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https://www.readbyqxmd.com/read/28441475/2-2-spirobis-chromene-derivatives-chemistry-and-their-relation-with-the-multistate-system-of-anthocyanins
#1
Artur J Moro, A Jorge Parola, Fernando Pina, Ana-Maria Pana, Valentin Badea, Iulia Pausescu, Sergiu Shova, Liliana Cseh
The chemistry of 2,2'-spirobis[chromene] derivatives is intimately related to the one of anthocyanins and similar compounds. The 2,2'-spirobis[chromene] species plays a central role in the network of chemical reactions connecting two different flavylium-based multistate systems. In the present work, a new asymmetric 2,2'-spirobis[chromene] intermediate possessing a constrained propylenic bridge between carbons 3 and 3' was isolated and its role as a pivot in the anthocyanins-type multistate of chemical reactions was investigated by the conjugation of absorption spectroscopy, stopped-flow, NMR and X-Ray crystallography...
April 25, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28436701/two-cytotoxic-6-7-seco-spiro-lacton-ent-kauranoids-from-isodon-rubescens
#2
Guo-Yong Luo, Rui Deng, Jing-Jie Zhang, Jiang-Hai Ye, Lu-Tai Pan
The present study was performed to investigate the chemical components of the branches and leaves of Isodon rubescens. Two 6,7-seco-spiro-lacton-ent-kauranoids were obtained. Based on the extensive spectroscopic analyses, their structures were elucidated as 6-epi-11-O-acetylangustifolin (1) and 11-O-acetylangustifolin (2), respectively. The structure of 2 was further comfirmed by X-ray crystallography analysis. MTT method was employed to evaluate their cytotoxity against human lung cancer cell lines A549 and leukemia cell lines K562...
April 24, 2017: Journal of Asian Natural Products Research
https://www.readbyqxmd.com/read/28428974/perspective-a-toolbox-for-protein-structure-determination-in-physiological-environment-through-oriented-2d-ordered-site-specific-immobilization
#3
M Altissimo, M Kiskinova, R Mincigrucci, L Vaccari, C Guarnaccia, C Masciovecchio
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based X-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals. They suffer from some limitations that have not been overcome, such as radiation damage, the natural inability to crystallize a number of proteins, and experimental conditions for structure determination that are incompatible with the physiological environment...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28385960/unequivocal-determination-of-complex-molecular-structures-using-anisotropic-nmr-measurements
#4
Yizhou Liu, Josep Saurí, Emily Mevers, Mark W Peczuh, Henk Hiemstra, Jon Clardy, Gary E Martin, R Thomas Williamson
Assignment of complex molecular structures from nuclear magnetic resonance (NMR) data can be prone to interpretational mistakes. Residual dipolar couplings and residual chemical shift anisotropy provide a spatial view of the relative orientations between bonds and chemical shielding tensors, respectively, regardless of separation. Consequently, these data constitute a reliable reporter of global structural validity. Anisotropic NMR parameters can be used to evaluate investigators' structure proposals or structures generated by computer-assisted structure elucidation...
April 7, 2017: Science
https://www.readbyqxmd.com/read/28383118/norovirus-rna-dependent-rna-polymerase-a-computational-study-of-metal-binding-preferences
#5
Md Munan Shaik, Nicholus Bhattacharjee, Mikolaj Feliks, Kenneth K-S Ng, Martin J Field
Norovirus (NV) RNA-dependent RNA polymerase (RdRP) is essential for replicating the genome of the virus, which makes this enzyme a key target for the development of antiviral agents against NV gastroenteritis. In this work, a complex of NV RdRP bound to manganese ions and an RNA primer-template duplex was investigated using X-ray crystallography and hybrid quantum chemical/molecular mechanical simulations. Experimentally, the complex crystallized in a tetragonal crystal form. The nature of the primer/template duplex binding in the resulting structure indicates that the complex is a closed back-tracked state of the enzyme, in which the 3'-end of the primer occupies the position expected for the post-incorporated nucleotide before translocation...
April 6, 2017: Proteins
https://www.readbyqxmd.com/read/28380256/investigation-of-the-mycobacterial-enzyme-hsad-as-a-potential-novel-target-for-anti-tubercular-agents-using-a-fragment-based-drug-design-approach
#6
Ali Ryan, Elena Polycarpou, Nathan A Lack, Dimitrios Evangelopoulos, Christian Sieg, Alice Halman, Sanjib Bhakta, Olga Eleftheriadou, Timothy D McHugh, Sebastian Keany, Edward D Lowe, Romain Ballet, Areej Abuhammad, William R Jacobs, Alessio Ciulli, Edith Sim
BACKGROUND AND PURPOSE: With the emergence of extensively drug-resistant tuberculosis there is a need for new anti-tubercular drugs that work through novel mechanisms of action. The meta cleavage product hydrolase, HsaD, has been demonstrated to be critical to the survival of Mycobacterium tuberculosis in macrophages and is encoded in an operon involved in cholesterol catabolism, which is identical in M. tuberculosis and M. bovis BCG. EXPERIMENTAL APPROACH: We generated a mutant strain of M...
April 5, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28376302/multimodal-recognition-of-diverse-peptides-by-the-c-terminal-sh2-domain-of-phospholipase-c-%C3%AE-1-protein
#7
Marissa A McKercher, Xiaoyang Guan, Zhongping Tan, Deborah S Wuttke
SH2 domains recognize phosphotyrosine (pY)-containing peptide ligands and play key roles in the regulation of receptor tyrosine kinase pathways. Each SH2 domain has individualized specificity, encoded in the amino acids neighboring the pY, for defined targets that convey their distinct functions. The C-terminal SH2 domain (PLCC) of the phospholipase C-γ1 full-length protein (PLCγ1) typically binds peptides containing small and hydrophobic amino acids adjacent to the pY, including a peptide derived from platelet-derived growth factor receptor B (PDGFRB) and an intraprotein recognition site (Y783 of PLCγ1) involved in the regulation of the protein's lipase activity...
April 11, 2017: Biochemistry
https://www.readbyqxmd.com/read/28375690/ultrafast-x-ray-crystallography-and-liquidography
#8
Hosung Ki, Key Young Oang, Jeongho Kim, Hyotcherl Ihee
Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers...
March 27, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28368100/halogen-%C3%AF-interactions-in-the-cytochrome-p450-active-site-structural-insights-into-human-cyp2b6-substrate-selectivity
#9
Manish B Shah, Jingbao Liu, Qinghai Zhang, C David Stout, James R Halpert
Numerous cytochrome P450 (CYP) 2B6 substrates including drugs and environmental chemicals are halogenated. To assess the role of halogen-π bonds in substrate selectivity and orientation in the active site, structures of four CYP2B6 monoterpenoid complexes were solved by X-ray crystallography. Bornyl bromide exhibited dual orientations in the active site with the predominant orientation revealing a bromine-π bond with the Phe108 side chain. Bornane demonstrated two orientations with equal occupancy; in both, the C2 atom that bears the bromine in bornyl bromide was displaced by more than 2...
April 6, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28357862/bio-inspired-herringbone-foldamers-strategy-for-changing-the-structure-of-helices
#10
Abdulselam Adam, Gebhard Haberhauer, Christoph Wölper
Cyclic oligomers of azole peptides were isolated from a multitude of marine organisms and were used for a large number of molecular machines. As shown previously, oligomers derived from achiral imidazole amino acids fold into canonical helices. Here we show that a minor change, the introduction of a methyl group in the δ position, results in a significant change in the secondary structure of the corresponding oligomers. Instead of a canonical helix, a noncanonical herringbone helix is formed. In the latter, the slope along the helix changes its sign at least twice per turn...
April 12, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28355539/opposing-intermolecular-tuning-of-ca-2-affinity-for-calmodulin-by-neurogranin-and-camkii-peptides
#11
Pengzhi Zhang, Swarnendu Tripathi, Hoa Trinh, Margaret S Cheung
We investigated the impact of bound calmodulin (CaM)-target compound structure on the affinity of calcium (Ca(2+)) by integrating coarse-grained models and all-atomistic simulations with nonequilibrium physics. We focused on binding between CaM and two specific targets, Ca(2+)/CaM-dependent protein kinase II (CaMKII) and neurogranin (Ng), as they both regulate CaM-dependent Ca(2+) signaling pathways in neurons. It was shown experimentally that Ca(2+)/CaM (holoCaM) binds to the CaMKII peptide with overwhelmingly higher affinity than Ca(2+)-free CaM (apoCaM); the binding of CaMKII peptide to CaM in return increases the Ca(2+) affinity for CaM...
March 28, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28353338/proton-based-ultrafast-magic-angle-spinning-solid-state-nmr-spectroscopy
#12
Rongchun Zhang, Kamal H Mroue, Ayyalusamy Ramamoorthy
Protons are vastly abundant in a wide range of exciting macromolecules and thus can be a powerful probe to investigate the structure and dynamics at atomic resolution using solid-state NMR (ssNMR) spectroscopy. Unfortunately, the high signal sensitivity, afforded by the high natural-abundance and high gyromagnetic ratio of protons, is greatly compromised by severe line broadening due to the very strong (1)H-(1)H dipolar couplings. As a result, protons are rarely used, in spite of the desperate need for enhancing the sensitivity of ssNMR to study a variety of systems that are not amenable for high resolution investigation using other techniques including X-ray crystallography, cryo-electron microscopy, and solution NMR spectroscopy...
March 29, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28350168/-thalianatriene-and-retigeranin-b-catalyzed-by-sesterterpene-synthases-from-arabidopsis-thaliana
#13
Jie Shao, Qing-Wen Chen, Hua-Jun Lv, Juan He, Zhi-Feng Liu, Yan-Na Lu, Hai-Li Liu, Guo-Dong Wang, Yong Wang
Two GFPPS linked (+)-thalianatriene (1) and (-)-retigeranin B (2) sesterterpene synthase genes were identified from the genome of Arabidopsis thaliana. 1 possesses an unprecedented 11-6-5 tricyclic ring system, while 2 contains a characteristic 5-5-5-6-5 pentacyclic ring system. Their structures were determined by extensive NMR spectroscopy, chemical derivatization, and X-ray crystallography. The variable-temp NMR measurement of 3, a diepoxy-bearing derivative of 1, enables us to completely assign the NMR signals of the two conformers as 3a (67%, UUU) and 3b (33%, UUD)...
April 7, 2017: Organic Letters
https://www.readbyqxmd.com/read/28346776/proton-exchange-in-a-paramagnetic-chemical-exchange-saturation-transfer-agent-from-experimental-studies-and-ab-initio-metadynamics-simulation
#14
Rodolphe Pollet, Célia S Bonnet, Pascal Retailleau, Philippe Durand, Éva Tóth
The proton-exchange process between water and a carbamate has been studied experimentally and theoretically in a lanthanide-based paramagnetic chemical exchange saturation transfer agent endowed with potential multimodality detection capabilities (optical imaging, or T1 MRI for the Gd(III) analogue). In addition to an in-depth structural analysis by a combined approach (using X-ray crystallography, NMR, and molecular dynamics), our ab initio simulation in aqueous solution sheds light on the reaction mechanism for this proton exchange, which involves structural Grotthuss diffusion...
March 27, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28345709/a-study-of-asymmetrical-mixed-valent-mo2-mo2-complexes-in-the-class-iii-regime
#15
Suman Mallick, Tao Cheng, Lu Chen, Miao Meng, Yu Yu Zhang, Chun Y Liu
Three novel asymmetrical dimolybdenum dimers, [Mo2(DAniF)3]2(μ-OOCCOS) (DAniF = N,N'-di(p-anisyl)formamidinate) ([OO-OS]), [Mo2(DAniF)3]2(μ-S2CCO2) ([SS-OO]), and [Mo2(DAniF)3]2(μ-SSCCOS) ([SS-OS]), have been synthesized and characterized by either single-crystal X-ray crystallography or (1)H NMR spectroscopy. The structural asymmetry for these compounds gives rise to a redox asymmetry, which enlarges the potential separation (ΔE1/2) between the two [Mo2] units. The mixed-valance (MV) species [OO-OS](+), [SS-OO](+) and [SS-OS](+), prepared by one-electron chemical oxidation of the neutral precursors, exhibit an intense and symmetrical intervalence charge transfer (IVCT) absorption band in the near-IR region, along with the high energy metal (δ) to ligand (π*) (ML) and ligand (π) to metal (δ) charge transfer (LMCT) absorptions...
March 27, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28338136/investigation-of-the-complexation-of-nat-zr-iv-and-89-zr-iv-by-hydroxypyridinones-for-the-development-of-chelators-for-pet-imaging-applications
#16
F Guérard, M Beyler, Y-S Lee, R Tripier, J-F Gestin, M W Brechbiel
Three hydroxypyridinone (HOPO) positional isomers - 1,2-HOPO (L1H) and its water soluble analogue (L1'H), 3,2-HOPO (L2H) and 3,4-HOPO (L3H) have been investigated for the complexation of Zr(iv). Potentiometric and UV-Vis spectrometric studies show a higher thermodynamic stability for the formation of Zr(L1')4 in comparison with Zr(L2)4 and Zr(L3)4 as well as a higher kinetic inertness in competition studies with EDTA or Fe(3+) at a radiotracer concentration with (89)Zr. Besides the low pKa of L1H or L1'H (pKa = 5...
March 24, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28319851/-31-p-dephased-13-c-detected-redor-for-nmr-crystallography-at-natural-isotopic-abundance
#17
Alexander I Greenwood, Mary C Clay, Chad M Rienstra
Typically, the process of NMR-based structure determination relies on accurately measuring a large number of internuclear distances to serve as restraints for simulated annealing calculations. In solids, the rotational-echo double-resonance (REDOR) experiment is a widely used approach to determine heteronuclear dipolar couplings corresponding to distances usually in the range of 1.5-8Å. A challenge in the interpretation of REDOR data is the degeneracy of symmetric subunits in an oligomer or equivalent molecules in a crystal lattice, which produce REDOR trajectories that depend explicitly on two or more distances instead of one...
May 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28318239/trapping-experiments-on-a-trichlorosilanide-anion-a-key-intermediate-of-halogenosilane-chemistry
#18
Julian Teichmann, Markus Bursch, Benedikt Köstler, Michael Bolte, Hans-Wolfram Lerner, Stefan Grimme, Matthias Wagner
Treatment of Si2Cl6 with [Et4N][BCl4] in CH2Cl2 furnished the known products of a chloride-induced disproportionation reaction of the disilane, such as SiCl4, [Si(SiCl3)3](-), and [Si6Cl12·2Cl](2-). No Si-B-bonded products were detectable. In contrast, the addition of Si2Cl6 to [Et4N][BI3Cl] afforded the Si-B adduct [Et4N][I3SiBI3]. Thus, a quantitative Cl/I exchange at the silicon atom accompanies the trihalogenosilanide formation. [Et4N][I3SiBI3] was also accessible from a mixture of Si2I6, [Et4N]I, and BI3...
March 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28277547/backbone-assignment-of-perdeuterated-proteins-by-solid-state-nmr-using-proton-detection-and-ultrafast-magic-angle-spinning
#19
Pascal Fricke, Veniamin Chevelkov, Maximilian Zinke, Karin Giller, Stefan Becker, Adam Lange
Solid-state NMR (ssNMR) is a technique that allows the study of protein structure and dynamics at atomic detail. In contrast to X-ray crystallography and cryo-electron microscopy, proteins can be studied under physiological conditions-for example, in a lipid bilayer and at room temperature (0-35 °C). However, ssNMR requires considerable amounts (milligram quantities) of isotopically labeled samples. In recent years, (1)H-detection of perdeuterated protein samples has been proposed as a method of alleviating the sensitivity issue...
April 2017: Nature Protocols
https://www.readbyqxmd.com/read/28261207/investigating-substitutions-in-antibody-antigen-complexes-using-molecular-dynamics-a-case-study-with-broad-spectrum-influenza-a-antibodies
#20
William D Lees, Lenka Stejskal, David S Moss, Adrian J Shepherd
In studying the binding of host antibodies to the surface antigens of pathogens, the structural and functional characterization of antibody-antigen complexes by X-ray crystallography and binding assay is important. However, the characterization requires experiments that are typically time consuming and expensive: thus, many antibody-antigen complexes are under-characterized. For vaccine development and disease surveillance, it is often vital to assess the impact of amino acid substitutions on antibody binding...
2017: Frontiers in Immunology
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