scholarly journals Remodeling of Conformational Dynamics Enhances Catalytic Activities of M1 Zinc-metallopeptidases from Lanthipeptide Biosynthesis

2021 ◽  
Author(s):  
chang zhao ◽  
Wang-Jian Sheng ◽  
ying wang ◽  
Jie Zheng ◽  
Xiangqian Xie ◽  
...  
Keyword(s):  
Conformational Equilibrium ◽  
Regulatory Element ◽  
Conformational Dynamics ◽  
Biological Functions ◽  
Class Iii ◽  
X Ray ◽  
Catalytic Activities ◽  
Leader Peptides ◽  
Domain Dynamics

Abstract Lanthipeptides are an important group of natural products with diverse biological functions, and their biosynthesis requires the removal of N-terminal leader peptides (LPs) by designated proteases. LanPM1 enzymes, a subgroup of M1 zinc-metallopeptidases, are recently identified as bifunctional proteases with both endo- and aminopeptidase activities to remove LPs of class III and class IV lanthipeptides. Herein, we report the biochemical and structural characterization of EryP as the LanPM1 enzyme from the biosynthesis of class III lanthipeptide erythreapeptin. We determined X-ray crystal structures of EryP in three conformational states, the open, intermediate and closed states and identified a unique inter-domain Ca binding site as a regulatory element to modulate its domain dynamics and proteolytic activity. Inspired by the regulatory Ca binding, we develop a strategy to engineer LanPM1 enzymes for enhanced catalytic activities by strengthening inter-domain associations and driving the conformational equilibrium toward their closed forms.

scholarly journals In-Exchanged CHA Zeolites for Selective Dehydrogenation of Ethane: Characterization and Effect of Zeolite Framework Type

Catalysts ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 807
Author(s):  
Zen Maeno ◽  
Xiaopeng Wu ◽  
Shunsaku Yasumura ◽  
Takashi Toyao ◽  
Yasuharu Kanda ◽  
...  
Keyword(s):  
Active Sites ◽  
Temperature Programmed Desorption ◽  
X Ray Diffraction ◽  
Zeolite Framework ◽  
X Ray ◽  
Catalytic Activities ◽  
Ethane Dehydrogenation ◽  
Temperature Programmed

In this study, the characterization of In-exchanged CHA zeolite (In-CHA (SiO2/Al2O3 = 22.3)) was conducted by in-situ X-ray diffraction (XRD) and ammonia temperature-programmed desorption (NH3-TPD). We also prepared other In-exchanged zeolites with different zeolite structures (In-MFI (SiO2/Al2O3 = 22.3), In-MOR (SiO2/Al2O3 = 20), and In-BEA (SiO2/Al2O3 = 25)) and different SiO2/Al2O3 ratios (In-CHA(Al-rich) (SiO2/Al2O3 = 13.7)). Their catalytic activities in nonoxidative ethane dehydrogenation were compared. Among the tested catalysts, In-CHA(Al-rich) provided the highest conversion. From kinetic experiments and in-situ Fourier transform infrared (FTIR) spectroscopy, [InH2]+ ions are formed regardless of SiO2/Al2O3 ratio, serving as the active sites.

scholarly journals Structural characterization of gephyrin by AFM and SAXS reveals a mixture of compact and extended states

2013 ◽  
Vol 69 (10) ◽  
pp. 2050-2060 ◽  
Author(s):  
Bodo Sander ◽  
Giancarlo Tria ◽  
Alexander V. Shkumatov ◽  
Eun-Young Kim ◽  
J. Günter Grossmann ◽  
...  
Keyword(s):  
Conformational Dynamics ◽  
Cd Spectroscopy ◽  
X Ray ◽  
Force Microscopy ◽  
X Ray Scattering ◽  
Atomic Force ◽  
Extended States ◽  
High Degree

Gephyrin is a trimeric protein involved in the final steps of molybdenum-cofactor (Moco) biosynthesis and in the clustering of inhibitory glycine and GABAAreceptors at postsynaptic specializations. Each protomer consists of stably folded domains (referred to as the G and E domains) located at either terminus and connected by a proteolytically sensitive linker of ∼150 residues. Both terminal domains can oligomerize in their isolated forms; however, in the context of the full-length protein only the G-domain trimer is permanently present, whereas E-domain dimerization is prevented. Atomic force microscopy (AFM) and small-angle X-ray scattering (SAXS) reveal a high degree of flexibility in the structure of gephyrin. The results imply an equilibrium between compact and extended conformational states in solution, with a preference for compact states. CD spectroscopy suggests that a partial compaction is achieved by interactions of the linker with the G and E domains. Taken together, the data provide a rationale for the role of the linker in the overall structure and the conformational dynamics of gephyrin.

scholarly journals Synthesis and characterization of nickel oxide and evaluation of its catalytic activities for degradation of methyl orange in aqueous medium

2020 ◽  
Vol 3 (2) ◽  
pp. 47
Author(s):  
Muhammad Saeed ◽  
Muhammad Amjed ◽  
Attaul Haq ◽  
Muhammad Usman ◽  
Shahid Adeel
Keyword(s):  
Methyl Orange ◽  
Nickel Oxide ◽  
Aqueous Medium ◽  
Oxide Catalyst ◽  
X Ray ◽  
Catalytic Activities ◽  
Oxide Particles ◽  
Apparent Activation Energies ◽  
Degradation Of Methyl Orange

This study focuses on synthesis of nickel oxide catalyst and exploration of its catalytic activities for degradation of methyl orange in aqueous medium. Nickel oxide was prepared sole-gel method using nickel nitrate haxahydrate and citric acid as precursor materials. X-ray diffractometry and scanning electron microscopy were used for characterization of prepared nickel oxide particles. The prepared particles were used as the catalysts for the degradation of Methyl Orange in aqueous medium. The effects of different parameters on degradation of methyl orange were investigated. The degradation of methyl orange followed the Eley-Rideal (E-R) mechanism. The apparent activation energies for degradation of methyl orange determined was found as 36.4 kJ/mol.

Characterization of a tropical soil and a waste from kaolin mining and their suitability as heterogeneous catalysts for Fenton and Fenton-like reactions

Clay Minerals ◽  
2007 ◽  
Vol 42 (3) ◽  
pp. 299-306 ◽  
Author(s):  
M. C. Pereira ◽  
C. M. Tavares ◽  
J. D. Fabris ◽  
R. M. Lago ◽  
E. Murad ◽  
...  
Keyword(s):  
Methylene Blue ◽  
Chemical Analysis ◽  
Iron Oxides ◽  
Heterogeneous Catalysts ◽  
Tropical Soil ◽  
X Ray Diffraction ◽  
X Ray ◽  
Catalytic Activities ◽  
Fenton System

AbstractAlternative Fenton and Fenton-like systems based on natural Fe oxides are described. The collected materials were modified through controlled reduction with H2 and were characterized by chemical analysis, X-ray diffraction, saturation magnetization measurements, and Mössbauer spectroscopy at 298 and 110 K. The catalytic activities of these original and modified materials were tested by studying the decomposition of H2O2 and the discolouration of methylene blue. Iron oxides present in the samples were mainly hematite and subordinate goethite which, after controlled reduction, were converted to metallic iron and magnetite. The mixture of Fe0 and magnetite in one of these materials was significantly more efficient at H2O2 decomposition and the discolouration of methylene blue than the original Fe3+ oxides. These results suggest that Fe2+ is essential to produce an active Fenton system.

scholarly journals Molecular recognition and dynamics of linear poly-ubiquitins: integrating coarse-grain simulations and experiments

2020 ◽  
Author(s):  
Alexander Jussupow ◽  
Ana C. Messias ◽  
Ralf Stehle ◽  
Arie Geerlof ◽  
Sara M. Ø. Solbak ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Small Angle ◽  
Conformational Dynamics ◽  
Conformational Space ◽  
Coarse Grain ◽  
X Ray ◽  
X Ray Scattering ◽  
Linear Poly ◽  
Ray Scattering

AbstractPoly-ubiquitin chains are flexible multidomain proteins, whose conformational dynamics enable their molecular recognition by a large number of partners in multiple biological pathways. By using alternative linkage, it is possible to obtain poly-ubiquitin molecules with different dynamical properties. This flexibility is further increased by the possibility to tune the length of poly-ubiquitin chains. Characterizing the dynamics of poly-ubiquitins as a function of their length is thus relevant to understand their biology. Structural characterization of poly-ubiquitin conformational dynamics is challenging both experimentally and computationally due to increasing system size and conformational variability. Here, by developing highly efficient and accurate small-angle X-ray scattering driven Martini coarse-grain simulations, we characterize the dynamics of linear M1-linked di-, tri- and tetra-ubiquitin chains. Our data show that the behavior of the di-ubiquitin subunits is independent of the presence of additional ubiquitin modules. We propose that the conformational space sampled by linear poly-ubiquitins, in general, may follow a simple self-avoiding polymer model. These results, combined with experimental data from small angle X-ray scattering, biophysical techniques and additional simulations show that binding of NEMO, a central regulator in the NF-κB pathway, to linear poly-ubiquitin obeys a 2:1 (NEMO:poly-ubiquitin) stoichiometry in solution, even in the context of four ubiquitin units. Eventually, we show how the conformational properties of long poly-ubiquitins may modulate the binding with their partners in a length-dependent manner.SignificanceProtein conformational dynamics plays an essential role in molecular recognition mechanisms. The characterization of conformational dynamics is hampered by the conformational averaging of observable in experimental structural biology techniques and by the limitations in the accuracy of computational methods. By developing an efficient and accurate approach to combine small-angle X-ray scattering solution experiments and coarse-grain Martini simulations, we show that the conformational dynamics of linear poly-ubiquitins can be efficiently determined and to rationalize the role of poly-ubiquitin dynamic in the molecular recognition of the UBAN domain upon binding to the signaling regulator NEMO. The analysis of the conformational ensembles allows us to propose a general model of the dynamics of linear poly-ubiquitin chains where they can be described as a self-avoiding polymer with a characteristic length associated with their specific linkage.

Characterization of Antimony-Doped TIN Oxide Catalysts

2001 ◽  
Vol 7 (S2) ◽  
pp. 1094-1095
Author(s):  
K. Sun ◽  
J. Liu ◽  
N.D. Browning
Keyword(s):  
Tin Oxide ◽  
Photoelectron Spectroscopy ◽  
Contrast Imaging ◽  
X Ray ◽  
Catalytic Activities ◽  
Valence States ◽  
Z Contrast ◽  
Electron Energy Loss ◽  
X Ray Absorption

Antimony-doped tin oxide (ATO) catalysts are used for the oxidation of propylene to acrolein, the ammoxidation of propylene to acrylonitrile and the oxidative dehydrogenation of butanes to 1,3- butadiene. The distribution and valence states of Sb in ATOs are key in determining their catalytic activities. While these materials have been subjects of intensive studies for more than 20 years, X-ray photoelectron spectroscopy, Mössbauer spectrometry, and X-ray absorption spectroscopy4 have so far provided only indirect data for the distribution of Sb and its valence states. in particular, while has been hypothesized that the tin (IV) oxide contains Sb (V) within the bulk lattice and Sb (III) located at surface sites, no direct experimental evidence for this has been provided.Here we use electron energy loss spectroscopy (EELS) combined with Z-contrast imaging in a JEOL 2010F field emission STEM/TEM operating at 200 KV to analyze ATO catalysts.

The Use of Advanced Analytical Techniques for Characterization of the Chemical, Physical, and Crystallographic Nature of a Surface

1973 ◽  
Vol 31 ◽  
pp. 132-133 ◽  
Author(s):  
R. E. Herfert
Keyword(s):  
Surface Characterization ◽  
Analytical Techniques ◽  
X Ray Diffraction ◽  
Depth Of Penetration ◽  
X Ray ◽  
The Past ◽  
Transmission Electron ◽  
Scanning Electron

Studies of the nature of a surface, either metallic or nonmetallic, in the past, have been limited to the instrumentation available for these measurements. In the past, optical microscopy, replica transmission electron microscopy, electron or X-ray diffraction and optical or X-ray spectroscopy have provided the means of surface characterization. Actually, some of these techniques are not purely surface; the depth of penetration may be a few thousands of an inch. Within the last five years, instrumentation has been made available which now makes it practical for use to study the outer few 100A of layers and characterize it completely from a chemical, physical, and crystallographic standpoint. The scanning electron microscope (SEM) provides a means of viewing the surface of a material in situ to magnifications as high as 250,000X.

High Resolution Replication of Organoclay Surfaces

1982 ◽  
Vol 40 ◽  
pp. 576-577
Author(s):  
W. W. Barker ◽  
W. E. Rigsby ◽  
V. J. Hurst ◽  
W. J. Humphreys
Keyword(s):  
Clay Mineral ◽  
Organic Molecule ◽  
Organic Molecules ◽  
X Ray Diffraction ◽  
Xrd Pattern ◽  
X Ray ◽  
Naturally Occurring ◽  
Silicate Layers ◽  
Mineral Identification

Experimental clay mineral-organic molecule complexes long have been known and some of them have been extensively studied by X-ray diffraction methods. The organic molecules are adsorbed onto the surfaces of the clay minerals, or intercalated between the silicate layers. Natural organo-clays also are widely recognized but generally have not been well characterized. Widely used techniques for clay mineral identification involve treatment of the sample with H2 O2 or other oxidant to destroy any associated organics. This generally simplifies and intensifies the XRD pattern of the clay residue, but helps little with the characterization of the original organoclay. Adequate techniques for the direct observation of synthetic and naturally occurring organoclays are yet to be developed.

Digital x-ray mapping of nanometer-size supported bimetallic catalysts

1988 ◽  
Vol 46 ◽  
pp. 530-531
Author(s):  
L. T. Germinario
Keyword(s):  
Background Radiation ◽  
Metal Cluster ◽  
Single Element ◽  
Beam Diameter ◽  
X Rays ◽  
X Ray ◽  
Major Interest ◽  
Induced Changes

Understanding the role of metal cluster composition in determining catalytic selectivity and activity is of major interest in heterogeneous catalysis. The electron microscope is well established as a powerful tool for ultrastructural and compositional characterization of support and catalyst. Because the spatial resolution of x-ray microanalysis is defined by the smallest beam diameter into which the required number of electrons can be focused, the dedicated STEM with FEG is the instrument of choice. The main sources of errors in energy dispersive x-ray analysis (EDS) are: (1) beam-induced changes in specimen composition, (2) specimen drift, (3) instrumental factors which produce background radiation, and (4) basic statistical limitations which result in the detection of a finite number of x-ray photons. Digital beam techniques have been described for supported single-element metal clusters with spatial resolutions of about 10 nm. However, the detection of spurious characteristic x-rays away from catalyst particles produced images requiring several image processing steps.

Plant Pathology Diagnosed by X-Ray Microanalysis

1987 ◽  
Vol 45 ◽  
pp. 974-975
Author(s):  
J. H. Resau ◽  
N. Howell ◽  
S. H. Chang
Keyword(s):  
Electron Microscopy ◽  
Plant Pathology ◽  
Biochemical Characterization ◽  
Nutrient Deficiency ◽  
Green Leaf ◽  
Parasitic Infestation ◽  
X Ray

Spinach grown in Texas developed “yellow spotting” on the peripheral portions of the leaves. The exact cause of the discoloration could not be determined as there was no evidence of viral or parasitic infestation of the plants and biochemical characterization of the plants did not indicate any significant differences between the yellow and green leaf portions of the spinach. The present study was undertaken using electron microscopy (EM) to determine if a micro-nutrient deficiency was the cause for the discoloration.Green leaf spinach was collected from the field and sent by express mail to the EM laboratory. The yellow and equivalent green portions of the leaves were isolated and dried in a Denton evaporator at 10-5 Torr for 24 hrs. The leaf specimens were then examined using a JEOL 100 CX analytical microscope. TEM specimens were prepared according to the methods of Trump et al.

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