scholarly journals Mass Spectral Signatures of Complex Post-Translational Modifications in Proteins: A Proof-of-Principle Based on X-ray Irradiated Vancomycin

2020 ◽  
Vol 31 (8) ◽  
pp. 1738-1743
Author(s):  
Marwa Abdelmouleh ◽  
Mathieu Lalande ◽  
Johnny El Feghaly ◽  
Violaine Vizcaino ◽  
André Rebelo ◽  
...  
Keyword(s):  
Post Translational Modifications ◽  
X Ray ◽  
Mass Spectral ◽  
Spectral Signatures ◽  
Proof Of Principle

scholarly journals Background X-Ray Emission from Hot Gas in CDM and CDM+ Lambda Universes: Spectral Signatures

1995 ◽  
Vol 451 ◽  
pp. 436 ◽  
Author(s):  
Renyue Cen ◽  
Hyesung Kang ◽  
Jeremiah P. Ostriker ◽  
Dongsu Ryu
Keyword(s):  
X Ray ◽  
Spectral Signatures ◽  
Hot Gas

scholarly journals PDBrenum: a webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences

2021 ◽  
Author(s):  
Bulat Faezov ◽  
Roland L. Dunbrack
Keyword(s):  
Protein Data Bank ◽  
Data Bank ◽  
Post Translational Modifications ◽  
X Ray ◽  
X Ray Crystallography ◽  
Link Type ◽  
Binding Partners ◽  
Cryo Electron Microscopy ◽  
Comparative Structure ◽  
In The Beginning

AbstractThe Protein Data Bank (PDB) was established at Brookhaven National Laboratories in 1971 as an archive for biological macromolecular crystal structures. In the beginning the archive held only seven structures but in early 2021, the database has more than 170,000 structures solved by X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy, and other methods. Many proteins have been studied under different conditions (e.g., binding partners such as ligands, nucleic acids, or other proteins; mutations and post-translational modifications), thus enabling comparative structure-function studies. However, these studies are made more difficult because authors are allowed by the PDB to number the amino acids in each protein sequence in any manner they wish. This results in the same protein being numbered differently in the available PDB entries. In addition to the coordinates, there are many fields that contain information regarding specific residues in the sequence of each protein in the entry. Here we provide a webserver and Python3 application that fixes the PDB sequence numbering problem by replacing the author numbering with numbering derived from the corresponding UniProt sequences. We obtain this correspondence from the SIFTS database from PDBe. The server and program can take a list of PDB entries and provide renumbered files in mmCIF format and the legacy PDB format for both asymmetric unit files and biological assembly files provided by PDBe. The server can also take a list of UniProt identifiers (“P04637” or “P53_HUMAN”) and return the desired files.AvailabilitySource code is freely available at https://github.com/Faezov/PDBrenum. The webserver is located at: http://dunbrack3.fccc.edu/[email protected] or [email protected].

scholarly journals Generation of photoionized plasmas in the laboratory: Analogues to astrophysical sources

2019 ◽  
Vol 15 (S350) ◽  
pp. 321-325
Author(s):  
S. White ◽  
R. Irwin ◽  
R. Warwick ◽  
G. Sarri ◽  
G. F. Gribakin ◽  
...  
Keyword(s):  
Experimental Approach ◽  
Argon Plasma ◽  
Time Dependent ◽  
X Ray ◽  
Photoionized Plasma ◽  
Photoionized Plasmas ◽  
Laboratory Analogue ◽  
Bright Source ◽  
Proof Of Principle ◽  
Gas Pressures

AbstractImplementation of a novel experimental approach using a bright source of narrowband x-ray emission has enabled the production of a photoionized argon plasma of relevance to astrophysical modelling codes such as Cloudy. We present results showing that the photoionization parameter ζ = 4πF/ne generated using the VULCAN laser was ≈ 50 erg cm s−1, higher than those obtained previously with more powerful facilities. Comparison of our argon emission-line spectra in the 4.15 - 4.25 Å range at varying initial gas pressures with predictions from the Cloudy code and a simple time-dependent code are also presented. Finally we briefly discuss how this proof-of-principle experiment may be scaled to larger facilities such as ORION to produce the closest laboratory analogue to a photoionized plasma.

scholarly journals Theory of Accretion Disk Coronae

1990 ◽  
Vol 115 ◽  
pp. 187-196
Author(s):  
T. R. Kallman
Keyword(s):  
Active Galactic Nuclei ◽  
Accretion Disk ◽  
Cataclysmic Variables ◽  
Galactic Nuclei ◽  
X Ray ◽  
Spectral Signatures ◽  
Low Mass ◽  
X Ray Absorption ◽  
X Ray Binaries ◽  
Theoretical Issues

AbstractAccretion disk coronae are likely to be the dominant site for X-ray absorption and reprocessed emission in low mass X-ray binaries, and may be present in other classes of compact X-ray sources such as active galactic nuclei and cataclysmic variables. In spite of this fact, and in spite of the observational evidence for their existence, there remain many uncertainties about the structure of accretion disk coronae. This paper will discuss the coronal structure and dynamics, their X-ray spectral signatures including coupling to the variability behavior of compact X-ray sources, and the major unsolved theoretical issues surrounding them.

scholarly journals Determining paediatric patient thickness from a single digital radiograph—a proof of principle

2018 ◽  
Vol 91 (1087) ◽  
pp. 20180139 ◽  
Author(s):  
Mark Worrall ◽  
Sarah Vinnicombe ◽  
David G Sutton
Keyword(s):  
Paediatric Patient ◽  
Attenuation Coefficient ◽  
A Priori ◽  
A Priori Knowledge ◽  
Linear Attenuation Coefficient ◽  
Clinical Tool ◽  
X Ray ◽  
Pixel Value ◽  
Solid Water ◽  
Proof Of Principle

Objective: This work presents a proof of principle for a method of estimating the thickness of an attenuator from a single radiograph using the image, the exposure factors with which it was acquired and a priori knowledge of the characteristics of the X-ray unit and detector used for the exposure. It is intended this could be developed into a clinical tool to assist with paediatric patient dose audit, for which a measurement of patient size is required. Methods: The proof of principle used measured pixel value and effective linear attenuation coefficient to estimate the thickness of a Solid Water attenuator. The kerma at the detector was estimated using a measurement of pixel value on the image and measured detector calibrations. The initial kerma was estimated using a lookup table of measured output values. The effective linear attenuation coefficient was measured for Solid Water at varying kVp. 11 test images of known and varying thicknesses of Solid Water were acquired at 60, 70 and 81 kVp. Estimates of attenuator thickness were made using the model and the results compared to the known thickness. Results: Estimates of attenuator thickness made using the model differed from the known thickness by 3.8 mm (3.2%) on average, with a range of 0.5–10.8 mm (0.5–9%). Conclusion: A proof of principle is presented for a method of estimating the thickness of an attenuator using a single radiograph of the attenuator. The method has been shown to be accurate using a Solid Water attenuator, with a maximum difference between estimated and known attenuator thickness of 10.8 mm (9%). The method shows promise as a clinical tool for estimating abdominal paediatric patient thickness for paediatric patient dose audit, and is only contingent on the type of data routinely collected by Medical Physics departments. Advances in knowledge: A computational model has been created that is capable of accurately estimating the thickness of a uniform attenuator using only the radiographic image, the exposure factors with which it was acquired and a priori knowledge of the characteristics of the X-ray unit and detector used for the exposure.

scholarly journals Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Zachary Lee Johnson ◽  
Jun-Ho Lee ◽  
Kiyoun Lee ◽  
Minhee Lee ◽  
Do-Yeon Kwon ◽  
...  
Keyword(s):  
Antiviral Agents ◽  
Nucleoside Transporters ◽  
Structural Basis ◽  
Biological Processes ◽  
Functional Information ◽  
Binding Studies ◽  
X Ray ◽  
Equilibrium Binding ◽  
Drug Selectivity ◽  
Proof Of Principle

Concentrative nucleoside transporters (CNTs) are responsible for cellular entry of nucleosides, which serve as precursors to nucleic acids and act as signaling molecules. CNTs also play a crucial role in the uptake of nucleoside-derived drugs, including anticancer and antiviral agents. Understanding how CNTs recognize and import their substrates could not only lead to a better understanding of nucleoside-related biological processes but also the design of nucleoside-derived drugs that can better reach their targets. Here, we present a combination of X-ray crystallographic and equilibrium-binding studies probing the molecular origins of nucleoside and nucleoside drug selectivity of a CNT from Vibrio cholerae. We then used this information in chemically modifying an anticancer drug so that it is better transported by and selective for a single human CNT subtype. This work provides proof of principle for utilizing transporter structural and functional information for the design of compounds that enter cells more efficiently and selectively.

X-ray spectral signatures of photoionized plasmas

1990 ◽  
Vol 350 ◽  
pp. L37 ◽  
Author(s):  
Duane A. Liedahl ◽  
Steven M. Kahn ◽  
Albert L. Osterheld ◽  
William H. Goldstein
Keyword(s):  
X Ray ◽  
Spectral Signatures ◽  
Photoionized Plasmas

Meso-pyrrolyl BODIPY based colorimetric optical sensor for Cu2+ ions

2020 ◽  
Vol 24 (09) ◽  
pp. 1121-1128
Author(s):  
P. Sabari ◽  
Rima Sengupta ◽  
B. Umasekhar ◽  
Mangalampalli Ravikanth
Keyword(s):  
Schiff Base ◽  
2D Nmr ◽  
Spectral Studies ◽  
Strong Absorption Band ◽  
X Ray ◽  
Mass Spectral ◽  
Imine Nitrogen ◽  
Phenolic Oxygen ◽  
Td Dft ◽  
Cation Sensing

A simple meso-pyrrolyl BODIPY-Schiff base conjugate was synthesized by reacting ([Formula: see text]-formylpyrrolyl) BODIPY with 2-aminophenol in ethanol at reflux followed by recrystallization from CH2Cl2/petroleum ether, affording the conjugate in 72% yield. The conjugate was thoroughly characterized by HR-MS, 1D and 2D NMR and X-ray crystallographic techniques. The X-ray structure of the meso-pyrrolyl BODIPY-Schiff base conjugate revealed that the meso-pyrrole and the phenyl substituents were deviated by an angle of [Formula: see text] and [Formula: see text], respectively, from the plane of the BF2-dipyrrin core. The absorption spectrum of the conjugate was similar to the ([Formula: see text]-formylpyrrolyl) BODIPY with a strong absorption band at 508 nm, whereas the fluorescence of the ([Formula: see text]-formylpyrrolyl) BODIPY was completely quenched in the BODIPY-Schiff base conjugate. Furthermore, cation sensing studies revealed that the conjugate has a specific sensing ability for the Cu(II) ion even in the presence of the other metal ions, as verified by the visual, absorption and mass spectral studies. The DFT optimized structure revealed that the Cu(II) ion was bound to pyrrolic nitrogen, imine nitrogen, phenolic oxygen and two water molecules in a distorted square pyramidal fashion. TD-DFT studies accounted well for the absorption spectra of the BODIPY-Schiff base conjugate and its Cu[Formula: see text] bound complex.

scholarly journals The Dehydrogenation Mechanism and Reversibility of LiBH4 Doped by Active Al Derived from AlH3

Metals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 559 ◽  
Author(s):  
Qing He ◽  
Dongdong Zhu ◽  
Xiaocheng Wu ◽  
Duo Dong ◽  
Xiaoying Jiang ◽  
...  
Keyword(s):  
Reaction Products ◽  
X Ray Diffraction ◽  
Scanning Electronic Microscopy ◽  
Electronic Microscopy ◽  
Scanning Calorimetry ◽  
Mass Spectral Analysis ◽  
X Ray ◽  
Mass Spectral ◽  
Al Composite ◽  
Dehydrogenation Mechanism

A detailed analysis of the dehydrogenation mechanism and reversibility of LiBH4 doped by as-derived Al (denoted Al*) from AlH3 was performed by thermogravimetry (TG), differential scanning calorimetry (DSC), mass spectral analysis (MS), powder X-ray diffraction (XRD), scanning electronic microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR). The results show that the dehydrogenation of LiBH4/Al* is a five-step reaction: (1) LiBH4 + Al → LiH + AlB2 + “Li-Al-B-H” + B2H6 + H2; (2) the decomposition of “Li-Al-B-H” compounds liberating H2; (3) 2LiBH4 + Al → 2LiH + AlB2 + 3H2; (4) LiBH4 → LiH + B + 3/2H2; and (5) LiH + Al → LiAl + 1/2H2. Furthermore, the reversibility of the LiBH4/Al* composite is based on the following reaction: LiH + LiAl + AlB2 + 7/2H2 ↔ 2LiBH4 + 2Al. The extent of the dehydrogenation reaction between LiBH4 and Al* greatly depends on the precipitation and growth of reaction products (LiH, AlB2, and LiAl) on the surface of Al*. A passivation shell formed by these products on the Al* is the kinetic barrier to the dehydrogenation of the LiBH4/Al* composite.

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