategy for de novo sequence analysis using a maldi-tof/tof mass spectrometer. this approach allows ... | 2006 | 16739227 |
| photocycle and photoreversal of photoactive yellow protein at alkaline ph: kinetics, intermediates, and equilibria. | since the habitat of halorhodospira halophila is distinctly alkaline, we investigated the kinetics and intermediates of the photocycle and photoreversal of the photoreceptor photoactive yellow protein (pyp) from ph 8 to 11. svd analysis of the transient absorption time traces in a broad wavelength range (330-510 nm) shows the presence of three spectrally distinct species (i1, i1', and i2') at ph 10. the spectrum of i1' was obtained in two different ways. the maximal absorption is at 425 nm. i1' ... | 2006 | 16752896 |
| properties of the dark and signaling states of photoactive yellow protein probed by solution phase hydrogen/deuterium exchange and mass spectrometry. | the perturbations on conversion from the dark state to the signaling state in photoactive yellow protein have been determined by solution-phase hydrogen/deuterium exchange and mass spectrometry. both the wild type and m100a mutant are used in this study, with the mutant providing over 90% conversion to the bleached state under steady-state illumination. we found perturbations in both the wild type and the mutant on illumination, consistent with a more flexible structure in the long-lived signali ... | 2006 | 17002275 |
| ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein. | photoactive proteins such as pyp (photoactive yellow protein) are generally accepted as model systems for studying protein signal state formation. pyp is a blue-light sensor from the bacterium halorhodospira halophila. the formation of pyp's signaling state is initiated by trans-cis isomerization of the p-coumaric acid chromophore upon the absorption of light. the quantum yield of signaling state formation is approximately 0.3. using femtosecond visible pump/mid-ir probe spectroscopy, we investi ... | 2006 | 17015839 |
| predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein. | understanding the dynamics of large-scale conformational changes in proteins still poses a challenge for molecular simulations. we employ transition path sampling of explicit solvent molecular dynamics trajectories to obtain atomistic insight in the reaction network of the millisecond timescale partial unfolding transition in the photocycle of the bacterial sensor photoactive yellow protein. likelihood maximization analysis predicts the best model for the reaction coordinates of each substep as ... | 2010 | 20133754 |
| modulating native-like residual structure in the fully denatured state of photoactive yellow protein affects its refolding. | residual structure in the fully unfolded state is a key element for understanding protein folding. we show that the residual structure in fully denatured photoactive yellow protein (pyp) is affected by isomerization of its p-coumaric acid (pca) chromophore. the exposure of total surface area and hydrophobic surface area upon unfolding was quantified by denaturant m values and heat capacity changes (deltac(p)), respectively. the exposure of the buried surface area upon the unfolding of the acid-d ... | 2010 | 20178976 |
| spectral tuning of photoactive yellow protein. | we report a theoretical study on the optical properties of a small, water-soluble photosensory receptor, photoactive yellow protein (pyp). a hierarchical ab initio molecular orbital calculation accurately evaluated the optical absorption maximum of the wild-type, as well as the lambda(max) values of 12 mutants. electronic excitation of the chromophore directly affects the electronic state of nearby atoms in the protein environment. this effect is explicitly considered in the present study. furth ... | 2007 | 17017845 |
| trans-cis photoisomerization of a photoactive yellow protein model chromophore in crystalline phase. | we have studied the photoinduced trans/cis isomerization of the protonated form of p-hydroxycinnamic thiophenyl ester, a model chromophore of the photoactive yellow protein (pyp), in crystalline phase, by both fluorescence and infrared spectroscopies. the conversion from trans to cis configuration is revealed by a shift of the fluorescence peak and by inspection of the infrared maker bands. the crystal packing apparently stabilizes the cis photoproduct, suggesting different environmental effects ... | 2006 | 17034177 |
| preparation of large crystals of photoactive yellow protein for neutron diffraction and high resolution crystal structure analysis. | the exact positions of all the hydrogen atoms in photoactive yellow protein (pyp) is important for understanding the molecular mechanism of the photoreaction because the protonation/deprotonation of certain amino acid residues and rearrangements in the hydrogen bond network are involved in the conformational changes of pyp. neutron crystallography is one of the most effective methods to determine the hydrogen positions. however, a large crystal is required for neutron crystallography because a n ... | 2007 | 17052135 |
| phylogeny and evolution of the family ectothiorhodospiraceae based on comparison of 16s rrna, cbbl and nifh gene sequences. | the occurrence of genes encoding nitrogenase and ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) was investigated in the members of the family ectothiorhodospiraceae. this family forms a separate phylogenetic lineage within the gammaproteobacteria according to 16s rrna gene sequence analysis and mostly includes photo- and chemoautotrophic halophilic and haloalkaliphilic bacteria. the cbbl gene encoding the large subunit of 'green-like' form i rubisco was found in all strains, except th ... | 2007 | 17911316 |
| diversity of rubisco and atp citrate lyase genes in soda lake sediments. | sediments from six soda lakes of the kulunda steppe (altai, russia) and from hypersaline alkaline lakes of wadi natrun (egypt) were analyzed for the presence of cbb and aclb genes encoding key enzymes ci assimilation (rubisco in calvin-benson and atp citrate lyase in rtca cycles, respectively). the cbbl gene (rubisco form i) was found in all samples and was most diverse, while the cbbm (rubisco form ii) and aclb were detected only in few samples and with a much lower diversity. the cbbl librarie ... | 2010 | 21073490 |
| neutron and x-ray structural studies of short hydrogen bonds in photoactive yellow protein (pyp). | 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 blue light. the complete structure (including h atoms) of pyp has been determined in d(2)o-soaked crystals through the application of joint x-ray (1.1 a) and neutron (2.5 a) structure refinement in combi ... | 2007 | 18007033 |
| dodecins: a family of lumichrome binding proteins. | dodecin is a small dodecameric flavoprotein from halobacterium salinarum that contains two flavins stacked between two tryptophan residues to form an aromatic tetrade. the functional properties of heterologously expressed dodecin were investigated by fluorescence spectroscopy, which allowed the determination of dissociation constants for a number of protein-ligand complexes. the values obtained were in the nanomolar to micromolar range and correlate positively with the ligand size. these data we ... | 2006 | 16460756 |
| is the photoactive yellow protein a uv-b/blue light photoreceptor? | uv light below 300 nm is shown to generate the first photocycle intermediate in the blue light photoreceptor photoactive yellow protein. fluorescence and ultrafast transient absorption measurements indicate two excitation pathways: uv-b absorption by the chromophore and fluorescence resonant energy transfer (fret) from tryptophan and tyrosine residues. | 2011 | 21267495 |
| cloning and characterization of nif structural and regulatory genes in the purple sulfur bacterium, halorhodospira halophila. | halorhodospira halophila is a halophilic photosynthetic bacterium classified as a purple sulfur bacterium. we found that h. halophila generates hydrogen gas during photoautotrophic growth as a byproduct of a nitrogenase reaction. in order to consider the applied possibilities of this photobiological hydrogen generation, we cloned and characterized the structural and regulatory genes encoding the nitrogenase, nifh, nifd and nifa, from h. halophila. this is the first description of the nif genes f ... | 2006 | 16716929 |
| surface-enhanced raman scattering captures conformational changes of single photoactive yellow protein molecules under photoexcitation. | distinct conformational changes of single photoactive yellow protein (pyp) molecules were captured under photoexcitation, using a sers substrate approach. these steps conform to those in pyp's photocycle. at the single molecule level, sers of pyp yields well-resolved peaks, some of which were not reported earlier. further, exclusive peak pairs have been identified that can elucidate pyp's conformational steps and chemisorption configuration on ag using the sers selection rules. despite the "weak ... | 2010 | 19788179 |
| proline 68 enhances photoisomerization yield in photoactive yellow protein. | in proteins and enzymes, the local environment of an active cofactor plays an important role in controlling the outcome of a functional reaction. in photoactive yellow protein (pyp), it ensures photoisomerization of the chromophore, a prerequisite for formation of a signaling state. pyp is the prototype of a pas domain, and the preferred model system for the studies of molecular mechanisms of biological light sensing. we investigated the effect of replacing proline-68, positioned near but not in ... | 2011 | 21542640 |
| axis-dependent anisotropy in protein unfolding from integrated nonequilibrium single-molecule experiments, analysis, and simulation. | we present a comprehensive study that integrates experimental and theoretical nonequilibrium techniques to map energy landscapes along well defined pull-axis specific coordinates to elucidate mechanisms of protein unfolding. single-molecule force-extension experiments along two different axes of photoactive yellow protein combined with nonequilibrium statistical mechanical analysis and atomistic simulation reveal energetic and mechanistic anisotropy. steered molecular dynamics simulations and fr ... | 2007 | 18093935 |
| photoactive yellow protein from the halophilic bacterium salinibacter ruber. | a gene for photoactive yellow protein (pyp) was identified from the genome sequence of the extremely halophilic aerobic bacterium salinibacter ruber (sr). the sequence is distantly related to the prototypic pyp from halorhodospira halophila (hh) (37% identity) and contains most of the amino acid residues identified as necessary for function. however, the sr pyp gene is not flanked by its two biosynthetic genes as in other species. to determine as to whether the sr pyp gene encodes a functional p ... | 2008 | 18198898 |
| stress tensor analysis of the protein quake of photoactive yellow protein. | immediately after photon absorption, the photoenergy is converted to local stress energy via the ultrafast photoisomerization reaction of the p-coumaric acid (pca) chromophore in a small water-soluble blue light receptor, photoactive yellow protein (pyp), derived from the halophilic bacterium, halorhodospira halophila. a series of conformational changes are then induced, which are intimately related with the relaxation process on the energy landscape of pyp. in order to understand the signaling ... | 2008 | 18309395 |
| the photoreaction of the photoactive yellow protein domain in the light sensor histidine kinase ppr is influenced by the c-terminal domains. | 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 biosynthesi ... | 2008 | 18346084 |
| low-temperature spectroscopy of met100ala mutant of photoactive yellow protein. | 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 ... | 2008 | 18399916 |
| distinguishing chromophore structures of photocycle intermediates of the photoreceptor pyp by transient fluorescence and energy transfer. | the cinnamoyl chromophore is the light-activated switch of the photoreceptor photoactive yellow protein (pyp) and isomerizes during the functional cycle. the fluorescence of w119, the only tryptophan of pyp, is quenched by energy transfer to the chromophore. this depends on the chromophore's transition dipole moment orientation and spectrum, both of which change during the photocycle. the transient fluorescence of w119 thus serves as a sensitive kinetic monitor of the chromophore's structure and ... | 2008 | 18605685 |
| toxic introns and parasitic intein in coxiella burnetii: legacies of a promiscuous past. | the genome of the obligate intracellular pathogen coxiella burnetii contains a large number of selfish genetic elements, including two group i introns (cbu.l1917 and cbu.l1951) and an intervening sequence that interrupts the 23s rrna gene, an intein (cbu.dnab) within dnab and 29 insertion sequences. here, we describe the ability of the intron-encoded rnas (ribozymes) to retard bacterial growth rate (toxicity) and examine the functionality and phylogenetic history of cbu.dnab. when expressed in e ... | 2008 | 18606739 |
| ph dependence of the photoactive yellow protein photocycle recovery reaction reveals a new late photocycle intermediate with a deprotonated chromophore. | the recovery reaction of the signaling state of photoactive yellow protein includes the following: (i) deprotonation of the p-coumaryl chromophore, (ii) refolding of the protein, and (iii) chromophore re-isomerization from the cis to the trans configuration. through analysis of the ph dependence of this recovery reaction, we were able to provide proof for the existence of an additional photocycle intermediate. the spectral similarity between this new intermediate and the dark state indicates tha ... | 2009 | 19091750 |
| de novo sequence analysis of n-terminal sulfonated peptides after in-gel guanidination. | in this protocol, we describe an approach in which two-dimensional electrophoresis (2de)-separated proteins are guanidinated in-gel prior to enzymatic cleavage. in contrast to previously described techniques, this procedure allows the extracted tryptic peptides to be n-terminally sulfonated without any further sample purification. the protocol was applied on a proteomic study of 2de-separated proteins from halorhodospira halophila, an extremophilic eubacterium with an unsequenced genome at the m ... | 2009 | 19381605 |
| menaquinone as pool quinone in a purple bacterium. | purple bacteria have thus far been considered to operate light-driven cyclic electron transfer chains containing ubiquinone (uq) as liposoluble electron and proton carrier. we show that in the purple gamma-proteobacterium halorhodospira halophila, menaquinone-8 (mk-8) is the dominant quinone component and that it operates in the q(b)-site of the photosynthetic reaction center (rc). the redox potentials of the photooxidized pigment in the rc and of the rieske center of the bc(1) complex are signi ... | 2009 | 19429705 |
| hydrogen bond dynamics in the active site of photoactive yellow protein. | hydrogen bonds play major roles in biological structure and function. nonetheless, hydrogen-bonded protons are not typically observed by x-ray crystallography, and most structural studies provide limited insight into the conformational plasticity of individual hydrogen bonds or the dynamical coupling present within hydrogen bond networks. we report the nmr detection of the hydrogen-bonded protons donated by tyr-42 and glu-46 to the chromophore oxygen in the active site of the bacterial photorece ... | 2009 | 19470452 |
| preliminary x-ray analysis of twinned crystals of sarcosine dimethylglycine methyltransferase from halorhodospira halochoris. | sarcosine dimethylglycine methyltransferase (ec 2.1.1.157) is an enzyme from the extremely halophilic anaerobic bacterium halorhodospira halochoris. this enzyme catalyzes the twofold methylation of sarcosine to betaine, with s-adenosylmethionine (adomet) as the methyl-group donor. this study presents the crystallization and preliminary x-ray analysis of recombinant sarcosine dimethylglycine methyltransferase produced in escherichia coli. mass spectroscopy was used to determine the purity and hom ... | 2009 | 19652345 |
| color regulation and stabilization of chromophore by cys69 in photoactive yellow protein active center. | model compounds of pyp chromophore were synthesized and characterized to investigate the role of the cys69 residue in the active center, which has the intramolecular nhoc hydrogen bond to the conjugated carbonyl oxygen and thioester linkage of the chromophore. the results of uv-vis and (13)c nmr spectroscopy of the model compounds indicated that they delocalized the negative charge of the chromophore and increased the contribution of the quinoid-like resonance structure in the phenolate anion st ... | 2009 | 19707683 |
| prokaryotic phototaxis. | microorganisms have various mechanisms at their disposal to react to (changes in) their ambient light climate (i.e., intensity, color, direction, and degree of polarization). of these, one of the best studied mechanisms is the process of phototaxis. this process can be described as a behavioral migration-response of an organism toward a change in illumination regime. in this chapter we discuss three of these migration responses, based on swimming, swarming, and twitching motility, respectively. ... | 2009 | 19763957 |
| controlling the photoreactivity of the photoactive yellow protein chromophore by substituting at the p-coumaric acid group. | we have performed ab initio casscf, caspt2, and eom-ccsd calculations on doubly deprotonated p-coumaric acid (pca(2-)), the chromophore precursor of the photoactive yellow protein. the results of the calculations demonstrate that pca(2-) can undergo only photoisomerization of the double bond. in contrast, the chromophore derivative with the acid replaced by a ketone (p-hydroxybenzylidene acetone, pck(-)) undergoes both single- and double-bond photoisomerization, with the single-bond relaxation c ... | 2011 | 21561119 |
| hydrogen-bond network probed by time-resolved optoacoustic spectroscopy: photoactive yellow protein and the effect of e46q and e46a mutations. | the enthalpy and structural volume changes (delta hi and delta vi) produced upon photoinduced formation and decay of the red-shifted intermediate (pr = i1) in the photoactive yellow protein (wt-pyp) from halorhodospira halophila and the mutated e46q-pyp and e46a-pyp, were determined by laser-induced optoacoustic spectroscopy (lioas) using the two-temperatures method, at ph 8.5. these mutations alter the hydrogen bond between the phenolate oxygen of the chromophore and the residue at position 46. ... | 2005 | 19791418 |
| catching a protein in the act. | | 2010 | 20133629 |
| spectral tuning in photoactive yellow protein by modulation of the shape of the excited state energy surface. | protein-chromophore interactions in photoreceptors often shift the chromophore absorbance maximum to a biologically relevant spectral region. a fundamental question regarding such spectral tuning effects is how the electronic ground state s(0) and excited state s(1) are modified by the protein. it is widely assumed that changes in energy gap between s(0) and s(1) are the main factor in biological spectral tuning. we report a generally applicable approach to determine if a specific residue modula ... | 2010 | 20220103 |
| structure-based design of a photocontrolled dna binding protein. | photocontrolled transcription factors could be powerful tools for probing the role of transcriptional processes in settings that are spatially or temporally complex. we report the structure-based design of a photocontrolled bzip-type dna binding protein that is a hybrid of the prototypical homodimeric bzip protein gcn4 and photoactive yellow protein (pyp), a blue-light-sensitive protein from halorhodospira halophila. a fusion of the c-terminal zipper region of gcn4-bzip with the n-terminal cap o ... | 2010 | 20363227 |
| artificial metalloenzymes through cysteine-selective conjugation of phosphines to photoactive yellow protein. | | 2010 | 20432427 |