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Chemical crystallography

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https://www.readbyqxmd.com/read/29438671/the-structure-of-the-biofilm-controlling-response-regulator-bfmr-from-acinetobacter-baumannii-reveals-details-of-its-dna-binding-mechanism
#1
G Logan Draughn, Morgan E Milton, Erik A Feldmann, Benjamin G Bobay, Braden M Roth, Andrew L Olson, Richele J Thompson, Luis A Actis, Christopher Davies, John Cavanagh
The rise of drug-resistant bacterial infections coupled with decreasing antibiotic efficacy poses a significant challenge to global healthcare. Acinetobacter baumannii is an insidious, emerging bacterial pathogen responsible for severe nosocomial infections aided by its ability to form biofilms. The response regulator BfmR, from the BfmR/S two-component system, is the master regulator of biofilm initiation in A. baumannii and is a tractable therapeutic target. Here we present the structure of A. baumannii BfmR using a hybrid approach combining X-ray crystallography, nuclear magnetic resonance spectroscopy, chemical crosslinking mass spectrometry, and molecular modeling...
February 10, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29429876/-to-be-or-not-to-be-protonated-atomic-details-of-human-carbonic-anhydrase-clinical-drug-complexes-by-neutron-crystallography-and-simulation
#2
Andrey Kovalevsky, Mayank Aggarwal, Hector Velazquez, Matthew J Cuneo, Matthew P Blakeley, Kevin L Weiss, Jeremy C Smith, S Zoë Fisher, Robert McKenna
Human carbonic anhydrases (hCAs) play various roles in cells, and have been drug targets for decades. Sequence similarities of hCA isoforms necessitate designing specific inhibitors, which requires detailed structural information for hCA-inhibitor complexes. We present room temperature neutron structures of hCA II in complex with three clinical drugs that provide in-depth analysis of drug binding, including protonation states of the inhibitors, hydration water structure, and direct visualization of hydrogen-bonding networks in the enzyme's active site...
January 29, 2018: Structure
https://www.readbyqxmd.com/read/29405001/mapping-of-protein-interfaces-in-live-cells-using-genetically-encoded-crosslinkers
#3
Lisa Seidel, Irene Coin
Understanding the topology of protein-protein interactions is a matter of fundamental importance in the biomedical field. Biophysical approaches such as X-ray crystallography and nuclear magnetic resonance can investigate in detail only isolated protein complexes that are reconstituted in an artificial environment. Alternative methods are needed to investigate protein interactions in a physiological context, as well as to characterize protein complexes that elude the direct structural characterization. We describe here a general strategy to investigate protein interactions at the molecular level directly in the live mammalian cell, which is based on the genetic incorporation of photo- and chemical crosslinking noncanonical amino acids...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29404547/mechanistic-understanding-of-tungsten-oxide-in-plane-nanostructure-growth-via-sequential-infiltration-synthesis
#4
Jae Jin Kim, Hyo Seon Suh, Chun Zhou, Anil U Mane, Byeongdu Lee, Soojeong Kim, Jonathan D Emery, Jeffrey W Elam, Paul F Nealey, Paul Fenter, Timothy T Fister
Tungsten oxide (WO3-x) nanostructures with hexagonal in-plane arrangements were fabricated by sequential infiltration synthesis (SIS), using the selective interaction of gas phase precursors with functional groups in one domain of a block copolymer (BCP) self-assembled template. Such structures are highly desirable for various practical applications and as model systems for fundamental studies. The nanostructures were characterized by cross-sectional scanning electron microscopy, grazing-incidence small/wide-angle X-ray scattering (GISAXS/GIWAXS), and X-ray absorption near edge structure (XANES) measurements at each stage during the SIS process and subsequent thermal treatments, to provide a comprehensive picture of their evolution in morphology, crystallography and electronic structure...
February 6, 2018: Nanoscale
https://www.readbyqxmd.com/read/29394051/structural-elucidation-and-bio-inspired-total-syntheses-of-ascorbylated-diterpenoid-hongkonoids-a-d
#5
Jin-Xin Zhao, Yan-Yan Yu, Sha-Sha Wang, Su-Ling Huang, Yu Shen, Xin-Hua Gao, Li Sheng, Jing-Ya Li, Ying Leng, Jia Li, Jian-Min Yue
Hongkonoids AD (1-4), the first example of ascorbylated terpenoids featuring a unique 5,5,5-fused tricyclic spiroketal butyrolactone moiety and diterpenoid-derived long chain, were isolated from Dysoxylum hongkongense. Their structures were unambiguously assigned by a combination of spectroscopic data, chemical degradation, X-ray crystallography, CD analysis, and total synthesis. The total syntheses of compounds 1-4 were effectively accomplished by a convergent strategy with the longest linear sequences of 12-14 steps and overall yields of 5...
February 2, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29385686/new-antibacterial-phenone-derivatives-asperphenone-a-c-from-mangrove-derived-fungus-aspergillus-sp-yhz-1
#6
Zhi-Kai Guo, Yi-Qin Zhou, Hao Han, Wen Wang, Lang Xiang, Xin-Zhao Deng, Hui-Ming Ge, Rui-Hua Jiao
Marine fungi are a promising source of novel bioactive natural products with diverse structure. In our search for new bioactive natural products from marine fungi, three new phenone derivatives, asperphenone A-C (1-3), have been isolated from the ethyl acetate extract of the fermentation broth of the mangrove-derived fungus, Aspergillus sp. YHZ-1. The chemical structures of these natural products were elucidated on the basis of mass spectrometry, one- and two-dimensional NMR spectroscopic analysis and asperphenone A and B were confirmed by single-crystal X-ray crystallography...
January 30, 2018: Marine Drugs
https://www.readbyqxmd.com/read/29376653/redox-chemistry-of-bis-pyrrolyl-pyridine-chromium-and-molybdenum-complexes-an-experimental-and-density-functional-theoretical-study
#7
Anitha S Gowda, Jeffrey L Petersen, Carsten Milsmann
The three- and four-membered redox series [Cr(MePDP)2]z (z = 1-, 2-, 3-) and [Mo(MePDP)2]z (z = 0, 1-, 2-, 3-) were synthesized to study the redox properties of the pincer ligand MePDP2- (H2MePDP = 2,6-bis(5-methyl-3-phenyl-1H-pyrrol-2-yl)pyridine). The monoanionic complexes were characterized by X-ray crystallography, UV/vis/NIR spectroscopy, and magnetic susceptibility measurements. Experimental and density functional theory (DFT) studies are consistent with closed-shell MePDP2- ligands and +III oxidation states (d3, S = 3/2) for the central metal ions...
January 27, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29337573/cryoprotectants-severely-exacerbate-x-ray-induced-photoreduction
#8
Kurt H Nienaber, M Jake Pushie, Julien J H Cotelesage, Ingrid J Pickering, Graham N George
Approximately 11% of enzymes contain a transition metal ion that is essential for catalytic function. Such metalloenzymes catalyze much of the most chemically challenging and biologically essential chemistry carried out by life. X-ray based methods, predominantly macromolecular crystallography (MX) and also X-ray absorption spectroscopy (XAS), have proved essential for determining structures of transition metal ion-containing active sites in order to deduce enzyme catalytic mechanisms. However, X-ray irradiation can induce change in both oxidation state and structure of the metal, which is problematic in structure determination...
January 16, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29334167/cross-linking-mass-spectrometry-for-studying-protein-structures-and-protein-protein-interactions-where-are-we-now-and-where-should-we-go-from-here
#9
Andrea Sinz
Structural mass spectrometry (MS) is gaining increasing importance in deriving valuable three-dimensional structural information on proteins and protein complexes and complements existing techniques, such as NMR spectroscopy and X-ray crystallography. Structural MS unites different MS-based techniques, i.e, hydrogen-deuterium exchange, native MS, ion-mobility MS, protein footprinting, and chemical cross-linking/MS, and allows fundamental questions in structural biology to be addressed. In this article, I will focus on the cross-linking/MS strategy...
January 15, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29332299/similarity-search-combined-with-docking-and-molecular-dynamics-for-novel-hache-inhibitor-scaffolds
#10
Nadia Melo Borges, Geraldo Rodrigues Sartori, Jean F R Ribeiro, Josmar R Rocha, João B L Martins, Carlos A Montanari, Ricardo Gargano
The main purpose of this study was to address the performance of virtual screening methods based on ligands and the protein structure of acetylcholinesterase (AChE) in order to retrieve novel human AChE (hAChE) inhibitors. In addition, a protocol was developed to identify novel hit compounds and propose new promising AChE inhibitors from the ZINC database with 10 million commercially available compounds. In this sense, 3D similarity searches using rapid overlay of chemical structures and similarity analysis through comparison of electrostatic overlay of docked hits were used to retrieve AChE inhibitors from collected databases...
January 13, 2018: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29327921/the-nature-and-reactivity-of-ferryl-heme-in-compounds-i-and-ii
#11
Peter C E Moody, Emma L Raven
Aerobic organisms have evolved to activate oxygen from the atmosphere, which allows them to catalyze the oxidation of different kinds of substrates. This activation of oxygen is achieved by a metal center (usually iron or copper) buried within a metalloprotein. In the case of iron-containing heme enzymes, the activation of oxygen is achieved by formation of transient iron-oxo (ferryl) intermediates; these intermediates are called Compound I and Compound II. The Compound I and II intermediates were first discovered in the 1930s in horseradish peroxidase, and it is now known that these same species are used across the family of heme enzymes, which include all of the peroxidases, the heme catalases, the P450s, cytochrome c oxidase, and NO synthase...
January 12, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29300483/unexpected-diffusion-anisotropy-of-carbon-dioxide-in-the-metal-organic-framework-zn2-dobpdc
#12
Alexander C Forse, Miguel I Gonzalez, Rebecca L Siegelman, Velencia J Witherspoon, Sudi Jawahery, Rocio Mercado, Phillip J Milner, Jeffrey D Martell, Berend Smit, Bernhard Blümich, Jeffrey R Long, Jeffrey A Reimer
Metal-organic frameworks are promising materials for energy-efficient gas separations, but little is known about the diffusion of adsorbates in materials featuring one-dimensional porosity at the nanoscale. An understanding of the interplay between framework structure and gas diffusion is crucial for the practical application of these materials as adsorbents or in mixed-matrix membranes, since the rate of gas diffusion within the adsorbent pores impacts the required size (and therefore cost) of the adsorbent column or membrane...
January 4, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29288772/ph-driven-fibrillar-aggregation-of-the-super-sweet-protein-y65r-mnei-a-step-by-step-structural-analysis
#13
Andrea Pica, Serena Leone, Rocco Di Girolamo, Federica Donnarumma, Alessandro Emendato, Michele Fortunato Rega, Antonello Merlino, Delia Picone
BACKGROUND: MNEI and its variant Y65R-MNEI are sweet proteins with potential applications as sweeteners in food industry. Also, they are often used as model systems for folding and aggregation studies. METHODS: X-ray crystallography was used to structurally characterize Y65R-MNEI at five different pHs, while circular dichroism and fluorescence spectroscopy their thermal and chemical stability. ThT assay and AFM were used for studying the kinetics of aggregation and morphology of the aggregates...
December 27, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29281006/pine-sparky-2-for-automated-nmr-based-protein-structure-research
#14
Woonghee Lee, John L Markley
Summary: NMR (nuclear magnetic resonance) spectroscopy, along with X-ray crystallography and Cryo-EM, is one of the three major tools that enable the determination of atomic-level structural models of biological macromolecules. Of these, NMR has the unique ability to follow important processes in solution, including conformational changes, internal dynamics and protein-ligand interactions. As a means for facilitating the handling and analysis of spectra involved in these types of NMR studies, we have developed PINE-SPARKY...
December 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29277259/exciton-states-and-optical-properties-of-the-cp26-photosynthetic-protein
#15
Daniil V Khokhlov, Aleksandr S Belov, Vadim V Eremin
The photosynthetic complex CP26, one of the minor antennae of the photosystem II, plays an important role in regulation of the excitation energy transfer in the PSII. Due to instability during isolation and purification, it remained poorly studied from the viewpoint of theoretical chemistry because of the absence of X-ray crystallography data. In this work, using the recently determined three-dimensional structure of the complex we apply the quantum chemical approach to study the properties of exciton states in it...
December 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29243923/crystalline-superlattices-of-nanoscopic-cds-molecular-clusters-an-x-ray-crystallography-and-111cd-ssnmr-spectroscopy-study
#16
Tetyana I Levchenko, Bryan E G Lucier, John F Corrigan, Yining Huang
Systematic 111Cd solid-state (SS) NMR experiments were performed to correlate X-ray crystallographic data with SSNMR parameters for a set of CdS-based materials, varying from molecular crystals of small complexes [Cd(SPh)4]2- and [Cd4(SPh)10]2- to superlattices of large monodisperse clusters [Cd54S32(SPh)48(dmf)4]4- and 1.9 nm CdS. Methodical data analysis allowed for assigning individual resonances or resonance groups to particular types of cadmium sites residing in different chemical and/or crystallographic environments...
December 15, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/29233219/a-molecular-engineering-toolbox-for-the-structural-biologist
#17
Galia T Debelouchina, Tom W Muir
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29215275/x-shaped-oligomeric-pyromellitimide-polyradicals
#18
Yilei Wu, Ji-Min Han, Michael Hong, Matthew D Krzyaniak, Anthea K Blackburn, Isurika R Fernando, Dennis D Cao, Michael R Wasielewski, J Fraser Stoddart
The synthesis of stable organic polyradicals is important for the development of magnetic materials. Herein, we report the synthesis, isolation, and characterization of a series of X-shaped pyromellitimide (PI) oligomers (Xn-R, n = 2-4, R = Hex or Ph) linked together by single C-C bonds between their benzenoid cores. We hypothesize that these oligomers might form high-spin states in their reduced forms because of the nearly orthogonal conformations adopted by their PI units. 1H and 13C nuclear magnetic resonance (NMR) spectroscopies confirmed the isolation of the dimeric, trimeric, and tetrameric homologues...
December 7, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29214549/synthesis-structure-and-toxicity-evaluation-of-ethanolamine-nitro-chloronitrobenzoates-a-combined-experimental-and-theoretical-study
#19
Manuela Crisan, Liliana Halip, Paulina Bourosh, Sergiu Adrian Chicu, Yurii Chumakov
BACKGROUND: Nitroaromatic and chloronitroaromatic compounds have been a subject of great interest in industry and recently in medical-pharmaceutic field. 2-Chloro-4-nitro/2-chloro-5-nitrobenzoic acids and 4-nitrobenzoic acid are promising new agents for the treatment of main infectious killing diseases in the world: immunodeficiency diseases and tuberculosis. RESULTS: New ethanolamine nitro/chloronitrobenzoates were synthesized and characterized by X-ray crystallography, UV-vis, FT-IR and elementary analysis techniques...
December 6, 2017: Chemistry Central Journal
https://www.readbyqxmd.com/read/29208708/aminoglycoside-interactions-and-impacts-on-the-eukaryotic-ribosome
#20
Irina Prokhorova, Roger B Altman, Muminjon Djumagulov, Jaya P Shrestha, Alexandre Urzhumtsev, Angelica Ferguson, Cheng-Wei Tom Chang, Marat Yusupov, Scott C Blanchard, Gulnara Yusupova
Aminoglycosides are chemically diverse, broad-spectrum antibiotics that target functional centers within the bacterial ribosome to impact all four principle stages (initiation, elongation, termination, and recycling) of the translation mechanism. The propensity of aminoglycosides to induce miscoding errors that suppress the termination of protein synthesis supports their potential as therapeutic interventions in human diseases associated with premature termination codons (PTCs). However, the sites of interaction of aminoglycosides with the eukaryotic ribosome and their modes of action in eukaryotic translation remain largely unexplored...
December 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
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