Genomes and Genes
Summary: Light absorbing proteins and protein prosthetic groups found in certain microorganisms. Some microbial photoreceptors initiate specific chemical reactions which signal a change in the environment, while others generate energy by pumping specific ions across a cellular membrane.
- Schmidt M, Ihee H, Pahl R, Srajer V. Protein-ligand interaction probed by time-resolved crystallography. Methods Mol Biol. 2005;305:115-54 pubmed..The time-resolved technique, combined with trapping methods and computational approaches, holds the promise for a complete structure-based description of biomolecular reactions. ..
- Nutsch T, Marwan W, Oesterhelt D, Gilles E. Signal processing and flagellar motor switching during phototaxis of Halobacterium salinarum. Genome Res. 2003;13:2406-12 pubmed..Moreover, the simulations demonstrate that motor switching occurs through subsequent rate-limiting steps, which are both under sensory control, suggesting that two signals may be involved in halobacterial phototaxis. ..
- Lammich L, Rajput J, Andersen L. Photodissociation pathways of gas-phase photoactive yellow protein chromophores. Phys Rev E Stat Nonlin Soft Matter Phys. 2008;78:051916 pubmed..For the trans-thiophenyl-p-coumarate model, despite its more complex molecular structure, simpler decay dynamics showing only fragmentation were observed...
- Pieroni O, Plaza P, Mahet M, Angelini N, Checcucci G, Malatesta M, et al. Circular dichroism of the photoreceptor pigment oxyblepharismin. Photochem Photobiol. 2005;81:1343-6 pubmed..This experimental result is related to the existence of a high-energy interconversion barrier between two enantiomeric structures of the molecule and discussed on the basis of an asymmetric biosynthesis of its precursor, blepharismin. ..
- Koch M, Staudinger W, Siedler F, Oesterhelt D. Physiological sites of deamidation and methyl esterification in sensory transducers of Halobacterium salinarum. J Mol Biol. 2008;380:285-302 pubmed publisher..Compared to previously reported methods, the described approach significantly facilitates the identification of physiological transducer modification sites. ..
- Diller R, Jakober R, Schumann C, Peters F, Klare J, Engelhard M. The trans-cis isomerization reaction dynamics in sensory rhodopsin II by femtosecond time-resolved midinfrared spectroscopy: chromophore and protein dynamics. Biopolymers. 2006;82:358-62 pubmed..Similar observations, yet not as strongly expressed, have been made earlier in bacteriorhodopsin and halorhodopsin. ..
- Coureux P, Fan Z, Stojanoff V, Genick U. Picometer-scale conformational heterogeneity separates functional from nonfunctional states of a photoreceptor protein. Structure. 2008;16:863-72 pubmed publisher..82 A crystal structure in fact comprises an ensemble of conformational states, in which subpopulations with nearly identical structures display dramatically different functional properties. ..
- Kamikubo H, Koyama T, Hayashi M, Shirai K, Yamazaki Y, Imamoto Y, et al. The photoreaction of the photoactive yellow protein domain in the light sensor histidine kinase Ppr is influenced by the C-terminal domains. Photochem Photobiol. 2008;84:895-902 pubmed publisher..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...
- Hendriks J, van Stokkum I, Hellingwerf K. Deuterium isotope effects in the photocycle transitions of the photoactive yellow protein. Biophys J. 2003;84:1180-91 pubmed..This is supported in our data through the combination of the observed pOH and pH dependence, together with the kinetic deuterium isotope effect. ..
- Lee B, Croonquist P, Sosnick T, Hoff W. PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation. J Biol Chem. 2001;276:20821-3 pubmed..Our results show that receptor activation by light converts PYP to a molten globule and indicate stimulus-induced unfolding to a partially unstructured molten globule as a novel theme in signaling. ..
- Genick U, Soltis S, Kuhn P, Canestrelli I, Getzoff E. Structure at 0.85 A resolution of an early protein photocycle intermediate. Nature. 1998;392:206-9 pubmed..The resultant stored energy is used to drive the PYP light cycle. These results suggest a model for phototransduction, with implications for bacteriorhodopsin, photoactive proteins, PAS domains, and signalling proteins. ..
- del Rosario R, Staudinger W, Streif S, Pfeiffer F, Mendoza E, Oesterhelt D. Modelling the CheY(D10K,Yl00W) Halobacterium salinarum mutant: sensitivity analysis allows choice of parameter to be modified in the phototaxis model. IET Syst Biol. 2007;1:207-21 pubmed..Thus, those experimental data that could previously be explained only by ad hoc assumptions are now obtained 'naturally' from the revised model...
- Malo G, Pouwels L, Wang M, Weichsel A, Montfort W, Rizzo M, et al. X-ray structure of Cerulean GFP: a tryptophan-based chromophore useful for fluorescence lifetime imaging. Biochemistry. 2007;46:9865-73 pubmed..Possible interpretations in terms of chromophore isomerization are presented. ..
- Leenders E, Guidoni L, Rothlisberger U, Vreede J, Bolhuis P, Meijer E. Protonation of the chromophore in the photoactive yellow protein. J Phys Chem B. 2007;111:3765-73 pubmed..Combining these simulations with more QMMM calculations enabled us to check the stability of protonation states and clarify the initial requirements for the proton transfer in PYP. ..
- Shirai K, Yamazaki Y, Kamikubo H, Imamoto Y, Kataoka M. Attempt to simplify the amino-acid sequence of photoactive yellow protein with a set of simple rules. Proteins. 2007;67:821-33 pubmed..The structural characterization of each chimeric protein indicates that the important information on the structure formation is encoded in the beta-scaffold region. ..
- Kamikubo H, Shimizu N, Harigai M, Yamazaki Y, Imamoto Y, Kataoka M. Characterization of the solution structure of the M intermediate of photoactive yellow protein using high-angle solution x-ray scattering. Biophys J. 2007;92:3633-42 pubmed..High-angle x-ray scattering with molecular fluctuation simulation allows us to derive the structural properties of the transient state of a protein in solution. ..
- Olmedo M, Ruger Herreros C, Luque E, Corrochano L. A complex photoreceptor system mediates the regulation by light of the conidiation genes con-10 and con-6 in Neurospora crassa. Fungal Genet Biol. 2010;47:352-63 pubmed publisher..In addition we show that the regulatory protein VE-1 is required for full photocarotenogenesis. We propose that these proteins may modulate the WCC in a gene-specific way. ..
- Masuda S, Bauer C. AppA is a blue light photoreceptor that antirepresses photosynthesis gene expression in Rhodobacter sphaeroides. Cell. 2002;110:613-23 pubmed..These results establish AppA as a transcription factor that controls both redox and blue light repression of photosystem gene expression by mediating DNA binding activity of PpsR. ..
- Imamoto Y, Harigai M, Morimoto T, Kataoka M. Low-temperature spectroscopy of Met100Ala mutant of photoactive yellow protein. Photochem Photobiol. 2008;84:970-6 pubmed publisher..5 A), 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...
- van Aalten D, Haker A, Hendriks J, Hellingwerf K, Joshua Tor L, Crielaard W. Engineering photocycle dynamics. Crystal structures and kinetics of three photoactive yellow protein hinge-bending mutants. J Biol Chem. 2002;277:6463-8 pubmed
- den Heeten R, Muñoz B, Popa G, Laan W, Kamer P. Synthesis of hybrid transition-metalloproteins via thiol-selective covalent anchoring of Rh-phosphine and Ru-phenanthroline complexes. Dalton Trans. 2010;39:8477-83 pubmed publisher..In addition wild-type PYP (PYP WT), PYP R52G and ALBP were successfully modified with a (eta(6)-arene) ruthenium(II) phenanthroline complex via a maleimide linker. ..
- van der Horst M, Van Stokkum I, Crielaard W, Hellingwerf K. The role of the N-terminal domain of photoactive yellow protein in the transient partial unfolding during signalling state formation. FEBS Lett. 2001;497:26-30 pubmed..Furthermore, deletion of the N-terminal domain completely abolishes the non-linearity of the Arrhenius plot of the rate of ground state recovery. ..
- Fiedler B, Börner T, Wilde A. Phototaxis in the cyanobacterium Synechocystis sp. PCC 6803: role of different photoreceptors. Photochem Photobiol. 2005;81:1481-8 pubmed
- Khan J, Imamoto Y, Kataoka M, Tokunaga F, Terazima M. Time-resolved thermodynamics: heat capacity change of transient species during photoreaction of PYP. J Am Chem Soc. 2006;128:1002-8 pubmed..This technique can be used for photochemical reactions in general to investigate the conformational change and the hydrophobic interaction in a time domain...
- Ko C, Levine B, Toniolo A, Manohar L, Olsen S, Werner H, et al. Ab initio excited-state dynamics of the photoactive yellow protein chromophore. J Am Chem Soc. 2003;125:12710-1 pubmed
- Chen C, DeMay B, Gladfelter A, Dunlap J, Loros J. Physical interaction between VIVID and white collar complex regulates photoadaptation in Neurospora. Proc Natl Acad Sci U S A. 2010;107:16715-20 pubmed publisher..Thus, our results demonstrate a direct molecular connection between two of the most essential light signaling components in Neurospora, VVD and WCC, illuminating a previously uncharacterized process for light-sensitive eukaryotic cells. ..
- Froehlich A, Pregueiro A, Lee K, Denault D, Colot H, Nowrousian M, et al. The molecular workings of the Neurospora biological clock. Novartis Found Symp. 2003;253:184-98; discussion 102-9, 198-202, 281-4 pubmed..This gene may be an entry point to study the connection between the biological clock and other basic cellular mechanisms. ..
- Ryan W, Gordon D, Levy D. Gas-phase photochemistry of the photoactive yellow protein chromophore trans-p-coumaric acid. J Am Chem Soc. 2002;124:6194-201 pubmed..Although trans-CA was excited in all three regions, a significant cis-CA peak appeared only in region II, though a small cis peak was observed in region III. ..
- Kyndt J, Meyer T, Cusanovich M, Van Beeumen J. Characterization of a bacterial tyrosine ammonia lyase, a biosynthetic enzyme for the photoactive yellow protein. FEBS Lett. 2002;512:240-4 pubmed..To our knowledge it is the first time this type of enzyme has been found in bacteria. ..
- Ishizuka T, Narikawa R, Kohchi T, Katayama M, Ikeuchi M. Cyanobacteriochrome TePixJ of Thermosynechococcus elongatus harbors phycoviolobilin as a chromophore. Plant Cell Physiol. 2007;48:1385-90 pubmed..The results indicated that the chromophore of TePixJ is not PCB, but its isomer, phycoviolobilin (PVB). It is suggested that the GAF domain of TePixJ has auto-lyase and auto-isomerase activities. ..
- van der Horst M, Hellingwerf K. Photoreceptor proteins, "star actors of modern times": a review of the functional dynamics in the structure of representative members of six different photoreceptor families. Acc Chem Res. 2004;37:13-20 pubmed..Some members of the rhodopsins, the xanthopsins, and the phototropins are so well characterized that they function as model systems to study (receptor) protein dynamics and (un)folding. ..
- van Aalten D, Crielaard W, Hellingwerf K, Joshua Tor L. Conformational substates in different crystal forms of the photoactive yellow protein--correlation with theoretical and experimental flexibility. Protein Sci. 2000;9:64-72 pubmed..We show that these differences can be used to obtain a description of the flexibility of the protein that is consistent with the motions observed in solution. ..
- Brudler R, Rammelsberg R, Woo T, Getzoff E, Gerwert K. Structure of the I1 early intermediate of photoactive yellow protein by FTIR spectroscopy. Nat Struct Biol. 2001;8:265-70 pubmed..This excludes an I1 structural model proposed on the basis of time resolved Laue crystallography, but does agree with the cryotrapped structure of an I1 precursor...
- Rossle S, Frank I. First-principles simulation of photoreactions in biological systems. Front Biosci (Landmark Ed). 2009;14:4862-77 pubmed..Like this, bonds can be formed and broken, that is, chemical reactions can be simulated. The review focuses on applications of first-principles molecular dynamics to photoactive proteins. ..
- Kyndt J, Savvides S, Memmi S, Koh M, Fitch J, Meyer T, et al. Structural role of tyrosine 98 in photoactive yellow protein: effects on fluorescence, gateway, and photocycle recovery. Biochemistry. 2007;46:95-105 pubmed..We tested the recovery kinetics of mutant P68A and found that, although the gateway may be important for photocycle initiation, its role in recovery to the ground state is minimal...
- Brudler R, Gessner C, Li S, Tyndall S, Getzoff E, Woods V. PAS domain allostery and light-induced conformational changes in photoactive yellow protein upon I2 intermediate formation, probed with enhanced hydrogen/deuterium exchange mass spectrometry. J Mol Biol. 2006;363:148-60 pubmed
- Yeremenko S, Hellingwerf K. Resolving protein structure dynamically. Structure. 2005;13:4-6 pubmed
- Du L, Zhao Y, Chen J, Yang L, Zheng Y, Tang Y, et al. D77, one benzoic acid derivative, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular LEDGF/p75. Biochem Biophys Res Commun. 2008;375:139-44 pubmed publisher..As the firstly discovered small molecular compound targeting HIV-1 integrase interaction with LEDGF/p75, D77 might supply useful structural information for further anti-HIV agent discovery. ..
- Baca M, Borgstahl G, Boissinot M, Burke P, Williams D, Slater K, et al. Complete chemical structure of photoactive yellow protein: novel thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry. Biochemistry. 1994;33:14369-77 pubmed
- Groot M, van Wilderen L, Di Donato M. Time-resolved methods in biophysics. 5. Femtosecond time-resolved and dispersed infrared spectroscopy on proteins. Photochem Photobiol Sci. 2007;6:501-7 pubmed..We further discuss a few examples of experiments performed on the photoactive yellow protein and photosynthetic complexes in more detail. ..
- Khan J, Imamoto Y, Yamazaki Y, Kataoka M, Tokunaga F, Terazima M. A biosensor in the time domain based on the diffusion coefficient measurement: intermolecular interaction of an intermediate of photoactive yellow protein. Anal Chem. 2005;77:6625-9 pubmed..The characteristic advantages and limitations are summarized. ..
- Mullineaux C. How do cyanobacteria sense and respond to light?. Mol Microbiol. 2001;41:965-71 pubmed..Some problems in characterizing cyanobacterial signal transduction pathways are outlined and alternative experimental strategies are discussed. ..
- Kirik I, Nefedova L, Fantin I, Babykin M. [Inversion of phototaxis in cells of Synechocystis sp. PCC 6803 determined by a mutation in the regulatory gene prqR]. Genetika. 2008;44:474-82 pubmed..These data imply that mutation prqRL17Q changes the specificity of the PrqR repressor protein and thereby affects the regulation of phototaxis at the level of photoperception and signal transduction in cells. ..
- Tanaka K, Nakasone Y, Okajima K, Ikeuchi M, Tokutomi S, Terazima M. Oligomeric-state-dependent conformational change of the BLUF protein TePixD (Tll0078). J Mol Biol. 2009;386:1290-300 pubmed..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. ..
- Unno M, Kumauchi M, Sasaki J, Tokunaga F, Yamauchi S. Resonance Raman spectroscopy and quantum chemical calculations reveal structural changes in the active site of photoactive yellow protein. Biochemistry. 2002;41:5668-74 pubmed..This large motion of the chromophore is potentially correlated with the succeeding global conformational changes in the protein, which ultimately leads to transduction of a biological signal...
- Philip A, Nome R, Papadantonakis G, Scherer N, Hoff W. Spectral tuning in photoactive yellow protein by modulation of the shape of the excited state energy surface. Proc Natl Acad Sci U S A. 2010;107:5821-6 pubmed publisher..These results reveal that residue 46 tunes the absorbance spectrum of PYP largely by modulating the width of the S(1) energy surface...
- Meyer T, Tollin G, Hazzard J, Cusanovich M. Photoactive yellow protein from the purple phototrophic bacterium, Ectothiorhodospira halophila. Quantum yield of photobleaching and effects of temperature, alcohols, glycerol, and sucrose on kinetics of photobleaching and recovery. Biophys J. 1989;56:559-64 pubmed
- Jurk M, Dorn M, Kikhney A, Svergun D, Gartner W, Schmieder P. The switch that does not flip: the blue-light receptor YtvA from Bacillus subtilis adopts an elongated dimer conformation independent of the activation state as revealed by a combined AUC and SAXS study. J Mol Biol. 2010;403:78-87 pubmed publisher..In addition, we show that YtvA does not change its oligomerization state or its overall shape upon light activation. ..
- de Groot M, Buma W. Comment on "Gas-phase photochemistry of the photoactive yellow protein chromophore trans-p-coumaric acid". J Phys Chem A. 2005;109:6135-6 pubmed
- Bernard C, Houben K, Derix N, Marks D, van der Horst M, Hellingwerf K, et al. The solution structure of a transient photoreceptor intermediate: Delta25 photoactive yellow protein. Structure. 2005;13:953-62 pubmed..Thus, the partially unfolded nature of the presumed signaling state of PYP in solution, as suggested previously, has now been structurally demonstrated...
- Kyndt J, Fitch J, Meyer T, Cusanovich M. Thermochromatium tepidum photoactive yellow protein/bacteriophytochrome/diguanylate cyclase: characterization of the PYP domain. Biochemistry. 2005;44:4755-64 pubmed..However, it is kinetically most similar to Rhodocista centenaria PYP (Ppr) despite the very different absorption spectra due to the lack of E46...
- Anderson S, Srajer V, Pahl R, Rajagopal S, Schotte F, Anfinrud P, et al. Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein. Structure. 2004;12:1039-45 pubmed