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https://www.readbyqxmd.com/read/29778646/the-fine-art-of-integral-membrane-protein-crystallisation
#1
REVIEW
James Birch, Danny Axford, James Foadi, Arne Meyer, Annette Eckardt, Yvonne Thielmann, Isabel Moraes
Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral membrane proteins has proven to be far from trivial, hence they are underrepresented in the protein data bank. Low expression levels, insolubility and instability are just a few of the many hurdles one faces when studying these proteins...
May 17, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29777317/using-smiles-strings-for-the-description-of-chemical-connectivity-in-the-crystallography-open-database
#2
Miguel Quirós, Saulius Gražulis, Saulė Girdzijauskaitė, Andrius Merkys, Antanas Vaitkus
Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for predicting chemical properties from molecular structure. In this article, the ongoing work to describe the chemical connectivity of entries contained in the Crystallography Open Database (COD) in SMILES format is reported. This collection of SMILES is publicly available for chemical (substructure) search or for any other purpose on an open-access basis, as is the COD itself. The conventions that have been followed for the representation of compounds that do not fit into the valence bond theory are outlined for the most frequently found cases...
May 18, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29776116/depletion-zones-and-crystallography-on-pinched-spheres
#3
Jingyuan Chen, Xiangjun Xing, Zhenwei Yao
Understanding the interplay between ordered structures and substrate curvature is an interesting problem with versatile applications, including functionalization of charged supramolecular surfaces and modern microfluidic technologies. In this work, we investigate the two-dimensional packing structures of charged particles confined on a pinched sphere. By continuously pinching the sphere, we observe cleavage of elongated scars into pleats, proliferation of disclinations, and subsequently, emergence of a depletion zone at the negatively curved waist that is completely void of particles...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29775936/from-hit-to-lead-structure-based-discovery-of-naphthalene-1-sulfonamide-derivatives-as-potent-and-selective-inhibitors-of-fatty-acid-binding-protein-4
#4
Ding-Ding Gao, Hui-Xia Dou, Hai-Xia Su, Ming-Ming Zhang, Ting Wang, Qiu-Feng Liu, Hai-Yan Cai, Hai-Peng Ding, Zhuo Yang, Wei-Liang Zhu, Ye-Chun Xu, He-Yao Wang, Ying-Xia Li
Fatty acid binding protein 4 (FABP4) plays a critical role in metabolism and inflammatory processes and therefore is a potential therapeutic target for immunometabolic diseases such as diabetes and atherosclerosis. Herein, we reported the identification of naphthalene-1-sulfonamide derivatives as novel, potent and selective FABP4 inhibitors by applying a structure-based design strategy. The binding affinities of compounds 16dk, 16do and 16du to FABP4, at the molecular level, are equivalent to or even better than that of BMS309403...
May 9, 2018: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29775229/synthesis-of-an-all-ferric-cuboidal-cluster-feiii%C3%A2-s%C3%A2-sar-%C3%A2
#5
Golam Moula, Tsuyoshi Matsumoto, Matthias E Miehlich, Karsten Meyer, Kazuyuki Tatsumi
An unprecedented, super oxidized all-ferric iron-sulfur cubanoid cluster with all terminal thiolates, Fe₄S₄(STbt)₄ (3) [Tbt = 2,4,6-tris{bis(trimethylsilyl)methyl}phenyl], has been isolated from the reaction of the bis-thiolate complex Fe(STbt)₂ (2) with elemental sulfur. This cluster 3 has been characterized by X-ray crystallography, zero-field ⁵⁷Fe Mössbauer spectroscopy, cyclic voltammetry, and other relevant physico-chemical methods. Based on all data, the electronic ground state of the cluster has been assigned to be Stot = 0...
May 18, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29774643/a-nona-nuclear-heterometallic-pd3pt6-donut-shaped-cage-molecular-recognition-and-photocatalysis
#6
Dan Preston, Keith C Gordon, Joshua J Sutton, James D Crowley
We report a simple, low symmetry 2-(1-(pyridine-4-methyl)-1H-1,2,3-triazol-4-yl)pyridine ligand which has both monodentate and bidentate binding sites. With platinumII and/or palladiumII ions, two examples of a new nona-nuclear metallo-assembly have been accessed. These complexes have been characterized by nuclear magnetic resonance (NMR) spectroscopies, electrospray mass spectrometry (ESI-MS), and in key cases, X-ray crystallography. The cages possess three clefts comprised of planar cationic panels. This structural feature enables the binding of planar aromatic guests such as anthracene...
May 18, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29773785/revealing-isoelectronic-size-conversion-dynamics-of-metal-nanoclusters-by-a-noncrystallization-approach
#7
Qiaofeng Yao, Victor Fung, Cheng Sun, Sida Huang, Tiankai Chen, De-En Jiang, Jim Yang Lee, Jianping Xie
Atom-by-atom engineering of nanomaterials requires atomic-level knowledge of the size evolution mechanism of nanoparticles, which remains one of the greatest mysteries in nanochemistry. Here we reveal atomic-level dynamics of size evolution reaction of molecular-like nanoparticles, i.e., nanoclusters (NCs) by delicate mass spectrometry (MS) analyses. The model size-conversion reaction is [Au23 (SR)16 ]- → [Au25 (SR)18 ]- (SR = thiolate ligand). We demonstrate that such isoelectronic (valence electron count is 8 in both NCs) size-conversion occurs by a surface-motif-exchange-induced symmetry-breaking core structure transformation mechanism, surfacing as a definitive reaction of [Au23 (SR)16 ]-  + 2 [Au2 (SR)3 ]- → [Au25 (SR)18 ]-  + 2 [Au(SR)2 ]- ...
May 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29772085/ligand-induced-conformational-changes-in-hsp90-monitored-time-resolved-and-label-free-towards-a-conformational-activity-screening-for-drug-discovery
#8
Jörn Güldenhaupt, Marta Amaral, Carsten Kötting, Djordje Musil, Jonas Schartner, Matthias Frech, Klaus Gerwert
A detailed investigation of protein-ligand interactions is crucial during the early drug discovery process. However, most available techniques lack either structural or temporal resolution. In contrast, ATR-FTIR spectroscopy can monitor protein-ligand interactions label-free with high spatiotemporal resolution. Here we immobilize as example the heat shock protein HSP90 on an ATR-crystal. This protein is an important molecular target for drugs against several diseases including cancer. With our novel approach we investigated a ligand induced secondary structural change...
May 17, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29771936/assigning-crystallographic-electron-densities-with-free-energy-calculations-the-case-of-the-fluoride-channel-fluc
#9
Igor Ariz-Extreme, Jochen S Hub
Approximately 90% of the structures in the Protein Data Bank (PDB) were obtained by X-ray crystallography or electron microscopy. Whereas the overall quality of structure is considered high, thanks to a wide range of tools for structure validation, uncertainties may arise from density maps of small molecules, such as organic ligands, ions or water, which are non-covalently bound to the biomolecules. Even with some experience and chemical intuition, the assignment of such disconnected electron densities is often far from obvious...
2018: PloS One
https://www.readbyqxmd.com/read/29771342/recent-progress-in-structural-biology-lessons-from-our-research-history
#10
Ryo Nitta, Tsuyoshi Imasaki, Eriko Nitta
The recent 'resolution revolution' in structural analyses of cryo-electron microscopy (cryo-EM) has drastically changed the research strategy for structural biology. In addition to X-ray crystallography and nuclear magnetic resonance spectroscopy, cryo-EM has achieved the structural analysis of biological molecules at near-atomic resolution, resulting in the Nobel Prize in Chemistry 2017. The effect of this revolution has spread within the biology and medical science fields affecting everything from basic research to pharmaceutical development by visualizing atomic structure...
May 16, 2018: Microscopy
https://www.readbyqxmd.com/read/29769723/structure-of-a-volume-regulated-anion-channel-of-the-lrrc8-family
#11
Dawid Deneka, Marta Sawicka, Andy K M Lam, Cristina Paulino, Raimund Dutzler
Volume-regulated anion channels are activated in response to hypotonic stress. These channels are composed of closely related paralogues of the leucine-rich repeat-containing protein 8 (LRRC8) family that co-assemble to form hexameric complexes. Here, using cryo-electron microscopy and X-ray crystallography, we determine the structure of a homomeric channel of the obligatory subunit LRRC8A. This protein conducts ions and has properties in common with endogenous heteromeric channels. Its modular structure consists of a transmembrane pore domain followed by a cytoplasmic leucine-rich repeat domain...
May 16, 2018: Nature
https://www.readbyqxmd.com/read/29769649/organoruthenium-ii-complexes-ameliorates-oxidative-stress-and-impedes-the-age-associated-deterioration-in-caenorhabditis-elegans-through-jnk-1-daf-16-signalling
#12
G Devagi, A Mohankumar, G Shanmugam, S Nivitha, F Dallemer, P Kalaivani, P Sundararaj, R Prabhakaran
New ruthenium(II) complexes were synthesised and characterized by various spectro analytical techniques. The structure of the complexes 3 and 4 has been confirmed by X-ray crystallography. The complexes were subjected to study their anti-oxidant profile and were exhibited significantly greater in vitro DPPH radical scavenging activity than vitamin C. We found that complexes 1-4 confered tolerance to oxidative stress and extend the mean lifespan of mev-1 mutant worms and wild-type Caenorhabditis elegans. Further, mechanistic study and reporter gene expression analysis revealed that Ru(ƞ6 -p-cymene) complexes maintained the intracellular redox status and offers stress resistance through activating JNK-1/DAF-16 signaling axis and possibly by other antioxidant response pathway...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769321/lectin-mediated-binding-and-sialoglycans-of-porcine-surfactant-protein-d-synergistically-neutralize-influenza-a-virus
#13
Martin van Eijk, Michael J Rynkiewicz, Kshitij Khatri, Nancy Leymarie, Joseph Zaia, Mitchell R White, Kevan L Hartshorn, Tanya R Cafarella, Irma Van Die, Martin Hessing, Barbara A Seaton, Henk P Haagsman
Innate immunity is critical in the early containment of influenza A virus (IAV) infection, and surfactant protein D (SP-D) plays a crucial role in the pulmonary defense against IAV. In pigs, which are important intermediate hosts during the generation of pandemic IAVs, SP-D uses its unique carbohydrate recognition domain (CRD) to interact with IAV. An N-linked CRD-glycosylation provides interactions with the sialic acid binding site of IAV, and a tripeptide loop at the lectin binding site facilitates enhanced interactions with IAV glycans...
May 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29767971/structural-characterization-and-photochemical-properties-of-mono-and-bimetallic-cu-mabiq-complexes
#14
H Sophia Stark, Philipp J Altmann, Stephen Sproules, Corinna R Hess
We present a series of monometallic ([Cu(Mabiq)OTf] (1) and [Cu(Mabiq)] (2)) and bimetallic copper-Mabiq complexes ([Cu2 (Mabiq)(PPh3 )2 (OTf)2 ] (3) and [Cu2 (Mabiq)(PPh3 )2 ]PF6 (4)). The latter compounds contain an additional CuI center that binds in a tetrahedral fashion to the external bipyrimidine nitrogens of the macrocyclic ligand. Compounds 3 and 4 represent the first examples of bimetallic transition metal Mabiq complexes, stable both in solution and in the solid state. The structural and electronic properties of compounds 1-4 were analyzed by means of X-ray crystallography, cyclic voltammetry, and spectroscopic methods...
May 16, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29766578/self-assembly-of-fluorescent-dehydroberberine-enhances-mitochondria-dependent-antitumor-efficacy
#15
Ruibing An, Zhanni Gu, Haifeng Sun, Yuxuan Hu, Runqi Yan, Deju Ye, Hong Liu
Selective imaging and inducing mitochondrial dysfunction in tumor cells using mitochondria-targeting probes has become as a promising approach for cancer diagnosis and therapy. Here, we report the design of a fluorescent berberine analog, dehydroberberine (DH-BBR), as a new mitochondria-targeting probe capable of self-assembling into monodisperse organic nanoparticles (DTNPs) upon integration with a lipophilic counter anion, allowing for enhanced fluorescence imaging and treatment of tumors in living mice. X-ray crystallography revealed that the self-assembly process was attributed to a synergy of different molecular interactions, including π-π stacking, O···π interaction and electrostatic interaction between DH-BBR and counter anions...
May 15, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29765609/electron-crystallography-with-the-eiger-detector
#16
Gemma Tinti, Erik Fröjdh, Eric van Genderen, Tim Gruene, Bernd Schmitt, D A Matthijs de Winter, Bert M Weckhuysen, Jan Pieter Abrahams
Electron crystallography is a discipline that currently attracts much attention as method for inorganic, organic and macromolecular structure solution. EIGER, a direct-detection hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland, has been tested for electron diffraction in a transmission electron microscope. EIGER features a pixel pitch of 75 × 75 µm2 , frame rates up to 23 kHz and a dead time between frames as low as 3 µs. Cluster size and modulation transfer functions of the detector at 100, 200 and 300 keV electron energies are reported and the data quality is demonstrated by structure determination of a SAPO-34 zeotype from electron diffraction data...
March 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29765598/crystallography-and-the-development-of-therapeutic-medicines
#17
EDITORIAL
Edward N Baker
Advances in crystallography and cryo-EM promise to further enhance the proud role crystallography has played in the development of new medicines.
March 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29765041/nanographenes-as-electron-deficient-cores-of-donor-acceptor-systems
#18
Yu-Min Liu, Hao Hou, Yan-Zhen Zhou, Xin-Jing Zhao, Chun Tang, Yuan-Zhi Tan, Klaus Müllen
Conjugation of nanographenes (NGs) with electro-active molecules can establish donor-acceptor π-systems in which the former generally serve as the electron-donating moieties due to their electronic-rich nature. In contrast, here we report a series of reversed donor-acceptor structures are obtained by C-N coupling of electron-deficient perchlorinated NGs with electron-rich anilines. Selective amination at the vertexes of the NGs is unambiguously shown through X-ray crystallography. By varying the donating ability of the anilino groups, the optical and assembly properties of donor-acceptor NGs can be finely modulated...
May 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29764757/synthesis-and-profiling-of-a-3-aminopyridin-2-one-based-kinase-targeted-fragment-library-identification-of-3-amino-5-pyridin-4-yl-pyridin-2-1h-one-scaffold-for-monopolar-spindle-1-mps1-and-aurora-kinases-inhibition
#19
Daren Fearon, Isaac M Westwood, Rob L M van Montfort, Richard Bayliss, Keith Jones, Vassilios Bavetsias
Screening a 3-aminopyridin-2-one based fragment library against a 26-kinase panel representative of the human kinome identified 3-amino-5-(1-methyl-1H-pyrazol-4-yl)pyridin-2(1H)-one (2) and 3-amino-5-(pyridin-4-yl)pyridin-2(1H)-one (3) as ligand efficient inhibitors of the mitotic kinase Monopolar Spindle 1 (MPS1) and the Aurora kinase family. These kinases are well recognised as attractive targets for therapeutic intervention for treating cancer. Elucidation of the binding mode of these fragments and their analogues has been carried out by X-ray crystallography...
April 17, 2018: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/29763607/biomedical-applications-of-lumazine-synthase
#20
Yangjie Wei, Prashant Kumar, Newton Wahome, Nicholas J Mantis, C Russell Middaugh
Lumazine synthase (LS) is a family of enzyme involved in the penultimate step in the biosynthesis of riboflavin. Its enzymatic mechanism has been well defined and many LS structures have been solved using x-ray crystallography or cryo-electron microscopy. LS is composed of homo-oligomers, which vary in size and subunit number, including pentamers, decamers, and icosahedral sixty-mers, depending on its species of origin. Research on LS has expanded beyond the initial focus on its enzymatic function to properties related to its oligomeric structure and exceptional conformational stability...
May 12, 2018: Journal of Pharmaceutical Sciences
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