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Chemical crystallography

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https://www.readbyqxmd.com/read/28817770/photoinduced-copper-catalyzed-alkylation-of-amines-a-mechanistic-study-of-the-cross-coupling-of-carbazole-with-alkyl-bromides
#1
Jun Myun Ahn, Tanvi S Ratani, Kareem Hannoun, Gregory C Fu, Jonas C Peters
We have recently reported that a variety of couplings of nitrogen, sulfur, oxygen, and carbon nucleophiles with organic halides can be achieved under mild conditions (-40 to 30 °C) through the use of light and a copper catalyst. Insight into the various mechanisms by which these reactions proceed may enhance our understanding of chemical reactivity and facilitate the development of new methods. In this report, we apply an array of tools (EPR, NMR, transient absorption, and UV-vis spectroscopy; ESI-MS; X-ray crystallography; DFT calculations; reactivity, stereochemical, and product studies) to investigate the photoinduced, copper-catalyzed coupling of carbazole with alkyl bromides...
August 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28808891/nmr-backbone-resonance-assignment-of-new-delhi-metallo-beta-lactamase
#2
Chendie Yao, Qiong Wu, Guohua Xu, Conggang Li
The emerging of the New Delhi metallo-beta-lactamase (NDM-1) has become one of the greatest threats to the clinical treatment. Although the structure of NDM-1 has been determined by X-ray crystallography, the molecular mechanism and process of catalysis reaction remain elusive. NMR spectroscopy plays a unique role in the characterization of conformational dynamics. Here we report the backbone (1)H, (15)N and (13)C chemical shift assignments of NDM-1 by heteronuclear multidimensional NMR spectroscopy as well as its secondary structure in solution as predicted by TALOS+...
August 14, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28808437/how-to-assign-a-3%C3%A2-%C3%A2-1-dimensional-superspace-group-to-an-incommensurately-modulated-biological-macromolecular-crystal
#3
Jason Porta, Jeff Lovelace, Gloria E O Borgstahl
Periodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28807997/phosphoantigen-induced-conformational-change-of-butyrophilin-3a1-btn3a1-and-its-implication-on-v%C3%AE-9v%C3%AE-2-t-cell-activation
#4
Siyi Gu, Joseph R Sachleben, Christopher T Boughter, Wioletta I Nawrocka, Marta T Borowska, Jeffrey T Tarrasch, Georgios Skiniotis, Benoît Roux, Erin J Adams
Human Vγ9Vδ2 T cells respond to microbial infections as well as certain types of tumors. The key initiators of Vγ9Vδ2 activation are small, pyrophosphate-containing molecules called phosphoantigens (pAgs) that are present in infected cells or accumulate intracellularly in certain tumor cells. Recent studies demonstrate that initiation of the Vγ9Vδ2 T cell response begins with sensing of pAg via the intracellular domain of the butyrophilin 3A1 (BTN3A1) molecule. However, it is unknown how downstream events can ultimately lead to T cell activation...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28799326/glp-1-conjugated-to-rhsa-variants-with-modified-fcrn-binding-properties-impact-on-molecular-structure-and-half-life
#5
Jens Thostrup Bukrinski, Pernille Sønderby, Filipa Antunes, Birgitte Andersen, Esben Gjerloeff Wedebye Schmidt, Guenther H H J Peters, Pernille Harris
Glucagon-like peptide 1 (GLP-1) is a small incretin hormone stimulated by food intake, resulting in an amplification of the insulin response. Though interesting as a drug candidate for the treatment of type 2 diabetes mellitus, its short plasma half-life of less than 3 minutes limits its clinical use. A strategy to extend the half-life of GLP-1 utilizes the long half-life of human serum albumin (HSA) by combining the two via chemical conjugation or genetic fusion. HSA has a plasma half-life of around 21 days owing to its interaction with the neonatal Fc receptor (FcRn) expressed in endothelial cells of blood vessels, which rescues circulating HSA from lysosomal degradation...
August 11, 2017: Biochemistry
https://www.readbyqxmd.com/read/28781083/kras-g12c-drug-development-discrimination-between-switch-ii-pocket-configurations-using-hydrogen-deuterium-exchange-mass-spectrometry
#6
Jia Lu, Rane A Harrison, Lianbo Li, Mei Zeng, Sudershan Gondi, David Scott, Nathanael S Gray, John R Engen, Kenneth D Westover
KRAS G12C, the most common RAS mutation found in non-small-cell lung cancer, has been the subject of multiple recent covalent small-molecule inhibitor campaigns including efforts directed at the guanine nucleotide pocket and separate work focused on an inducible pocket adjacent to the switch motifs. Multiple conformations of switch II have been observed, suggesting that switch II pocket (SIIP) binders may be capable of engaging a range of KRAS conformations. Here we report the use of hydrogen/deuterium-exchange mass spectrometry (HDX MS) to discriminate between conformations of switch II induced by two chemical classes of SIIP binders...
July 25, 2017: Structure
https://www.readbyqxmd.com/read/28780862/structure-and-dynamics-of-an-intrinsically-disordered-protein-region-that-partially-folds-upon-binding-by-chemical-exchange-nmr
#7
Cyril Charlier, Guillaume Bouvignies, Philippe Pelupessy, Astrid Walrant, Rodrigue Marquant, Mikhail Kozlov, Pablo De Ioannes, Nicolas Bolik-Coulon, Sandrine Sagan, Patricia Cortes, Aneel K Aggarwal, Ludovic Carlier, Fabien Ferrage
Many intrinsically disordered proteins (IDPs) and protein regions (IDRs) engage in transient, yet specific, interactions with a variety of protein partners. Often, if not always, interactions with a protein partner lead to partial folding of the IDR. Characterizing the conformational space of such complexes is challenging: in solution-state NMR, signals of the IDR in the interacting region become broad, weak and often invisible; while X-ray crystallography only provides information on fully ordered regions...
August 7, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28759020/modulating-the-dna-polymerase-%C3%AE-reaction-equilibrium-to-dissect-the-reverse-reaction
#8
David D Shock, Bret D Freudenthal, William A Beard, Samuel H Wilson
DNA polymerases catalyze efficient and high-fidelity DNA synthesis. While this reaction favors nucleotide incorporation, polymerases also catalyze a reverse reaction, pyrophosphorolysis, that removes the DNA primer terminus and generates deoxynucleoside triphosphates. Because pyrophosphorolysis can influence polymerase fidelity and sensitivity to chain-terminating nucleosides, we analyzed pyrophosphorolysis with human DNA polymerase β and found the reaction to be inefficient. The lack of a thio-elemental effect indicated that this reaction was limited by a nonchemical step...
July 31, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28751927/an-nmr-crystallographic-investigation-of-the-relationships-between-the-crystal-structure-and-29-si-isotropic-chemical-shift-in-silica-zeolites
#9
Daniel M Dawson, Robert F Moran, Sharon E Ashbrook
NMR crystallography has recently been applied to great effect for silica zeolites. Here we investigate whether it is possible to extend the structural information available from routine NMR spectra via a simple structure-spectrum relationship. Unlike previous empirically derived relationships that have compared experimental crystal structures for (often disordered) silicates with experimental NMR spectra, where the structure may not be an accurate representation of the material studied experimentally, we use NMR parameters calculated by density functional theory (DFT) for both model Si(OSi(OH)3)4 clusters and also extended zeolitic SiO2 frameworks, for which the input structure corresponding to the NMR parameters is known exactly...
July 20, 2017: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
https://www.readbyqxmd.com/read/28750804/ligand-assisted-protein-structure-laps-an-experimental-paradigm-for-characterizing-cannabinoid-receptor-ligand-binding-domains
#10
David R Janero, Anisha Korde, Alexandros Makriyannis
Detailed characterization of the ligand-binding motifs and structure-function correlates of the principal GPCRs of the endocannabinoid-signaling system, the cannabinoid 1 (CB1R) and cannabinoid 2 (CB2R) receptors, is essential to inform the rational design of drugs that modulate CB1R- and CB2R-dependent biosignaling for therapeutic gain. We discuss herein an experimental paradigm termed "ligand-assisted protein structure" (LAPS) that affords a means of characterizing, at the amino acid level, CB1R and CB2R structural features key to ligand engagement and receptor-dependent information transmission...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28743589/density-functionalized-ru-ii-no-salen-cl-complex-computational-photodynamics-and-in-vitro-anticancer-facets
#11
Jan Mohammad Mir, N Jain, P S Jaget, R C Maurya
Photodynamic therapy (PDT) is a treatment that uses photosensitizing agents to kill cancer cells. Scientific community has been eager for decades in enduring curiosity to design an efficient PDT drug. Under such purview, the current report deals with the computational photodynamic behavior of ruthenium(II) nitrosyl complex containing N, N'-salicyldehyde-ethylenediimine (SalenH2), the synthesis and X-ray crystallography of which is already known [Ref. 36]. Gaussian 09W software package was employed to carry out the density functional (DFT) studies...
July 22, 2017: Photodiagnosis and Photodynamic Therapy
https://www.readbyqxmd.com/read/28737940/defining-the-structural-basis-for-allosteric-product-release-from-e-coli-dihydrofolate-reductase-using-nmr-relaxation-dispersion
#12
David Oyen, R Bryn Fenwick, Phillip C Aoto, Robyn L Stanfield, Ian A Wilson, H Jane Dyson, Peter E Wright
The rate-determining step in the catalytic cycle of E. coli dihydrofolate reductase is tetrahydrofolate (THF) product release, which can occur via an allosteric or an intrinsic pathway. The allosteric pathway, which becomes accessible when the reduced cofactor NADPH is bound, involves transient sampling of a higher energy conformational state, greatly increasing the product dissociation rate as compared to the intrinsic pathway that obtains when NADPH is absent. Although the kinetics of this process are known, the enzyme structure and the THF product conformation in the transiently formed excited state remain elusive...
August 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28705433/recent-advances-in-racemic-protein-crystallography
#13
REVIEW
Bingjia Yan, Linzhi Ye, Weiliang Xu, Lei Liu
Solution of the three-dimensional structures of proteins is a critical step in deciphering the molecular mechanisms of their bioactivities. Among the many approaches for obtaining protein crystals, racemic protein crystallography has been developed as a unique method to solve the structures of an increasing number of proteins. Exploiting unnatural protein enantiomers in crystallization and resolution, racemic protein crystallography manifests two major advantages that are 1) to increase the success rate of protein crystallization, and 2) to obviate the phase problem in X-ray diffraction...
May 10, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28703597/natural-and-semisynthetic-tigliane-diterpenoids-with-new-carbon-skeletons-from-euphorbia-dracunculoides-as-a-wnt-signaling-pathway-inhibitor
#14
Li Wang, Jing Yang, Ling-Mei Kong, Jun Deng, Zijun Xiong, Jianping Huang, Jianying Luo, Yijun Yan, Yikao Hu, Xiao-Nian Li, Yan Li, Yong Zhao, Sheng-Xiong Huang
Euphordraculoates A (1) and B (2), featuring tigliane diterpenoids with two new carbon skeletons, were characterized as metabolites of Euphorbia dracunculoides and semisynthetic products, respectively. Their structures were determined by spectroscopic analyses and X-ray crystallography. The respective biosynthetic and chemical formation mechanisms for 1 and 2 from a known tigliane 3 was proposed. The detailed decarbonization mechanism from 3 to 2 was further explored by (18)O-labeling experiment. Compound 2 could inhibit Wnt pathway in a dose- and time-dependent manner...
July 13, 2017: Organic Letters
https://www.readbyqxmd.com/read/28695248/divergent-effects-of-anesthetics-on-lipid-bilayer-properties-and-sodium-channel-function
#15
REVIEW
Karl F Herold, Olaf S Andersen, Hugh C Hemmings
General anesthetics revolutionized medicine by allowing surgeons to perform more complex and much longer procedures. This widely used class of drugs is essential to patient care, yet their exact molecular mechanism(s) are incompletely understood. One early hypothesis over a century ago proposed that nonspecific interactions of anesthetics with the lipid bilayer lead to changes in neuronal function via effects on membrane properties. This model was supported by the Meyer-Overton correlation between anesthetic potency and lipid solubility and despite more recent evidence for specific protein targets, in particular ion-channels, lipid bilayer-mediated effects of anesthetics is still under debate...
July 10, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28694484/self-assembled-%C3%AE-tocopherol-transfer-protein-nanoparticles-promote-vitamin-e-delivery-across-an-endothelial-barrier
#16
Walter Aeschimann, Stefanie Staats, Stephan Kammer, Natacha Olieric, Jean-Marc Jeckelmann, Dimitrios Fotiadis, Thomas Netscher, Gerald Rimbach, Michele Cascella, Achim Stocker
Vitamin E is one of the most important natural antioxidants, protecting polyunsaturated fatty acids in the membranes of cells. Among different chemical isoforms assimilated from dietary regimes, RRR-α-tocopherol is the only one retained in higher animals. This is possible thanks to α-Tocopherol Transfer Protein (α-TTP), which extracts α-tocopherol from endosomal compartments in liver cells, facilitating its distribution into the body. Here we show that, upon binding to its substrate, α-TTP acquires tendency to aggregation into thermodynamically stable high molecular weight oligomers...
July 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28693671/100-years-of-x-ray-crystallography
#17
Terence J Kemp, W Alcock
The developments in crystallography, since it was first covered in Science Progress in 1917, following the formulation of the Bragg equation, are described. The advances in instrumentation and data analysis, coupled with the application of computational methods to data analysis, have enabled the solution of molecular structures from the simplest binary systems to the most complex of biological structures. These developments are shown to have had major impacts in the development of chemical bonding theory and in offering an increasing understanding of enzyme-substrate interactions...
March 1, 2017: Science Progress
https://www.readbyqxmd.com/read/28692285/raman-optical-activity-reveals-carotenoid-photoactivation-events-in-the-orange-carotenoid-protein-in-solution
#18
Tomotsumi Fujisawa, Ryan L Leverenz, Momoka Nagamine, Cheryl A Kerfeld, Masashi Unno
The orange carotenoid protein (OCP) plays an important role in photoprotection in cyanobacteria, which is achieved by the photoconversion from the orange dark state (OCP(O)) to the red active state (OCP(R)). Using Raman optical activity (ROA), we studied the conformations of the carotenoid chromophore in the active sites of OCP(O) and OCP(R). This ROA measurement directly observed the chromophore conformation of native OCP in solution, and the measurement of OCP(R) first demonstrated the ROA spectroscopy for the transient species...
July 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28686035/nanoscale-chemical-processes-affecting-storage-capacities-and-seals-during-geologic-co2-sequestration
#19
Young-Shin Jun, Lijie Zhang, Yujia Min, Qingyun Li
Geologic CO2 sequestration (GCS) is a promising strategy to mitigate anthropogenic CO2 emission to the atmosphere. Suitable geologic storage sites should have a porous reservoir rock zone where injected CO2 can displace brine and be stored in pores, and an impermeable zone on top of reservoir rocks to hinder upward movement of buoyant CO2. The injection wells (steel casings encased in concrete) pass through these geologic zones and lead CO2 to the desired zones. In subsurface environments, CO2 is reactive as both a supercritical (sc) phase and aqueous (aq) species...
July 7, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28681606/identification-of-two-secondary-ligand-binding-sites-in-14-3-3-proteins-using-fragment-screening
#20
Eline Sijbesma, Lukasz Skora, Seppe Leysen, Luc Brunsveld, Uwe Koch, Peter Nussbaumer, Wolfgang Jahnke, Christian Ottmann
Proteins typically interact with multiple binding partners, and often different parts of their surfaces are employed to establish these protein-protein interactions (PPIs). Members of the class of 14-3-3 adapter proteins bind to several hundred other proteins in the cell. Multiple small molecules for the modulation of 14-3-3 PPIs have been disclosed; however, they all target the conserved phosphopeptide binding channel, so that selectivity is difficult to achieve. Here we report on the discovery of two individual secondary binding sites that have been identified by combining nuclear magnetic resonance-based fragment screening and X-ray crystallography...
August 1, 2017: Biochemistry
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