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Chemical crystallography

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https://www.readbyqxmd.com/read/29031269/visualising-crystal-packing-interactions-in-solid-state-nmr-concepts-and-applications
#1
Miri Zilka, Simone Sturniolo, Steven P Brown, Jonathan R Yates
In this article, we introduce and apply a methodology, based on density functional theory and the gauge-including projector augmented wave approach, to explore the effects of packing interactions on solid-state nuclear magnetic resonance (NMR) parameters. A visual map derived from a so-termed "magnetic shielding contribution field" can be made of the contributions to the magnetic shielding of a specific site-partitioning the chemical shift to specific interactions. The relation to the established approaches of examining the molecule to crystal change in the chemical shift and the nuclear independent chemical shift is established...
October 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29028171/structure-based-design-of-non-natural-macrocyclic-peptides-that-inhibit-protein-protein-interactions
#2
Dennis M Krüger, Adrian Glas, David Bier, Nicole Pospiech, Kerstin Wallraven, Laura Dietrich, Christian Ottmann, Oliver Koch, Sven Hennig, Tom N Grossmann
Macrocyclic peptides can interfere with challenging biomolecular targets including protein‒protein interactions. Whereas there are various approaches that facilitate the identification of peptide-derived ligands, their evolution into higher affinity binders remains a major hurdle. We report a virtual screen based on molecular docking that allows the affinity maturation of macrocyclic peptides taking non-natural amino acids into consideration. These macrocycles bear large and flexible substituents which usually complicate the use of docking approaches...
October 13, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29021733/berkeley-screen-a-set-of-96-solutions-for-general-macromolecular-crystallization
#3
Jose H Pereira, Ryan P McAndrew, Giovani P Tomaleri, Paul D Adams
Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing...
October 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28989600/chemical-tuning-of-dynamic-cation-off-centering-in-the-cubic-phases-of-hybrid-tin-and-lead-halide-perovskites
#4
Geneva Laurita, Douglas H Fabini, Constantinos C Stoumpos, Mercouri G Kanatzidis, Ram Seshadri
Hybrid halide perovskites combine ease of preparation and relatively abundant constituent elements with fascinating photophysical properties. Descriptions of the chemical and structural drivers of the remarkable properties have often focused on the potential role of the dynamic order/disorder of the molecular A-site cations. We reveal here a key aspect of the inorganic framework that potentially impacts the electronic, thermal, and dielectric properties. The temperature evolution of the X-ray pair distribution functions of hybrid perovskites ABX3 [A(+) = CH3NH3 (MA) or CH(NH2)2 (FA); B(2+) = Sn or Pb; X(-) = Br, or I] in their cubic phases above 300 K reveals temperature-activated displacement (off-centering) of the divalent group 14 cations from their nominal, centered sites...
August 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28986384/mass-spectrometry-for-fragment-screening
#5
REVIEW
Daniel Shiu-Hin Chan, Andrew J Whitehouse, Anthony G Coyne, Chris Abell
Fragment-based approaches in chemical biology and drug discovery have been widely adopted worldwide in both academia and industry. Fragment hits tend to interact weakly with their targets, necessitating the use of sensitive biophysical techniques to detect their binding. Common fragment screening techniques include differential scanning fluorimetry (DSF) and ligand-observed NMR. Validation and characterization of hits is usually performed using a combination of protein-observed NMR, isothermal titration calorimetry (ITC) and X-ray crystallography...
October 6, 2017: Essays in Biochemistry
https://www.readbyqxmd.com/read/28983993/synthesis-and-demonstration-of-the-biological-relevance-of-sp-3-rich-scaffolds-distantly-related-to-natural-product-frameworks
#6
Daniel J Foley, Philip G E Craven, Patrick M Collins, Richard G Doveston, Anthony Aimon, Romain Talon, Ian Churcher, Frank von Delft, Stephen P Marsden, Adam Nelson
The productive exploration of chemical space is an enduring challenge in chemical biology and medicinal chemistry. Natural products are biologically relevant, and their frameworks have facilitated chemical tool and drug discovery. A "top-down" synthetic approach is described that enabled a range of complex bridged intermediates to be converted with high step efficiency into 26 diverse sp(3) -rich scaffolds. The scaffolds have local natural product-like features, but are only distantly related to specific natural product frameworks...
October 6, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28973862/de-novo-design-of-covalently-constrained-mesosize-protein-scaffolds-with-unique-tertiary-structures
#7
Bobo Dang, Haifan Wu, Vikram Khipple Mulligan, Marco Mravic, Yibing Wu, Thomas Lemmin, Alexander Ford, Daniel-Adriano Silva, David Baker, William F DeGrado
The folding of natural proteins typically relies on hydrophobic packing, metal binding, or disulfide bond formation in the protein core. Alternatively, a 3D structure can be defined by incorporating a multivalent cross-linking agent, and this approach has been successfully developed for the selection of bicyclic peptides from large random-sequence libraries. By contrast, there is no general method for the de novo computational design of multicross-linked proteins with predictable and well-defined folds, including ones not found in nature...
September 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28972618/a-carbon-free-inorganic-metal-complex-consisting-of-an-all-nitrogen-pentazole-anion-a-zn-ii-cation-and-h2o
#8
Yuangang Xu, Pengcheng Wang, Qiuhan Lin, Ming Lu
A carbon-free inorganic-metal complex [Zn(H2O)4(N5)2]·4H2O was synthesized by the ion metathesis of [Na(H2O)(N5)]·2H2O solution with Zn(NO3)2·6H2O. The complex was well characterized by IR and Raman spectroscopy, elemental analysis (EA), powder X-ray diffraction (PXRD), and differential scanning calorimetry (DSC). The structure of the complex was confirmed by single-crystal X-ray crystallography and a Zn(ii) ion is coordinated in a quadrilateral bipyramid environment in which the axial position is formed by two nitrogen atoms (N1) from two pentazolate rings (cyclo-N5(-)) and the equatorial plane is formed by four oxygen atoms (O1) from four coordinated water molecules...
October 3, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28967262/chemical-validation-of-methionyl-trna-synthetase-as-a-druggable-target-in-leishmania-donovani
#9
Leah S Torrie, Stephen Brand, David A Robinson, Eun Jung Ko, Laste Stojanovski, Frederick R C Simeons, Susan Wyllie, John Thomas, Lucy Ellis, Maria Osuna-Cabello, Ola Epemolu, Andrea Nühs, Jennifer Riley, Lorna MacLean, Sujatha Manthri, Kevin D Read, Ian H Gilbert, Alan H Fairlamb, Manu De Rycker
Methionyl-tRNA synthetase (MetRS) has been chemically validated as a drug target in the kinetoplastid parasite Trypanosoma brucei. In the present study, we investigate the validity of this target in the related trypanosomatid Leishmania donovani. Following development of a robust high-throughput compatible biochemical assay, a compound screen identified DDD806905 as a highly potent inhibitor of LdMetRS (Ki of 18 nM). Crystallography revealed this compound binds to the methionine pocket of MetRS with enzymatic studies confirming DDD806905 displays competitive inhibition with respect to methionine and mixed inhibition with respect to ATP binding...
October 13, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/28956438/regioselective-synthesis-of-3-naphthylenes-and-tuning-of-their-antiaromaticity
#10
Zexin Jin, Yew Chin Teo, Simon J Teat, Yan Xia
Polycyclic conjugated hydrocarbons containing four-membered cyclobutadienoids (CBDs) are of great fundamental and technical interest due to the antiaromaticity brought by CBD circuits. However, their synthesis has been challenging, hampering the exploration and understanding of such systems. We report efficient synthesis of a series of unprecedented [3]naphthylene regioisomers in high yields, where three naphthalenoids are fused through two CBDs in linear, angular, and bent regioconnectivity. Their synthesis was enabled by exclusively regioselective catalytic arene-norbornene annulation (CANAL) between dibromonaphthalenes and benzooxanorbornadienes, followed by aromatization...
October 9, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28950050/the-impact-of-azidohomoalanine-incorporation-on-protein-structure-and-ligand-binding
#11
Florian Lehner, Denis Kudlinzki, Christian Richter, Henrike Müller-Werkmeister, Katharina Eberl, Jens Bredenbeck, Harald Schwalbe, Robert Silvers
The impact of the incorporation of a non-natural amino acid (NNAA) onto protein structure, dynamics, and ligand binding has not been studied rigorously so far. NNAAs are regularly used to modify proteins post-translationally in vivo and in vitro using click-chemistry. Here, we present a structural characterization of the impact of the incorporation of azidohomoalanine (AZH) into the model protein domain PDZ3 using NMR spectroscopy and X-ray crystallography. The structure and dynamics of the apo state of the AZH-modified PDZ3 remains mostly unperturbed...
September 26, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28934505/combining-asymmetric-13c-labeling-and-isotopic-filter-edit-noesy-a-novel-strategy-for-rapid-and-logical-rna-resonance-assignment
#12
Regan M LeBlanc, Andrew P Longhini, Stuart F J Le Grice, Bruce A Johnson, Theodore K Dayie
Although ∼98% of the human genomic output is transcribed as non-protein coding RNA, <2% of the protein data bank structures comprise RNA. This huge structural disparity stems from combined difficulties of crystallizing RNA for X-ray crystallography along with extensive chemical shift overlap and broadened linewidths associated with NMR of RNA. While half of the deposited RNA structures in the PDB were solved by NMR methods, the usefulness of NMR is still limited by the high cost of sample preparation and challenges of resonance assignment...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28915017/cationic-and-anionic-disorder-in-cztsse-kesterite-compounds-a-chemical-crystallography-study
#13
Pierre Bais, Maria Teresa Caldes, Michaël Paris, Catherine Guillot-Deudon, Pierre Fertey, Bernadette Domengès, Alain Lafond
The cationic and anionic disorder in the Cu2ZnSnSe4-Cu2ZnSnS4 (CZTSe-CZTS) system has been investigated through a chemical crystallography approach including X-ray diffraction (in conventional and resonant setup), (119)Sn and (77)Se NMR spectroscopy, and high-resolution transmission electron microscopy (HRTEM) techniques. Single-crystal XRD analysis demonstrates that the studied compounds behave as a solid solution with the kesterite crystal structure in the whole S/(S + Se) composition range. As previously reported for pure sulfide and pure selenide compounds, the (119)Sn NMR spectroscopy study gives clear evidence that the level of Cu/Zn disorder in mixed S/Se compounds depends on the thermal history of the samples (slow cooled or quenched)...
October 2, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28894951/structural-and-functional-characterization-of-mercuric-reductase-from-lysinibacillus-sphaericus-strain-g1
#14
Amit Bafana, Farha Khan, Kaza Suguna
In response to the widespread presence of inorganic Hg in the environment, bacteria have evolved resistance systems with mercuric reductase (MerA) as the key enzyme. MerA enzymes have still not been well characterized from gram positive bacteria. Current study reports physico-chemical, kinetic and structural characterization of MerA from a multiple heavy metal resistant strain of Lysinibacillus sphaericus, and discusses its implications in bioremediation application. The enzyme was homodimeric with subunit molecular weight of about 60 kDa...
September 11, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28892510/structure-based-design-synthesis-and-crystallization-of-2-arylquinazolines-as-lipid-pocket-ligands-of-p38%C3%AE-mapk
#15
Mike Bührmann, Bianca M Wiedemann, Matthias P Müller, Julia Hardick, Maria Ecke, Daniel Rauh
In protein kinase research, identifying and addressing small molecule binding sites other than the highly conserved ATP-pocket are of intense interest because this line of investigation extends our understanding of kinase function beyond the catalytic phosphotransfer. Such alternative binding sites may be involved in altering the activation state through subtle conformational changes, control cellular enzyme localization, or in mediating and disrupting protein-protein interactions. Small organic molecules that target these less conserved regions might serve as tools for chemical biology research and to probe alternative strategies in targeting protein kinases in disease settings...
2017: PloS One
https://www.readbyqxmd.com/read/28878872/quantum-crystallography
#16
REVIEW
Simon Grabowsky, Alessandro Genoni, Hans-Beat Bürgi
Approximate wavefunctions can be improved by constraining them to reproduce observations derived from diffraction and scattering experiments. Conversely, charge density models, incorporating electron-density distributions, atomic positions and atomic motion, can be improved by supplementing diffraction experiments with quantum chemically calculated, tailor-made electron densities (form factors). In both cases quantum chemistry and diffraction/scattering experiments are combined into a single, integrated tool...
June 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28875027/viscous-hydrophilic-injection-matrices-for-serial-crystallography
#17
Gabriela Kovácsová, Marie Luise Grünbein, Marco Kloos, Thomas R M Barends, Ramona Schlesinger, Joachim Heberle, Wolfgang Kabsch, Robert L Shoeman, R Bruce Doak, Ilme Schlichting
Serial (femtosecond) crystallography at synchrotron and X-ray free-electron laser (XFEL) sources distributes the absorbed radiation dose over all crystals used for data collection and therefore allows measurement of radiation damage prone systems, including the use of microcrystals for room-temperature measurements. Serial crystallography relies on fast and efficient exchange of crystals upon X-ray exposure, which can be achieved using a variety of methods, including various injection techniques. The latter vary significantly in their flow rates - gas dynamic virtual nozzle based injectors provide very thin fast-flowing jets, whereas high-viscosity extrusion injectors produce much thicker streams with flow rates two to three orders of magnitude lower...
July 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28867801/an-unusual-dimeric-inhibitor-of-acetylcholinesterase-cooperative-binding-of-crystal-violet
#18
Anders Allgardsson, C David Andersson, Christine Akfur, Franz Worek, Anna Linusson, Fredrik Ekström
Acetylcholinesterase (AChE) is an essential enzyme that terminates cholinergic transmission by a rapid hydrolysis of the neurotransmitter acetylcholine. AChE is an important target for treatment of various cholinergic deficiencies, including Alzheimer's disease and myasthenia gravis. In a previous high throughput screening campaign, we identified the dye crystal violet (CV) as an inhibitor of AChE. Herein, we show that CV displays a significant cooperativity for binding to AChE, and the molecular basis for this observation has been investigated by X-ray crystallography...
August 30, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28866776/-1-h-15-n-13-c-backbone-resonance-assignments-of-human-phosphoglycerate-kinase-in-a-transition-state-analogue-complex-with-adp-3-phosphoglycerate-and-magnesium-trifluoride
#19
Zhalgas Serimbetov, Nicola J Baxter, Matthew J Cliff, Jonathan P Waltho
Human phosphoglycerate kinase (PGK) is an energy generating glycolytic enzyme that catalyses the transfer of a phosphoryl group from 1,3-bisphosphoglycerate (BPG) to ADP producing 3-phosphoglycerate (3PG) and ATP. PGK is composed of two α/β Rossmann-fold domains linked by a central α-helix and the active site is located in the cleft formed between the N-domain which binds BPG or 3PG, and the C-domain which binds the nucleotides ADP or ATP. Domain closure is required to bring the two substrates into close proximity for phosphoryl transfer to occur, however previous structural studies involving a range of native substrates and substrate analogues only yielded open or partly closed PGK complexes...
September 2, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28862425/btn3a1-discriminates-%C3%AE-%C3%AE-t-cell-phosphoantigens-from-nonantigenic-small-molecules-via-a-conformational-sensor-in-its-b30-2-domain
#20
Mahboob Salim, Timothy J Knowles, Alfie T Baker, Martin S Davey, Mark Jeeves, Pooja Sridhar, John Wilkie, Carrie R Willcox, Hachemi Kadri, Taher E Taher, Pierre Vantourout, Adrian Hayday, Youcef Mehellou, Fiyaz Mohammed, Benjamin E Willcox
Human Vγ9/Vδ2 T-cells detect tumor cells and microbial infections by recognizing small phosphorylated prenyl metabolites termed phosphoantigens (P-Ag). The type-1 transmembrane protein Butyrophilin 3A1 (BTN3A1) is critical to the P-Ag-mediated activation of Vγ9/Vδ2 T-cells; however, the molecular mechanisms involved in BTN3A1-mediated metabolite sensing are unclear, including how P-Ag's are discriminated from nonantigenic small molecules. Here, we utilized NMR and X-ray crystallography to probe P-Ag sensing by BTN3A1...
September 14, 2017: ACS Chemical Biology
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