Proton-Coupled Structural Changes upon Binding of Carbon Monoxide to Cytochromecd1:  A Combined Flash Photolysis and X-ray Crystallography Study†,‡

Biochemistry ◽  
2000 ◽  
Vol 39 (36) ◽  
pp. 10967-10974 ◽  
Author(s):  
Tove Sjögren ◽  
Margareta Svensson-Ek ◽  
Janos Hajdu ◽  
Peter Brzezinski
Keyword(s):  
Carbon Monoxide ◽  
Structural Changes ◽  
Flash Photolysis ◽  
X Ray ◽  
X Ray Crystallography

Bis(1-phenyl-1-propyne) complexes of tungsten(II): crystal structures of [WI2(CO)(NCR)(η2-MeC2Ph)2] (R = Me, Et, or Ph)

2001 ◽  
Vol 79 (3) ◽  
pp. 263-271
Author(s):  
Paul K Baker ◽  
Michael GB Drew ◽  
Deborah S Evans
Keyword(s):  
Carbon Monoxide ◽  
Solid State ◽  
Crystal Structures ◽  
Octahedral Geometry ◽  
X Ray ◽  
X Ray Crystallography ◽  
Alkyne Complexes ◽  
First Time

Reaction of [WI2(CO)3(NCMe)2] with two equivalents of 1-phenyl-1-propyne (MeC2Ph) in CH2Cl2, and in the absence of light, gave the bis(1-phenyl-1-propyne) complex [WI2(CO)(NCMe)(η2-MeC2Ph)2] (1) in 77% yield. Treatment of equimolar quantities of 1 and NCR (R = Et, i-Pr, t-Bu, Ph) in CH2Cl2 afforded the nitrile-exchanged products, [WI2(CO)(NCR)(η2-MeC2Ph)2] (2-5) (R = Et (2), i-Pr (3), t-Bu (4), Ph (5)). Complexes 1, 2, and 5 were structurally characterized by X-ray crystallography. All three structures have the same pseudo-octahedral geometry, with the equatorial sites being occupied by cis and parallel alkyne groups, which are trans to the cis-iodo groups. The trans carbon monoxide and acetonitrile ligands occupy the axial sites. In structures 1 and 2, the methyl and phenyl substituents of the 1-phenyl-1-propyne ligands are cis to each other, whereas for the bulkier NCPh complex (5), the methyl and phenyl groups are trans to one another. This is the first time that this arrangement has been observed in the solid state in bis(alkyne) complexes of this type.Key words: bis(1-phenyl-1-propyne), carbonyl, nitrile, diiodo, tungsten(II), crystal structures.

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

2017 ◽  
Vol 114 (9) ◽  
pp. 2247-2252 ◽  
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.

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

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130568 ◽  
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?

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

2003 ◽  
Vol 17 (2-3) ◽  
pp. 345-353 ◽  
Author(s):  
Eriko Mano ◽  
Hironari Kamikubo ◽  
Yasushi Imamoto ◽  
Mikio Kataoka
Keyword(s):  
Photochemical Reaction ◽  
Structural Changes ◽  
Spectroscopic Studies ◽  
Crystalline Lattice ◽  
Photoactive Yellow Protein ◽  
X Ray ◽  
X Ray Crystallography ◽  
Solution Condition ◽  
Active Intermediate ◽  
Ectothiorhodospira Halophila

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.

Formation and reactivity of the zirconium ethylene complexes [η5-C5H3-1,3-(SiMe2CH2PR2)2]Zr(η2-CH2=CH2)(X) (R = Me, Pr i; X = Br, C5H5)

2001 ◽  
Vol 79 (5-6) ◽  
pp. 536-545 ◽  
Author(s):  
Michael D Fryzuk ◽  
Paul B Duval ◽  
Steven J Rettig
Keyword(s):  
Carbon Monoxide ◽  
Solid State ◽  
Kinetic Parameters ◽  
Structure Determination ◽  
Exchange Process ◽  
Carbonyl Complex ◽  
Carbonyl Ligand ◽  
Minor Isomer ◽  
X Ray ◽  
X Ray Crystallography

The formation and reactivity of the zirconium ethylene complexes R[P2Cp]Zr(η2-CH2=CH2)(X) (2a: R = Pri, X = Br; 2b: R = Me, X = Br; 4a: R = Pri, X = C5H5; R[P2Cp] = (η5-C5H3-1,3-(SiMe2CH2PR2)2)) are described. Ethylene complexes 2a and 2b are prepared from a reaction of R[P2Cp]ZrCl3 (1a: R = Pri; 1b: R = Me) with 2 equiv of EtMgBr, presumably via β-H elimination from the diethyl intermediate R[P2Cp]ZrCl(CH2CH3)2. The structure of 2b was determined by X-ray crystallography. Addition of carbon monoxide to 16-electron 2 displaces the ethylene ligand to generate the carbonyl complex R[P2Cp]Zr(CO)2Br (5a: R = Pri; 5b: R = Me), which is stable only under an atmosphere of CO. The corresponding CO reaction with 18-electron 4a to give the metallocene monocarbonyl analogue Pr[P2Cp]Zr(η5-C5H5)(CO) (6a) is considerably slower. 2a exhibits fluxional exchange of one carbonyl ligand with bulk 13CO in solution; the kinetic parameters for this exchange process are ΔH ‡ = 9.2(5) kcal mol–1 and ΔS ‡ = –17(2) cal mol–1 K–1. The addition of diphenylacetylene to 2a yields the alkyne complex Pr[P2Cp]Zr(η2-PhCCPh)Br (7a), which exists in solution as two isomers in equilibrium. A solid-state X-ray structure determination for the minor isomer syn-7a was performed.Key words: zirconium, cyclopentadienyl phosphine, alkyne, metallocyclopropane.

scholarly journals Structural Changes ofEscherichia coliFerric Uptake Regulator during Metal-dependent Dimerization and Activation Explored by NMR and X-ray Crystallography

2006 ◽  
Vol 281 (30) ◽  
pp. 21286-21295 ◽  
Author(s):  
Ludovic Pecqueur ◽  
Benoît D'Autréaux ◽  
Jérome Dupuy ◽  
Yvain Nicolet ◽  
Lilian Jacquamet ◽  
...  
Keyword(s):  
Structural Changes ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Structures and functions of carotenoids bound to reaction centers from purple photosynthetic bacteria

2006 ◽  
Vol 78 (8) ◽  
pp. 1505-1518 ◽  
Author(s):  
Hideki Hashimoto ◽  
Ritsuko Fujii ◽  
Kazuhiro Yanagi ◽  
Toshiyuki Kusumoto ◽  
Alastair T. Gardiner ◽  
...  
Keyword(s):  
Electrostatic Field ◽  
Flash Photolysis ◽  
Purple Bacteria ◽  
Reaction Centers ◽  
Photosynthetic Reaction Centers ◽  
Triplet Energy ◽  
X Ray ◽  
X Ray Crystallography ◽  
Purple Photosynthetic Bacteria ◽  
Value Decomposition

The photoprotective function of 15,15'-cis-carotenoids bound to the photosynthetic reaction centers (RCs) of purple bacteria has been studied using carotenoids reconstituted into carotenoidless RCs from Rhodobacter sphaeroides strain R26.1. The triplet-energy level of the carotenoid has been proposed to affect the quenching of the triplet state of special-pair bacteriochlorophyll (P). This was investigated using microsecond flash photolysis to detect the carotenoid triplets as a function of the number of conjugated double bonds, n. The carotenoid triplet signals were extracted by using singular-value decomposition (SVD) of the huge matrices data, and were confirmed for those having n = 8 to 11. This interpretation assumes that the reconstituted carotenoids occupy the same binding site in the RC. We have been able to confirm this assumption using X-ray crystallography to determine the structures of carotenoidless, wild-type carotenoid-containing, and 3,4-dihydro-spheroidene-reconstituted RCs. The X-ray study also emphasized the importance of the methoxy group of the carotenoids for binding to the RCs. Electroabsorption (Stark) spectroscopy was used to investigate the effect of the carotenoid on the electrostatic field around P. This electrostatic field changed by 10 % in the presence of the carotenoid.

scholarly journals Structural changes of TasA in biofilm formation ofBacillus subtilis

2018 ◽  
Vol 115 (13) ◽  
pp. 3237-3242 ◽  
Author(s):  
Anne Diehl ◽  
Yvette Roske ◽  
Linda Ball ◽  
Anup Chowdhury ◽  
Matthias Hiller ◽  
...  
Keyword(s):  
Structural Change ◽  
Structural Changes ◽  
Analytical Ultracentrifugation ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
X Ray ◽  
X Ray Crystallography ◽  
Angle Spinning

Microorganisms form surface-attached communities, termed biofilms, which can serve as protection against host immune reactions or antibiotics.Bacillus subtilisbiofilms contain TasA as major proteinaceous component in addition to exopolysaccharides. In stark contrast to the initially unfolded biofilm proteins of other bacteria, TasA is a soluble, stably folded monomer, whose structure we have determined by X-ray crystallography. Subsequently, we characterized in vitro different oligomeric forms of TasA by NMR, EM, X-ray diffraction, and analytical ultracentrifugation (AUC) experiments. However, by magic-angle spinning (MAS) NMR on live biofilms, a swift structural change toward only one of these forms, consisting of homogeneous and protease-resistant, β-sheet–rich fibrils, was observed in vivo. Thereby, we characterize a structural change from a globular state to a fibrillar form in a functional prokaryotic system on the molecular level.

X-Ray Crystallography of Carbon Monoxide Dehydrogenases

2018 ◽  
pp. 167-178
Author(s):  
Jae-Hun Jeoung ◽  
Berta M. Martins ◽  
Holger Dobbek
Keyword(s):  
Carbon Monoxide ◽  
X Ray ◽  
X Ray Crystallography
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