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X-ray crystallography

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https://www.readbyqxmd.com/read/28106382/lactide-as-the-playmaker-of-the-rop-game-theoretical-and-experimental-investigation-of-ring-opening-polymerization-of-lactide-initiated-by-aminonaphtholate-zinc-complexes
#1
Dawid Jędrzkiewicz, Grażyna Adamus, Michał Kwiecień, Łukasz John, Jolanta Ejfler
A family of homo- and heteroleptic zinc complexes bearing aminonaphtholate ligands was synthesized and fully characterized. Using NMR spectroscopy and DFT calculation, bis-alkoxy-bridged complexes [LZn(μ-OR)]2 were confirmed to have dimeric structures in solution, analogous to those obtained via X-ray crystallography. Surprisingly, a detailed experimental and theoretical study of the catalytic activity of [LZn(μ-OR)]2 in the ring-opening polymerization (ROP) of lactides showed that although well-defined alkoxy dimers possess a single-site structural motif, the most active initiator is obtained during in situ alcoholysis of the alkylzinc precursor...
January 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28104837/the-role-of-dimer-asymmetry-and-protomer-dynamics-in-enzyme-catalysis
#2
Tae Hun Kim, Pedram Mehrabi, Zhong Ren, Adnan Sljoka, Christopher Ing, Alexandr Bezginov, Libin Ye, Régis Pomès, R Scott Prosser, Emil F Pai
Freeze-trapping x-ray crystallography, nuclear magnetic resonance, and computational techniques reveal the distribution of states and their interconversion rates along the reaction pathway of a bacterial homodimeric enzyme, fluoroacetate dehalogenase (FAcD). The crystal structure of apo-FAcD exhibits asymmetry around the dimer interface and cap domain, priming one protomer for substrate binding. This asymmetry is dynamically averaged through conformational exchange on a millisecond time scale. During catalysis, the protomer conformational exchange rate becomes enhanced, the empty protomer exhibits increased local disorder, and water egresses...
January 20, 2017: Science
https://www.readbyqxmd.com/read/28103782/structures-of-the-first-extracellular-domain-of-crf-receptors
#3
Viviane Zelenay, Marilyn Perrin, Roland Riek
Corticotropin releasing factor (CRF) receptors belong to the secretin family of G protein-coupled receptors (GPCRs) and are responsible for initiating endocrine stress responses and mediating anxiety related behaviors upon activation via stressors. The main binding site for the CRF ligands is the first extracellular domain (ECD) of the receptors. Several structures of ligand-free and ligand-bound ECDs were recently determined either by nuclear magnetic resonance (NMR) spectroscopy or X-ray crystallography. They reveal how the ligands bind through both hydrophobic and hydrophilic interactions to the ECDs, which is highly dynamic in absence of ligands...
January 10, 2017: Current Molecular Pharmacology
https://www.readbyqxmd.com/read/28101862/crystallographic-studies-of-intermediate-filament-proteins
#4
Dmytro Guzenko, Anastasia A Chernyatina, Sergei V Strelkov
Intermediate filaments (IFs), together with microtubules and actin microfilaments, are the three main cytoskeletal components in metazoan cells. IFs are formed by a distinct protein family, which is made up of 70 members in humans. Most IF proteins are tissue- or organelle-specific, which includes lamins, the IF proteins of the nucleus. The building block of IFs is an elongated dimer, which consists of a central α-helical 'rod' domain flanked by flexible N- and C-terminal domains. The conserved rod domain is the 'signature feature' of the IF family...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101544/tetrathienyl-functionalized-red-and-nir-absorbing-bodipy-dyes-appending-various-peripheral-substituents
#5
Ping Liu, Feng Gao, Lina Zhou, Yu Chen, Zhijian Chen
A series of boron-dipyrromethene dyes (BODIPYs) 4a-g with different thienyl moieties at 2,3,5,6-positions of the BODIPY core were synthesized by the Stille cross-coupling reaction. The new compounds were characterized by (1)H NMR, (13)C NMR, HRMS, and IR spectroscopy. The single crystal structure of compound 4e was obtained by X-ray crystallography. The optical and electrochemical properties of these dyes were studied by UV/Vis spectroscopy, fluorescence spectroscopy, and cyclic voltammetry. The DFT calculation of the frontier molecular orbitals of these dyes corroborates the observed effects of peripheral substituents on the optical and redox properties...
January 19, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28098154/structural-basis-of-ligand-interaction-with-atypical-chemokine-receptor-3
#6
Martin Gustavsson, Liwen Wang, Noortje van Gils, Bryan S Stephens, Penglie Zhang, Thomas J Schall, Sichun Yang, Ruben Abagyan, Mark R Chance, Irina Kufareva, Tracy M Handel
Chemokines drive cell migration through their interactions with seven-transmembrane (7TM) chemokine receptors on cell surfaces. The atypical chemokine receptor 3 (ACKR3) binds chemokines CXCL11 and CXCL12 and signals exclusively through β-arrestin-mediated pathways, without activating canonical G-protein signalling. This receptor is upregulated in numerous cancers making it a potential drug target. Here we collected over 100 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map the structures of ACKR3:CXCL12 and ACKR3:small-molecule complexes, including dynamic regions that proved unresolvable by X-ray crystallography in homologous receptors...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28097217/amylose-recognition-and-ring-size-determination-of-amylomaltase
#7
Christian Roth, Nicole Weizenmann, Nicola Bexten, Wolfram Saenger, Wolfgang Zimmermann, Timm Maier, Norbert Sträter
Starch is a major carbon and energy source throughout all kingdoms of life. It consists of two carbohydrate polymers, branched amylopectin and linear amylose, which are sparingly soluble in water. Hence, the enzymatic breakdown by glycoside hydrolases (GHs) is of great biological and societal importance. Amylomaltases (AMs) are GHs specialized in the hydrolysis of α-1,4-linked sugar chains such as amylose. They are able to catalyze an intramolecular transglycosylation of a bound sugar chain yielding polymeric sugar rings, the cycloamyloses (CAs), consisting of 20 to 100 glucose units...
January 2017: Science Advances
https://www.readbyqxmd.com/read/28096372/helical-structure-stability-and-dynamics-in-human-apolipoprotein-e3-and-e4-by-hydrogen-exchange-and-mass-spectrometry
#8
Palaniappan S Chetty, Leland Mayne, Sissel Lund-Katz, S Walter Englander, Michael C Phillips
Apolipoprotein E (apoE) plays a critical role in cholesterol transport in both peripheral circulation and brain. Human apoE is a polymorphic 299-residue protein in which the less common E4 isoform differs from the major E3 isoform only by a C112R substitution. ApoE4 interacts with lipoprotein particles and with the amyloid-β peptide, and it is associated with increased incidence of cardiovascular and Alzheimer's disease. To understand the structural basis for the differences between apoE3 and E4 functionality, we used hydrogen-deuterium exchange coupled with a fragment separation method and mass spectrometric analysis to compare their secondary structures at near amino acid resolution...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28094934/donor-acceptor-stabilized-tetra-silanimine
#9
Yu-Liang Shan, Bi-Xiang Leong, Yongxin Li, Rakesh Ganguly, Cheuk-Wai So
The synthesis of an oligo(silanimine) is described. The reaction of the amidinato silylene [LSiN(SiMe3)2] (1, L = PhC(NtBu)2) with SiI4 in toluene afforded a mixture of the silanimine [LSi(I)NSiI3] (2), SiMe3I, and Si2I6. The mechanistic studies showed that 1 reacts with SiI4 to form the silyl ionic intermediate "{LSi(I)N(SiMe3)2}(+){SiI3}(-)", which then eliminates SiMe3I and "SiI2" to form the silanimine intermediate "LSi(I)NSiMe3". It further undergoes a substitution with another molecule of SiI4 to form a mixture of 2 and SiMe3I...
January 17, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28092942/advances-in-structural-and-single-molecule-methods-for-investigating-dna-lesion-bypass-and-repair-polymerases
#10
Austin T Raper, Andrew J Reed, Varun V Gadkari, Zucai Suo
Innovative advances in X-ray crystallography and single-molecule biophysics have yielded unprecedented insight into the mechanisms of DNA lesion bypass and damage repair. Time-dependent X-ray crystallography has been successfully applied to view the bypass of 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), a major oxidative DNA lesion, and the incorporation of the triphosphate form, 8-oxo-dGTP, catalyzed by human DNA polymerase β. Significant findings of these studies are highlighted here, and their contributions to the current mechanistic understanding of mutagenic translesion DNA synthesis (TLS) and base excision repair are discussed...
January 17, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28092367/molecular-architecture-and-dynamics-of-ash1-mrna-recognition-by-its-mrna-transport-complex
#11
Franziska Theresia Edelmann, Andreas Schlundt, Roland Gerhard Heym, Andreas Jenner, Annika Niedner-Boblenz, Muhammad Ibrahim Syed, Jean-Christophe Paillart, Ralf Stehle, Robert Janowski, Michael Sattler, Ralf-Peter Jansen, Dierk Niessing
mRNA localization is an essential mechanism of gene regulation and is required for processes such as stem-cell division, embryogenesis and neuronal plasticity. It is not known which features in the cis-acting mRNA localization elements (LEs) are specifically recognized by motor-containing transport complexes. To the best of our knowledge, no high-resolution structure is available for any LE in complex with its cognate protein complex. Using X-ray crystallography and complementary techniques, we carried out a detailed assessment of an LE of the ASH1 mRNA from yeast, its complex with its shuttling RNA-binding protein She2p, and its highly specific, cytoplasmic complex with She3p...
January 16, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28092155/discovery-of-first-in-class-potent-and-orally-bioavailable-eed-inhibitor-with-robust-anti-cancer-efficacy
#12
Ying Huang, Jeff Zhang, Zhengtian Yu, Hailong Zhang, Youzhen Wang, Andreas Lingel, Wei Qi, X Justin Gu, Kehao Zhao, Michael David Shultz, Long Wang, Xingnian Fu, Yongfeng Sun, Qiong Zhang, Xiangqing Jiang, Jiang-Wei Zhang, Chunye Zhang, Ling Li, Jue Zeng, Lijian Feng, Chao Zhang, Yueqin Liu, Man Zhang, Lijun Zhang, Mengxi Zhao, Zhenting Gao, Xianghui Liu, Douglas Fang, Haibing Guo, Yuan Mi, Tobias Gabriel, Michael P Dillon, Peter Atadja, Counde Oyang
Overexpression and somatic heterozygous mutations of EZH2, the catalytic subunit Polycomb repressive complex 2 (PRC2), are associated with several tumor types. EZH2 inhibitor, EPZ-6438 (Tazemetostat), demonstrated clinical efficacy in patients with acceptable safety profile as monotherapy. EED, another subunit of PRC2 complex, is essential for its histone methyltransferase activity through direct binding to trimethylated lysine 27 on histone 3 (H3K27Me3). Herein we disclose the discovery of a first-in-class potent, selective and orally bioavailable EED inhibitor EED226 (compound 43)...
January 16, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28091659/borane-catalyzed-indole-synthesis-through-intramolecular-hydroamination
#13
Sebastian Tussing, Miriam Ohland, Garrit Wicker, Ulrich Flörke, Jan Paradies
The reaction of 2-alkynyl anilines with catalytic amounts of B(C6F5)3 (5 mol%) resulted in the formation of 2-substituted indoles according to an intramolecular hydroamination in good to excellent yields. Reaction intermediates as well as products were characterized by NMR spectroscopy and by X-ray crystallography. The domino hydroamination/hydrogenation sequence allowed the efficient synthesis of tetrahydroquinoline 8 in good yield.
January 16, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28091515/protein-crystal-nucleation-in-pores
#14
Christo N Nanev, Emmanuel Saridakis, Naomi E Chayen
The most powerful method for protein structure determination is X-ray crystallography which relies on the availability of high quality crystals. Obtaining protein crystals is a major bottleneck, and inducing their nucleation is of crucial importance in this field. An effective method to form crystals is to introduce nucleation-inducing heterologous materials into the crystallization solution. Porous materials are exceptionally effective at inducing nucleation. It is shown here that a combined diffusion-adsorption effect can increase protein concentration inside pores, which enables crystal nucleation even under conditions where heterogeneous nucleation on flat surfaces is absent...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28090689/%C3%AE-aminoxy-peptoids-a-unique-peptoid-backbone-with-a-preference-for-cis-amide-bonds
#15
Viktoria Krieger, Emanuele Ciglia, Roland Thoma, Vera Vasylyeva, Benedikt Frieg, Nader de Sousa Amadeu, Thomas Kurz, Christoph Janiak, Holger Gohlke, Finn Kristian Hansen
α-Peptoids, or N-substituted glycine oligomers, are an important class of peptidomimetic foldamers with proteolytic stability. Nevertheless, the presence of cis-/trans-amide bond conformers, which contribute to the high flexibility of α-peptoids, is considered as a major drawback. A modified peptoid backbone with an improved control of the amide bond geometry could therefore help to overcome this limitation. Here we have performed the first thorough analysis of the folding propensities of α-aminoxy peptoids (or N-substituted 2-aminoxyacetic acid oligomers)...
January 16, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28089448/structural-basis-for-the-interaction-of-a-human-small-heat-shock-protein-with-the-14-3-3-universal-signaling-regulator
#16
Nikolai N Sluchanko, Steven Beelen, Alexandra A Kulikova, Stephen D Weeks, Alfred A Antson, Nikolai B Gusev, Sergei V Strelkov
By interacting with hundreds of protein partners, 14-3-3 proteins coordinate vital cellular processes. Phosphorylation of the small heat shock protein, HSPB6, within its intrinsically disordered N-terminal domain activates its interaction with 14-3-3, ultimately triggering smooth muscle relaxation. After analyzing the binding of an HSPB6-derived phosphopeptide to 14-3-3 using isothermal calorimetry and X-ray crystallography, we have determined the crystal structure of the complete assembly consisting of the 14-3-3 dimer and full-length HSPB6 dimer and further characterized this complex in solution using fluorescence spectroscopy, small-angle X-ray scattering, and limited proteolysis...
December 30, 2016: Structure
https://www.readbyqxmd.com/read/28089412/whaddaya-know-a-guide-to-uncertainty-and-subjectivity-in-structural-biology
#17
REVIEW
Joel P Mackay, Michael J Landsberg, Andrew E Whitten, Charles S Bond
The methods of structural biology, while powerful, are technically complex. Although the Protein Data Bank (PDB) provides a repository that allows anyone to download any structure, many users would not appreciate the caveats that should be considered when examining a structure. Here, we describe several key uncertainties associated with the application of X-ray crystallography, NMR spectroscopy, single-particle electron microscopy (SPEM), and small-angle scattering (SAS) to biological macromolecules. The take-home message is that structures are not absolute truths - they are models that fit the experimental data and therefore have uncertainty and subjectivity associated with them...
January 11, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28077635/virion-structure-of-black-queen-cell-virus-a-common-honeybee-pathogen
#18
Radovan Spurny, Antonín Přidal, Lenka Pálková, Hoa Khanh Tran Kiem, Joachim R de Miranda, Pavel Plevka
: Viral diseases are a major threat to honeybee (Apis mellifera) populations world-wide and therefore an important factor in reliable crop pollination and food security. Black queen cell virus (BQCV) is the etiological agent of a fatal disease of honeybee queen larvae and pupae. The virus belongs to the genus Triatovirus from the family Dicistroviridae that is part of the order Picornavirales Here we present a crystal structure of BQCV determined to a resolution of 3.4 Å. The virion is formed by sixty copies of each of the major capsid proteins VP1, VP2, and VP3, however there is no density corresponding to a 75-residue-long minor capsid protein VP4 encoded by the BQCV genome...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28076415/structure-and-recognition-of-a-novel-hiv-1-gp120-gp41-interface-antibody-that-caused-mper-exposure-through-viral-escape
#19
Constantinos Kurt Wibmer, Jason Gorman, Gabriel Ozorowski, Jinal N Bhiman, Daniel J Sheward, Debra H Elliott, Julie Rouelle, Ashley Smira, M Gordon Joyce, Nonkululeko Ndabambi, Aliaksandr Druz, Mangai Asokan, Dennis R Burton, Mark Connors, Salim S Abdool Karim, John R Mascola, James E Robinson, Andrew B Ward, Carolyn Williamson, Peter D Kwong, Lynn Morris, Penny L Moore
A comprehensive understanding of the regions on HIV-1 envelope trimers targeted by broadly neutralizing antibodies may contribute to rational design of an HIV-1 vaccine. We previously identified a participant in the CAPRISA cohort, CAP248, who developed trimer-specific antibodies capable of neutralizing 60% of heterologous viruses at three years post-infection. Here, we report the isolation by B cell culture of monoclonal antibody CAP248-2B, which targets a novel membrane proximal epitope including elements of gp120 and gp41...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28075068/binding-and-processing-of-%C3%AE-lactam-antibiotics-by-the-transpeptidase-ldtmt2-from-mycobacterium-tuberculosis
#20
Eva Maria Steiner, Gunter Schneider, Robert Schnell
β-lactam antibiotics represent a novel direction in the chemotherapy of tuberculosis that brings the peptidoglycan layer of the complex mycobacterial cell wall in focus as therapeutic target. Peptidoglycan stability in Mycobacterium tuberculosis especially during infection relies on the non-conventional peptide cross-links formed by L,D-transpeptidases. These enzymes are known to be inhibited by β-lactams, primarily carbapenems, leading to a stable covalent modification at the enzyme active site. A panel of sixteen β-lactams antibiotics was characterized by inhibition kinetics, mass spectrometry and x-ray crystallography to identify efficient compounds and study their action on the essential transpeptidase LdtMt2 ...
January 11, 2017: FEBS Journal
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