The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism

2019 ◽  
Vol 75 (9) ◽  
pp. 804-816 ◽  
Author(s):  
Konstantin M. Polyakov ◽  
Sergei Gavryushov ◽  
Tatiana V. Fedorova ◽  
Olga A. Glazunova ◽  
Alexander N. Popov
Keyword(s):  
Molecular Oxygen ◽  
Enzymatic Reaction ◽  
Copper Ion ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Fluoride Ions ◽  
X Ray ◽  
Mechanism Of Inhibition ◽  
Wide Range ◽  
Oxygen Ligand

Laccases are enzymes that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of molecular oxygen to water. Here, a subatomic resolution X-ray crystallographic study of the mechanism of inhibition of the laccase from the basidiomycete fungus Steccherinum murashkinskyi by chloride and fluoride ions is presented. Three series of X-ray diffraction data sets were collected with increasing doses of absorbed X-ray radiation from a native S. murashkinskyi laccase crystal and from crystals of complexes of the laccase with chloride and fluoride ions. The data for the native laccase crystal confirmed the previously deduced enzymatic mechanism of molecular oxygen reduction. The structures of the complexes allowed the localization of chloride and fluoride ions in the channel near the T2 copper ion. These ions replace the oxygen ligand of the T2 copper ion in this channel and can play the role of this ligand in the enzymatic reaction. As follows from analysis of the structures from the increasing dose series, the inhibition of laccases by chloride and fluoride anions can be explained by the fact that the binding of these negatively charged ions at the position of the oxygen ligand of the T2 copper ion impedes the reduction of the T2 copper ion.

Structural study of the X-ray-induced enzymatic reduction of molecular oxygen to water bySteccherinum murashkinskyilaccase: insights into the reaction mechanism

2017 ◽  
Vol 73 (5) ◽  
pp. 388-401 ◽  
Author(s):  
K. M. Polyakov ◽  
S. Gavryushov ◽  
S. Ivanova ◽  
T. V. Fedorova ◽  
O. A. Glazunova ◽  
...  
Keyword(s):  
Molecular Oxygen ◽  
Catalytic Reduction ◽  
Copper Ions ◽  
Absorbed Dose ◽  
Large Family ◽  
Data Sets ◽  
X Ray ◽  
Substrate Complex ◽  
Enzymatic Reduction ◽  
Wide Range

The laccase fromSteccherinum murashkinskyiis a member of the large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates, accompanied by the reduction of dioxygen to water. The reducing properties of X-ray radiation and the high quality of the laccase crystals allow the study of the catalytic reduction of dioxygen to water directly in a crystal. A series of diffraction data sets with increasing absorbed radiation dose were collected from a single crystal ofSteccherinum murashkinskyilaccase at 1.35 Å resolution. Changes in the active-site structure associated with the reduction of molecular oxygen to water on increasing the absorbed dose of ionizing radiation were detected. The structures in the series are mixtures of different states of the enzyme–substrate complex. Nevertheless, it was possible to interpret these structures as complexes of various oxygen ligands with copper ions in different oxidation states. The results allowed the mechanism of oxygen reduction catalyzed by laccases to be refined.

scholarly journals Effect of the L499M mutation of the ascomycetousBotrytis acladalaccase on redox potential and catalytic properties

2014 ◽  
Vol 70 (11) ◽  
pp. 2913-2923 ◽  
Author(s):  
Evgeny Osipov ◽  
Konstantin Polyakov ◽  
Roman Kittl ◽  
Sergey Shleev ◽  
Pavel Dorovatovsky ◽  
...  
Keyword(s):  
Redox Potential ◽  
Catalytic Properties ◽  
Enzymatic Reaction ◽  
Copper Ion ◽  
Large Family ◽  
Redox Potentials ◽  
Wild Type ◽  
Wild Type Enzyme ◽  
X Ray ◽  
Wide Range

Laccases are members of a large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. These enzymes contain four Cu atoms per molecule organized into three sites: T1, T2 and T3. In all laccases, the T1 copper ion is coordinated by two histidines and one cysteine in the equatorial plane and is covered by the side chains of hydrophobic residues in the axial positions. The redox potential of the T1 copper ion influences the enzymatic reaction and is determined by the nature of the axial ligands and the structure of the second coordination sphere. In this work, the laccase from the ascomyceteBotrytis acladawas studied, which contains conserved Ile491 and nonconserved Leu499 residues in the axial positions. The three-dimensional structures of the wild-type enzyme and the L499M mutant were determined by X-ray crystallography at 1.7 Å resolution. Crystals suitable for X-ray analysis could only be grown after deglycosylation. Both structures did not contain the T2 copper ion. The catalytic properties of the enzyme were characterized and the redox potentials of both enzyme forms were determined:E0= 720 and 580 mV for the wild-type enzyme and the mutant, respectively. Since the structures of the wild-type and mutant forms are very similar, the change in the redox potential can be related to the L499M mutation in the T1 site of the enzyme.

scholarly journals Multidimensional Ln-Aminophthalate Photoluminescent Coordination Polymers

Materials ◽  
2021 ◽  
Vol 14 (7) ◽  
pp. 1786
Author(s):  
Carla Queirós ◽  
Chen Sun ◽  
Ana M. G. Silva ◽  
Baltazar de Castro ◽  
Juan Cabanillas-Gonzalez ◽  
...  
Keyword(s):  
Water Content ◽  
Coordination Polymers ◽  
Metal Ion ◽  
Low Cost ◽  
Microwave Assisted Synthesis ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range ◽  
Ft Ir ◽  
Ft Ir Spectroscopy

The development of straightforward reproducible methods for the preparation of new photoluminescent coordination polymers (CPs) is an important goal in luminescence and chemical sensing fields. Isophthalic acid derivatives have been reported for a wide range of applications, and in addition to their relatively low cost, have encouraged its use in the preparation of novel lanthanide-based coordination polymers (LnCPs). Considering that the photoluminescent properties of these CPs are highly dependent on the existence of water molecules in the crystal structure, our research efforts are now focused on the preparation of CP with the lowest water content possible, while considering a green chemistry approach. One- and two-dimensional (1D and 2D) LnCPs were prepared from 5-aminoisophthalic acid and Sm3+/Tb3+ using hydrothermal and/or microwave-assisted synthesis. The unprecedented LnCPs were characterized by single-crystal X-ray diffraction (SCRXD), powder X-ray diffraction (PXRD), Fourier transform infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM), and their photoluminescence (PL) properties were studied in the solid state, at room temperature, using the CPs as powders and encapsulated in poly(methyl methacrylate (PMMA) films, envisaging the potential preparation of devices for sensing. The materials revealed interesting PL properties that depend on the dimensionality, metal ion, co-ligand used and water content.

2D X-ray diffraction and molecular modelling of the crystalline structure of polyesters under uniaxial stress

2021 ◽  
pp. 096739112199822
Author(s):  
Ahmed I Abou-Kandil ◽  
Gerhard Goldbeck
Keyword(s):  
Crystalline Structure ◽  
Molecular Modelling ◽  
Three Dimensional ◽  
Uniaxial Stress ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range ◽  
Modelling Techniques ◽  
Diffraction Patterns

Studying the crystalline structure of uniaxially and biaxially drawn polyesters is of great importance due to their wide range of applications. In this study, we shed some light on the behaviour of PET and PEN under uniaxial stress using experimental and molecular modelling techniques. Comparing experiment with modelling provides insights into polymer crystallisation with extended chains. Experimental x-ray diffraction patterns are reproduced by means of models of chains sliding along the c-axis leading to some loss of three-dimensional order, i.e. moving away from the condition of perfect register of the fully extended chains in triclinic crystals of both PET and PEN. This will help us understand the mechanism of polymer crystallisation under uniaxial stress and the appearance of mesophases in some cases as discussed herein.

scholarly journals Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted PhyH-DI fromBacillussp. HJB17

2017 ◽  
Vol 73 (11) ◽  
pp. 607-611
Author(s):  
Fang Lu ◽  
Bei Zhang ◽  
Yong Liu ◽  
Ying Song ◽  
Gangxing Guo ◽  
...  
Keyword(s):  
Unit Cell ◽  
Diffusion Method ◽  
Data Sets ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Phytases are phosphatases that hydrolyze phytates to less phosphorylatedmyo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase fromBacillussp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate. Crystals of native and selenomethionine-substituted PhyH-DI were obtained using the vapour-diffusion method in a condition consisting of 0.2 Msodium chloride, 0.1 MTris pH 8.5, 25%(w/v) PEG 3350 at 289 K. X-ray diffraction data were collected to 3.00 and 2.70 Å resolution, respectively, at 100 K. Native PhyH-DI crystals belonged to space groupC121, with unit-cell parametersa = 156.84,b = 45.54,c = 97.64 Å, α = 90.00, β = 125.86, γ = 90.00°. The asymmetric unit contained two molecules of PhyH-DI, with a corresponding Matthews coefficient of 2.17 Å3 Da−1and a solvent content of 43.26%. Crystals of selenomethionine-substituted PhyH-DI belonged to space groupC2221, with unit-cell parametersa = 94.71,b= 97.03,c= 69.16 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.44 Å3 Da−1and a solvent content of 49.64%. Initial phases for PhyH-DI were obtained from SeMet SAD data sets. These data will be useful for further studies of the structure–function relationship of PhyH-DI.

Structural study of the X-ray-induced enzymatic reaction of octahaem cytochromecnitrite reductase

2015 ◽  
Vol 71 (5) ◽  
pp. 1087-1094 ◽  
Author(s):  
A. A. Trofimov ◽  
K. M. Polyakov ◽  
V. A. Lazarenko ◽  
A. N. Popov ◽  
T. V. Tikhonova ◽  
...  
Keyword(s):  
Nitrite Reductase ◽  
Catalytic Reaction ◽  
Active Sites ◽  
Enzymatic Reaction ◽  
Absorbed Dose ◽  
Free Form ◽  
Data Sets ◽  
X Rays ◽  
X Ray ◽  
Site Water

Octahaem cytochromecnitrite reductase from the bacteriumThioalkalivibrio nitratireducenscatalyzes the reduction of nitrite to ammonium and of sulfite to sulfide. The reducing properties of X-ray radiation and the high quality of the enzyme crystals allow study of the catalytic reaction of cytochromecnitrite reductase directly in a crystal of the enzyme, with the reaction being induced by X-rays. Series of diffraction data sets with increasing absorbed dose were collected from crystals of the free form of the enzyme and its complexes with nitrite and sulfite. The corresponding structures revealed gradual changes associated with the reduction of the catalytic haems by X-rays. In the case of the nitrite complex the conversion of the nitrite ions bound in the active sites to NO species was observed, which is the beginning of the catalytic reaction. For the free form, an increase in the distance between the oxygen ligand bound to the catalytic haem and the iron ion of the haem took place. In the case of the sulfite complex no enzymatic reaction was detected, but there were changes in the arrangement of the active-site water molecules that were presumably associated with a change in the protonation state of the sulfite ions.

scholarly journals Theoretical study of the properties of X-ray diffraction moiré fringes. II. Illustration of angularly integrated moiré images

2019 ◽  
Vol 75 (4) ◽  
pp. 610-623
Author(s):  
Jun-ichi Yoshimura
Keyword(s):  
Incident Wave ◽  
Angular Width ◽  
X Ray Diffraction ◽  
Experimental Conditions ◽  
Acta Cryst ◽  
Low Contrast ◽  
X Ray ◽  
Moiré Fringes ◽  
Wide Range ◽  
Fringe Patterns

Using a theory of X-ray diffraction moiré fringes developed in a previous paper, labelled Part I [Yoshimura (2015). Acta Cryst. A71, 368–381], the X-ray moiré images of a silicon bicrystal having a weak curvature strain and an interspacing gap, assumed to be integrated for an incident-wave angular width, are simulation-computed over a wide range of crystal thicknesses and incident-wave angular width, likely under practical experimental conditions. Along with the simulated moiré images, the graphs of characteristic quantities on the moiré images are presented for a full understanding of them. The treated moiré images are all of rotation moiré. Mo Kα1 radiation and the 220 reflection were assumed in the simulation. The results of this simulation show that fringe patterns, which are significantly modified from simple straight fringes of rotation moiré, appear in some ranges of crystal thicknesses and incident-wave angular width, due to a combined effect of Pendellösung oscillation and an added phase difference from the interspacing gap, under the presence of a curvature strain. The moiré fringes which slope to the perpendicular direction to the diffraction vector in spite of the assumed condition of rotation moiré, and fringe patterns where low-contrast bands are produced with a sharp bend of fringes arising along the bands are examples of the modified fringe pattern. This simulation study provides a wide theoretical survey of the type of bicrystal moiré image produced under a particular condition.

scholarly journals Charge Compensation in Europium-Doped Hafnia Nanoparticles: Solvothermal Synthesis and Colloidal Dispersion

Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1042
Author(s):  
Xavier H. Guichard ◽  
Francesco Bernasconi ◽  
Alessandro Lauria
Keyword(s):  
Low Temperature ◽  
Hafnium Oxide ◽  
Aqueous Media ◽  
Charge Compensation ◽  
Colloidal Dispersion ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range ◽  
Direct Formation ◽  
Enhanced Luminescence

Effective charge compensation of europium in hafnium oxide nanoparticles was achieved at low temperature, allowing high doping incorporation (up to 6 at.%) and enhanced luminescence. The efficiency of the incorporation and charge compensation was confirmed by scanning electron microscope energy dispersive X-ray spectroscopy and powder X-ray diffraction measurements. Despite the known polymorphism of hafnium oxide, when doped to a concentration above 3 at.%, only the pure monoclinic phase was observed up to 6 at.% of europium. Furthermore, the low-temperature solvothermal route allowed the direct formation of stable dispersions of the synthesized material over a wide range of concentrations in aqueous media. The dispersions were studied by diffuse light scattering (DLS) to evaluate their quality and by photoluminescence to investigate the incorporation of the dopants into the lattice.

scholarly journals In situ X-ray Diffraction Investigation of the Crystallisation of Perfluorinated Ce(IV)-based Metal-Organic Frameworks with UiO-66 and MIL-140 architectures

2020 ◽  
Author(s):  
Stephen Shearan ◽  
Jannick Jacobsen ◽  
Ferdinando Costantino ◽  
Roberto D’Amato ◽  
Dmitri Novikov ◽  
...  
Keyword(s):  
Crystal Growth ◽  
Metal Organic Frameworks ◽  
Building Blocks ◽  
Nucleation And Growth ◽  
X Ray Diffraction ◽  
X Ray ◽  
Rate Determining Step ◽  
Wide Range ◽  
Metal Organic

We report on the results of a thorough <i>in situ</i> synchrotron powder X-ray diffraction study of the crystallisation in aqueous medium of two recently discovered perfluorinated Ce(IV)-based metal-organic frameworks (MOFs), analogues of the already well investigated Zr(IV)-based UiO-66 and MIL-140A, namely, F4_UiO-66(Ce) and F4_MIL-140A(Ce). The two MOFs were originally obtained in pure form in similar conditions, using ammonium cerium nitrate and tetrafluoroterephthalic acid as building blocks, and small variations of the reaction parameters were found to yield mixed phases. Here, we investigate the crystallisation of these compounds <i>in situ</i> in a wide range of conditions, varying parameters such as temperature, amount of the protonation modulator nitric acid (HNO<sub>3</sub>) and amount of the coordination modulator acetic acid (AcOH). When only HNO<sub>3</sub> is present in the reaction environment, F4_MIL-140A(Ce) is obtained as a pure phase. Heating preferentially accelerates nucleation, which becomes rate determining below 57 °C, whereas the modulator influences nucleation and crystal growth to a similar extent. Upon addition of AcOH to the system, alongside HNO<sub>3</sub>, mixed-phased products, consisting of F4_MIL-140A(Ce) and F4_UiO-66(Ce), are obtained. In these conditions, F4_UiO-66(Ce) is always formed faster and no interconversion between the two phases occurs. In the case of F4_UiO-66(Ce), crystal growth is always the rate determining step. An increase in the amount of HNO<sub>3</sub> slows down both nucleation and growth rates for F4_MIL-140A(Ce), whereas nucleation is mainly affected for F4_UiO-66(Ce). In addition, a higher amount HNO<sub>3</sub> favours the formation of F4_MIL-140A(Ce). Similarly, increasing the amount of AcOH leads to slowing down of the nucleation and growth rate, but favours the formation of F4_UiO-66(Ce). The pure F4_UiO-66(Ce) phase could also be obtained when using larger amounts of AcOH in the presence of minimal HNO<sub>3</sub>. Based on these <i>in situ</i> results, a new optimised route to achieving a pure, high quality F4_MIL-140A(Ce) phase in mild conditions (60 °C, 1 h) is also identified.

Single Crystal Wurtzitic Aluminum Nitride Growth on Silicon Using Supersonic Gas Jets

1995 ◽  
Vol 395 ◽  
Author(s):  
S. A. Ustin ◽  
L. Lauhon ◽  
K. A. Brown ◽  
D. Q. Hu ◽  
W. Ho
Keyword(s):  
Aluminum Nitride ◽  
Growth Rates ◽  
High Energy ◽  
X Ray Diffraction ◽  
Rutherford Back Scattering ◽  
X Ray ◽  
Supersonic Molecular Beam ◽  
Supersonic Beams ◽  
Wide Range

ABSTRACTHighly oriented aluminum nitride (0001) films have been grown on Si(001) and Si (111) substrates at temperatures between 550° C and 775° C with dual supersonic molecular beam sources. Triethylaluminum (TEA;[(C2H5)3Al]) and ammonia (NH3) were used as precursors. Hydrogen, helium, and nitrogen were used as seeding gases for the precursors, providing a wide range of possible kinetic energies for the supersonic beams due to the disparate masses of the seed gases. Growth rates of AIN were found to depend strongly on the substrate orientation and the kinetic energy of the incident precursor; a significant increase in growth rate is seen when seeding in hydrogen or helium as opposed to nitrogen. Growth rates were 2–3 times greater on Si(001) than on Si(111). Structural characterization of the films was done by reflection high energy electron diffraction (RHEED) and x-ray diffraction (XRD). X-ray rocking curve (XRC) full-width half-maxima (FWHM) were seen as small as 2.5°. Rutherford back scattering (RBS) was used to determine the thickness of the films and their chemical composition. Films were shown to be nitrogen rich, deviating from perfect stoichiometry by 10%–20%. Surface analysis was performed by Auger electron spectroscopy (AES).

Sign in / Sign up

Export Citation Format

Share Document