Comparison of the Photochemical Reaction of Photoactive Yellow Protein in Crystal with Reaction in Solution1

Photoactive yellow protein (PYP) is a photoreceptor protein for the negative phototaxis ofEctothiorhodospira halophila. The crystal structures of several photo‒intermediates have been revealed by X-ray crystallography. In the crystal structure of the active intermediate, PYPM, no significant structural changes were observed except for the vicinity of the chromophore. On the contrary, spectroscopic studies with solution condition demonstrated that global structural changes occur during the photo‒cycle. In order to reveal the origin of the discrepancies, we measured the reaction kinetics upon illumination under crystal condition and to compare them with those observed under solution condition. The reactive portion decreases with the increase of crystallinity. The rate constant of PYPMdecay also decreases with the increase of crystallinity. These results suggest two possibilities: (1) PYP in crystal does not react by the illumination; (2) the photoreaction rate is highly accelerated in crystal. Consequently, the photoreaction in crystal is considered to be highly influenced by the force constraint from crystalline lattice.

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Syntheses and Spectroscopic Studies of Some New Diazaphospholes and Diazaphosphorinanes. Crystal Structure of 4

Zeitschrift für Naturforschung B ◽

10.1515/znb-2005-1001 ◽

2005 ◽

Vol 60 (10) ◽

pp. 1021-1026 ◽

Cited By ~ 12

Author(s):

Khodayar Gholivand ◽

Zahra Shariatinia ◽

Mehrdad Pourayoubi ◽

Sedigheh Farshadian

Keyword(s):

Crystal Structure ◽

Ir Spectroscopy ◽

Spectroscopic Studies ◽

Coupling Constants ◽

Crystalline Lattice ◽

Polymeric Chain ◽

Ring Strain ◽

One Dimensional ◽

X Ray ◽

X Ray Crystallography

New diazaphospholes and diazaphosphorinanes with formula were synthesized and characterized by 1H, 13C, 31P NMR and IR spectroscopy and elemental analysis. The structure of compound 1 has been determined by X-ray crystallography. A one-dimensional polymeric chain was observed in the crystalline lattice produced by intermolecular -P=O. . .H-N- and -C=O. . .H-N-hydrogen bonds. Compounds 1 and 2 contain five-membered rings and show high values for 2J(PNH) and 2J(P,C) coupling constants due to the ring strain. These constants are reduced seriously in compounds with six-membered rings. In compound 6 with CCl3C(O)NH moiety, all phosphorus-hydrogen couplings are zero.

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Synthesis and spectroscopic studies of cobalt(III) complexes with 5-methyl-3-formylpyrazole-N(4)-diethylthiosemicarbazone (HMPzNEt2): X-ray crystallography of [Co(MPzNEt2)2]ClO4·2H2O (I) and [Co(MPzNEt2)2]BF4·2H2O (II)

Polyhedron ◽

10.1016/s0277-5387(02)00847-1 ◽

2002 ◽

Vol 21 (7) ◽

pp. 779-785 ◽

Cited By ~ 13

Author(s):

Nitis Chandra Saha ◽

Ray J Butcher ◽

Siddhartha Chaudhuri ◽

Nityananda Saha

Keyword(s):

Spectroscopic Studies ◽

X Ray ◽

X Ray Crystallography

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Coordination chemistry of thioether–pyridazine macrocycles. III. Synthetic, structural, and spectroscopic studies of Cu(II), Cu(II)Cu(I), and Cu(I) complexes of a hexathiapyridazinophane macrocyclic ligand

Canadian Journal of Chemistry ◽

10.1139/v93-144 ◽

1993 ◽

Vol 71 (7) ◽

pp. 1086-1093 ◽

Cited By ~ 13

Author(s):

Liqin Chen ◽

Laurence K. Thompson ◽

John N. Bridson

Keyword(s):

Mass Spectrometry ◽

Macrocyclic Ligand ◽

Spectroscopic Studies ◽

Orthorhombic System ◽

Space Group ◽

X Ray ◽

X Ray Crystallography ◽

Triclinic System ◽

Square Planar ◽

Copper Centre

The preparation and properties of the thioether–pyridazine macrocycle (L4; C16H20S6N4) containing two pyridazine subunits, and its Cu(II), Cu(II)Cu(I), and Cu(I) complexes are described. The ligand is characterized by 1H nuclear magnetic resonance and mass spectrometry, and the complexes by infrared, eleetronic spectra, and magnetism, and in some cases by X-ray crystallography. The complex [Cu2(L4)Cl4]x, (1) crystallized in the triclinic system, space group [Formula: see text] with a = 8.6204(8) Å, b = 9.850(1) Å, c = 8.348(1) Å, α = 111.46(1)°, β = 102.50(1)°, γ = 71.818(9)°, V = 622.6(1) Å3, and Z = 1 (R = 0.043, Rw = 0.042 for 1312 reflections). Two monodentate pyridazine rings in the same ligand bind to one trans square-planar copper centre (CuN2Cl2) with two sulfurs from each ligand binding to another trans square-planar copper centre (CuS2Cl2) to form a polynuclear chain. The complex [Cu(L4)Cl2] (3) crystallized in the triclinic system, space group [Formula: see text] with a = 11.001(1) Å, b = 12.888(2) Å, c = 8.704(1) Å, α = 102.89(1)°, β = 103.36(1)°,γ = 75.84(1)°, V = 1145.8(3) Å3 and Z = 2 (R = 0.056, Rw = 0.044 for 2059 reflections). A trans square-planar structure (CuN2Cl2) exists for 3 with monodentate pyridazines. [Cu(L4)(NO3)2] (4) crystallized in the orthorhombic system, space group P212121, with a = 15.148(2) Å, b = 15.562(3) Å, c = 11.064(1) Å, V = 2608.2(7) Å3 and Z = 4 (R = 0.039, Rw = 0.034 for 1864 reflections). Two monodentate pyridazine rings and two bidentate nitrates bind to a pseudo-octahedral copper(II) centre.

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Fused Supracyclopentadienyl Ligand Precursors. Synthesis, Structure, and Some Reactions of 1,3-Diphenylcyclopenta[l]phenanthrene-2-one, 1,2,3-Triphenylcyclopenta[l]phenanthrene-2-ol, 1-Chloro-1,2,3-triphenylcyclopenta[l]phenanthrene, 1-Bromo-1,2,3-triphenylcyclopenta[l]phenanthrene, and 1,2,3-Triphenyl-1H-cyclopenta[l]phenanthrene

Australian Journal of Chemistry ◽

10.1071/ch05172 ◽

2006 ◽

Vol 59 (2) ◽

pp. 135 ◽

Cited By ~ 4

Author(s):

Glen D. Dennis ◽

David Edwards-Davis ◽

Leslie D. Field ◽

Anthony F. Masters ◽

Thomas Maschmeyer ◽

...

Keyword(s):

Acetic Acid ◽

Good Yield ◽

Photochemical Reaction ◽

Subsequent Reaction ◽

X Ray ◽

X Ray Crystallography ◽

Independent Synthesis ◽

Ligand Precursors

The photochemical reaction of 1,3-diphenylcyclopenta[l]phenanthrene-2-one 5 (phencyclone) with oxygen in acetone leads to the formation of 1,2,3-trihydro-1,2,3-triphenylcyclo-penta[l]phenanthrene 7 (9,10-dibenzoylphenanthrene) along with a trace of the lactone 1,4-diphenylcyclo-3-pyran[l]phenanthrene-2-one 8. An independent synthesis of 8 was achieved by the reaction of 5 with FeCl3 in CHCl3. The treatment of 5 with phenyllithium yields 1,2,3-triphenylcyclopenta[l]phenanthrene-2-ol 9-OH in good yield. Subsequent reaction of 9-OH with SOCl2 or SOBr2 in pyridine leads to the formation of the halo-analogues 1-chloro-1,2,3-triphenylcyclopenta[l]phenanthrene 9-Cl and 1-bromo-1,2,3-triphenylcyclopenta[l]phenanthrene 9-Br, respectively. Treatment of 9-OH with HBr in acetic acid affords the rearranged product 1,1,3-triphenylcyclopenta[l]phenanthrene-2-one 10 with a trace of 9-Br. Treatment of 9-Cl or 9-Br with zinc in acetic acid affords 1,2,3-tri-phenyl-1H-cyclopenta[l]phenanthrene 9-H. 9,10-Phenanthrenediylbis(phenyl)methanone 7 is formed in good yield upon treatment of 9-OH with HI in acetic acid followed by heating with H2PO4. Compounds 7, 8, 9-Cl, 9-Br, and 10 have been structurally characterized using X-ray crystallography.

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Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1609243114 ◽

2017 ◽

Vol 114 (9) ◽

pp. 2247-2252 ◽

Cited By ~ 41

Author(s):

Cornelius Gati ◽

Dominik Oberthuer ◽

Oleksandr Yefanov ◽

Richard D. Bunker ◽

Francesco Stellato ◽

...

Keyword(s):

High Resolution ◽

Single Molecule ◽

Free Electron ◽

Structural Changes ◽

Protein Crystals ◽

Experimental Conditions ◽

X Ray ◽

X Ray Crystallography ◽

Unit Cells ◽

Resolution Structure

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.

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Time-resolved crystallography and protein design: signalling photoreceptors and optogenetics

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2013.0568 ◽

2014 ◽

Vol 369 (1647) ◽

pp. 20130568 ◽

Cited By ~ 31

Author(s):

Keith Moffat

Keyword(s):

Protein Design ◽

Structural Changes ◽

Fast Time ◽

Free Electron Lasers ◽

Time Resolved ◽

X Ray ◽

Biological Targets ◽

X Ray Crystallography ◽

X Ray Scattering ◽

Exciting Possibility

Time-resolved X-ray crystallography and solution scattering have been successfully conducted on proteins on time-scales down to around 100 ps, set by the duration of the hard X-ray pulses emitted by synchrotron sources. The advent of hard X-ray free-electron lasers (FELs), which emit extremely intense, very brief, coherent X-ray pulses, opens the exciting possibility of time-resolved experiments with femtosecond time resolution on macromolecular structure, in both single crystals and solution. The X-ray pulses emitted by an FEL differ greatly in many properties from those emitted by a synchrotron, in ways that at first glance make time-resolved measurements of X-ray scattering with the required accuracy extremely challenging. This opens up several questions which I consider in this brief overview. Are there likely to be chemically and biologically interesting structural changes to be revealed on the femtosecond time-scale? How shall time-resolved experiments best be designed and conducted to exploit the properties of FELs and overcome challenges that they pose? To date, fast time-resolved reactions have been initiated by a brief laser pulse, which obviously requires that the system under study be light-sensitive. Although this is true for proteins of the visual system and for signalling photoreceptors, it is not naturally the case for most interesting biological systems. To generate more biological targets for time-resolved study, can this limitation be overcome by optogenetic, chemical or other means?

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