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https://www.readbyqxmd.com/read/29166012/the-use-of-fluoroproline-in-muc1-antigen-enables-efficient-detection-of-antibodies-in-patients-with-prostate-cancer
#1
Víctor Jesús Somovilla, Iris Alicia Bermejo, Inês S Albuquerque, Nuria Martínez-Sáez, Jorge Castro-López, Fayna Garcia Martin, Ismael Compañón, Hiroshi Hinou, Shin-Ichiro Nishimura, Jesús Jiménez-Barbero, Juan Luis Asensio, Alberto Avenoza, Jesús H Busto, Ramon Hurtado-Guerrero, Jesús M Peregrina, Gonçalo J L Bernardes, Francisco Corzana
A structure-based design of a new generation tumor-associated glycopeptides with improved affinity against two anti-MUC1 antibodies is described. These unique antigens feature a fluorinated proline residue, such as a (4S)-4-fluoro-L-proline or 4,4-difluoroproline, at the most immunogenic domain. Binding assays using bio-layer interferometry reveal 3-fold to 10-fold affinity improvement with respect to the natural (glyco)peptides. According to X-ray crystallography and MD simulations, the fluorinated residues stabilize the antigen-antibody complex by enhancing key CH/π interactions...
November 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29165665/novel-structural-features-drive-dna-binding-properties-of-cmr-a-crp-family-protein-in-tb-complex-mycobacteria
#2
Sridevi Ranganathan, Jonah Cheung, Michael Cassidy, Christopher Ginter, Janice D Pata, Kathleen A McDonough
Mycobacterium tuberculosis (Mtb) encodes two CRP/FNR family transcription factors (TF) that contribute to virulence, Cmr (Rv1675c) and CRPMt (Rv3676). Prior studies identified distinct chromosomal binding profiles for each TF despite their recognizing overlapping DNA motifs. The present study shows that Cmr binding specificity is determined by discriminator nucleotides at motif positions 4 and 13. X-ray crystallography and targeted mutational analyses identified an arginine-rich loop that expands Cmr's DNA interactions beyond the classical helix-turn-helix contacts common to all CRP/FNR family members and facilitates binding to imperfect DNA sequences...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165643/expanding-the-repertoire-of-dna-shape-features-for-genome-scale-studies-of-transcription-factor-binding
#3
Jinsen Li, Jared M Sagendorf, Tsu-Pei Chiu, Marco Pasi, Alberto Perez, Remo Rohs
Uncovering the mechanisms that affect the binding specificity of transcription factors (TFs) is critical for understanding the principles of gene regulation. Although sequence-based models have been used successfully to predict TF binding specificities, we found that including DNA shape information in these models improved their accuracy and interpretability. Previously, we developed a method for modeling DNA binding specificities based on DNA shape features extracted from Monte Carlo (MC) simulations. Prediction accuracies of our models, however, have not yet been compared to accuracies of models incorporating DNA shape information extracted from X-ray crystallography (XRC) data or Molecular Dynamics (MD) simulations...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165461/synthesis-structures-and-magnetic-properties-of-two-chiral-mixed-valence-iron-ii-iii-coordination-networks
#4
Yun-Shan Xue, Xu Tan, Mengjie Zhou, Hua Mei, Yan Xu
Two rare chiral mixed-valence iron(ii,iii) coordination networks d-and l-{[Fe(II)FeO(BTC)3(DEF)3]·0.5H2O}n (d-1 and l-1) (H3BTC = 1,3,5-benzenetricarboxylic acid; DEF = N,N-diethylformamide) have been synthesized without any chiral auxiliary under the solvothermal conditions and structurally characterized by single crystal X-ray crystallography. Structural analysis indicates that these two polymers d-1 and l-1 are enantiomers. The only difference between d-1 and l-1 is that the framework of compound l-1 consists of left-handed double helical chains, while d-1 consists of right-handed double helical chains...
November 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29163924/synthesis-of-a-terminal-ce-iv-oxo-complex-by-photolysis-of-a-ce-iii-nitrate-complex
#5
Mikiyas K Assefa, Guang Wu, Trevor W Hayton
Reaction of [Ce(NR2)3] (R = SiMe3) with LiNO3 in THF, in the presence of 2,2,2-cryptand, results in the formation of the Ce(iii) "ate" complex, [Li(2,2,2-cryptand)][Ce(κ(2)-O2NO)(NR2)3] (1) in 38% yield. Photolysis of 1 at 380 nm affords [Li(2,2,2-cryptand)][Ce(O)(NR2)3] (2), in 33% isolated yield after reaction work-up. Complex 2 is the first reported example of a Ce(iv) oxo complex where the oxo ligand is not supported by hydrogen bonding or alkali metal coordination. Also formed during photolysis are [Li(2,2,2-cryptand)]2[(μ3-O){Ce(μ-O)(NR2)2}3] (3) and [Li(2,2,2-cryptand)][Ce(OSiMe3)(NR2)3] (4)...
November 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29163894/comparisons-of-lanthanide-actinide-2-ions-in-a-tris-aryloxide-arene-coordination-environment
#6
Megan E Fieser, Chad T Palumbo, Henry S La Pierre, Dominik P Halter, Vamsee K Voora, Joseph W Ziller, Filipp Furche, Karsten Meyer, William J Evans
A new series of Ln(3+) and Ln(2+) complexes has been synthesized using the tris(aryloxide)arene ligand system, (((Ad,Me)ArO)3mes)(3-), recently used to isolate a complex of U(2+). The triphenol precursor, ((Ad,Me)ArOH)3mes, reacts with the Ln(3+) amides, Ln(NR2)3 (R = SiMe3), to form a series of [(((Ad,Me)ArO)3mes)Ln] complexes, 1-Ln. Crystallographic characterization was achieved for Ln = Nd, Gd, Dy, and Er. The complexes 1-Ln can be reduced with potassium graphite in the presence of 2.2.2-cryptand (crypt) to form highly absorbing solutions with properties consistent with Ln(2+) complexes, [K(crypt)][(((Ad,Me)ArO)3mes)Ln], 2-Ln...
November 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29160702/heterometallic-heptanuclear-cu5ln2-ln-tb-dy-and-ho-single-molecule-magnets-organized-in-one-dimensional-coordination-polymeric-network
#7
Atanu Dey, Sourav Das, Subrata Kundu, Abhishake Mondal, Mathieu Rouzières, Corine Mathonière, Rodolphe Clérac, Ramakirushnan Suriya Narayanan, Vadapalli Chandrasekhar
The reaction of a multisite coordination ligand, LH3, with Cu(II) salts and Ln(NO3)3·nH2O in a 1:2:1 stoichiometric ratio in the presence of triethylamine was found to afford a series of one-dimensional heterometallic [{Cu5Ln2(L)2(μ3-OH)4(ClO4)(NO3)3(OH2)5}(ClO4)2(H2O)x]∞ [Ln = Tb(1), Dy(2) and Ho(3), x = 4.25, 5.5, and 5 for 1-3, respectively] coordination polymers. Complexes 1-3 have been characterized by single crystal X-ray crystallography. The detailed study of the magnetic properties has also been performed and compared with the parent [Cu5Ln2] molecular analogues...
November 21, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/29158700/x-ray-crystallographic-and-validated-hptlc-analysis-of-the-biomarker-chromone-glucoside-schumanniofioside-a-isolated-from-acalypha-fruticosa-growing-in-saudi-arabia
#8
Areej M Al-Taweel, Ghada A Fawzy, Shagufta Perveen, Perwez Alam, Ali A El Gamal
A chromone glucoside 2-methyl-5,7-dihydroxychromone 5-O-β-D-glucopyranoside (schumanniofioside A, compound 1) was isolated from the methanol extract of Acalypha fruticosa. The structure of compound 1 was fully assigned based on nuclear magnetic resonance (NMR) ((1)H, (13)C and 2D) spectra and electrospray ionization mass spectrum (ESI-MS) in addition to X-ray Crystallography. The molecules were packed in the crystal structure by eight intermolecular O-H⋯O and C-H⋯O interactions. The structure of compound 1 belongs to monoclinic, P21, a = 9...
November 2017: Saudi Pharmaceutical Journal: SPJ: the Official Publication of the Saudi Pharmaceutical Society
https://www.readbyqxmd.com/read/29155569/redox-behavior-of-a-dinuclear-ruthenium-ii-complex-bearing-an-uncommon-bridging-ligand-insights-from-high-pressure-electrochemistry
#9
Maximilian Dürr, Johannes Klein, Axel Kahnt, Sabine Becker, Ralph Puchta, Biprajit Sarkar, Ivana Ivanović-Burmazović
A dinuclear ruthenium complex bridged by 2,3,5,6-pyrazinetetracarboxylic acid (μ-LH2(2-)) was synthesized and characterized by X-ray crystallography, cyclic voltammetry under ambient and elevated pressures, electron paramagnetic resonance (EPR) and UV/vis-NIR (NIR = near-infrared) spectroelectrochemistry, pulse radiolysis, and computational methods. We probed for the first time in the field of mixed-valency the use of high-pressure electrochemical methods. The investigations were directed toward the influence of the protonation state of the bridging ligand on the electronic communication between the ruthenium ions, since such behavior is interesting in terms of modulating redox chemistry by pH...
November 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/29154862/c21-steroidal-glycosides-and-sesquiterpenes-from-the-roots-of-cynanchum-bungei-and-their-inhibitory-activities-against-the-proliferation-of-b-and-t-lymphocytes
#10
Jun-Jun Qin, Xi Chen, Ze-Min Lin, Yan-Sheng Xu, Yi-Ming Li, Jian-Ping Zuo, Wei-Min Zhao
Phytochemical investigation of the roots of Cynanchum bungei Decne (Asclepiadaceae) led to the elucidation of seven C21-steroidal glycosides (1-7) including three new compounds (1-3), named cynabungosides A-C, one new eudesmane-type sesquiterpene (8), named cynabungone, and one new humulane-type sesquiterpene (9), named cynabungolide. Their structures were elucidated on the basis of extensive spectroscopic analysis. The absolute configurations of 8 and 9 were defined unequivocally by ECD analysis and X-ray crystallography, respectively...
November 14, 2017: Fitoterapia
https://www.readbyqxmd.com/read/29152535/time-zero-determination-for-fel-pump-probe-studies-based-on-ultrafast-melting-of-bismuth
#11
S W Epp, M Hada, Y Zhong, Y Kumagai, K Motomura, S Mizote, T Ono, S Owada, D Axford, S Bakhtiarzadeh, H Fukuzawa, Y Hayashi, T Katayama, A Marx, H M Müller-Werkmeister, R L Owen, D A Sherrell, K Tono, K Ueda, F Westermeier, R J D Miller
A common challenge for pump-probe studies of structural dynamics at X-ray free-electron lasers (XFELs) is the determination of time zero (T0)-the time an optical pulse (e.g., an optical laser) arrives coincidently with the probe pulse (e.g., a XFEL pulse) at the sample position. In some cases, T0 might be extracted from the structural dynamics of the sample's observed response itself, but generally, an independent robust method is required or would be superior to the inferred determination of T0. In this paper, we present how the structural dynamics in ultrafast melting of bismuth can be exploited for a quickly performed, reliable and accurate determination of T0 with a precision below 20 fs and an overall experimental accuracy of 50 fs to 150 fs (estimated)...
September 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/29151218/structures-of-dynamic-protein-complexes-hybrid-techniques-to-study-map-kinase-complexes-and-the-escrt-system
#12
Wolfgang Peti, Rebecca Page, Evzen Boura, Bartosz Różycki
The integration of complementary molecular methods (including X-ray crystallography, NMR spectroscopy, small angle X-ray/neutron scattering, and computational techniques) is frequently required to obtain a comprehensive understanding of dynamic macromolecular complexes. In particular, these techniques are critical for studying intrinsically disordered protein regions (IDRs) or intrinsically disordered proteins (IDPs) that are part of large protein:protein complexes. Here, we explain how to prepare IDP samples suitable for study using NMR spectroscopy, and describe a novel SAXS modeling method (ensemble refinement of SAXS; EROS) that integrates the results from complementary methods, including crystal structures and NMR chemical shift perturbations, among others, to accurately model SAXS data and describe ensemble structures of dynamic macromolecular complexes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29151208/strategies-for-efficient-sample-preparation-for-dynamic-nuclear-polarization-solid-state-nmr-of-biological-macromolecules
#13
Boris Itin, Ivan V Sergeyev
Solid-state NMR (SSNMR) is a powerful tool for the elucidation of structure and dynamics in biological macromolecules. Over the years, SSNMR spectroscopists have developed an array of techniques enabling the measurement of internuclear correlations, distances, and torsional angles; these have been applied to the study of a number of biological systems that are difficult to study by X-ray crystallography and solution NMR, including key biological targets such as membrane proteins and amyloid fibrils. Applications of SSNMR to other topic areas, including materials science, pharmaceuticals, and small molecules, have also flourished in recent years...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29149501/the-weakly-coordinating-tris-trichlorosilyl-silyl-anion
#14
Marian Olaru, Maxie F Hesse, Elena Rychagova, Sergey Ketkov, Stefan Mebs, Jens Beckmann
Closely following the procedure for the preparation of the base-stabilized dichlorosilylene complex NHCDipp∙SiCl2 by Roesky and Stalke et al. (Angew. Chem. Int. Ed. 2009, 48, 5683-5686), besides the reported by-product [NHCDipp-H+∙∙∙Cl-], few crystals of the salt [NHCDipp-H∙∙∙Cl∙∙∙H-NHCDipp]Si(SiCl3)3 were isolated and characterized by X-ray crystallography (NHCDipp = N,N-di(2,6-isopropylphenyl)-imidazo-2-ylidene). They feature the weakly-coordinating anion Si(SiCl3)3-, which was more rationally obtained in high yields upon deprotonation of conjugate Brønsted acid HSi(SiCl3)3 with NHCDipp or PMP (PMP = 1,2,2,6,6-pentamethylpiperidine)...
November 17, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29147561/synthesis-and-reactivity-of-a-4his-enzyme-model-complex
#15
Jia Li, Atanu Banerjee, Timothy A Hasse, Reza Loloee, Shannon M Biros, Richard J Staples, Ferman A Chavez
A new iron(II) complex has been prepared and characterized. [Fe(TrIm)4(OTf)2] (1, TrIm = 1-Tritylimidazole). The solid state structure of 1 has been determined by X-ray crystallography. Compound 1 crystallizes in triclinic space group P1̄, with a = 13.342(7) Å, b = 13.5131(7) Å and c = 13.7025(7) Å. The iron center resides in distorted octahedral geometry coordinated to four equatorial imidazole groups and two axial triflate oxygens groups. The complex is high spin between 20 K and 300 K as indicated by variable field variable temperature magnetic measurements...
2017: RSC Advances
https://www.readbyqxmd.com/read/29147002/capturing-an-initial-intermediate-during-the-p450nor-enzymatic-reaction-using-time-resolved-xfel-crystallography-and-caged-substrate
#16
Takehiko Tosha, Takashi Nomura, Takuma Nishida, Naoya Saeki, Kouta Okubayashi, Raika Yamagiwa, Michihiro Sugahara, Takanori Nakane, Keitaro Yamashita, Kunio Hirata, Go Ueno, Tetsunari Kimura, Tamao Hisano, Kazumasa Muramoto, Hitomi Sawai, Hanae Takeda, Eiichi Mizohata, Ayumi Yamashita, Yusuke Kanematsu, Yu Takano, Eriko Nango, Rie Tanaka, Osamu Nureki, Osami Shoji, Yuka Ikemoto, Hironori Murakami, Shigeki Owada, Kensuke Tono, Makina Yabashi, Masaki Yamamoto, Hideo Ago, So Iwata, Hiroshi Sugimoto, Yoshitsugu Shiro, Minoru Kubo
Time-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers a crystallographic method to track enzymatic reactions. Here we demonstrate the application of this method using fungal NO reductase, a heme-containing enzyme, at room temperature. Twenty milliseconds after caged-NO photolysis, we identify a NO-bound form of the enzyme, which is an initial intermediate with a slightly bent Fe-N-O coordination geometry at a resolution of 2...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142195/structural-basis-for-trna-dependent-cysteine-biosynthesis
#17
Meirong Chen, Koji Kato, Yume Kubo, Yoshikazu Tanaka, Yuchen Liu, Feng Long, William B Whitman, Pascal Lill, Christos Gatsogiannis, Stefan Raunser, Nobutaka Shimizu, Akira Shinoda, Akiyoshi Nakamura, Isao Tanaka, Min Yao
Cysteine can be synthesized by tRNA-dependent mechanism using a two-step indirect pathway, where O-phosphoseryl-tRNA synthetase (SepRS) catalyzes the ligation of a mismatching O-phosphoserine (Sep) to tRNA(Cys) followed by the conversion of tRNA-bounded Sep into cysteine by Sep-tRNA:Cys-tRNA synthase (SepCysS). In ancestral methanogens, a third protein SepCysE forms a bridge between the two enzymes to create a ternary complex named the transsulfursome. By combination of X-ray crystallography, SAXS and EM, together with biochemical evidences, here we show that the three domains of SepCysE each bind SepRS, SepCysS, and tRNA(Cys), respectively, which mediates the dynamic architecture of the transsulfursome and thus enables a global long-range channeling of tRNA(Cys) between SepRS and SepCysS distant active sites...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142015/aqueous-ball-milling-of-nacre-constituents-facilitates-directional-self-assembly-of-aragonite-nanoparticles-of-the-gastropod-haliotis-glabra
#18
Marie-Louise Lemloh, Andreas Verch, Ingrid M Weiss
A ball-milling approach was developed to investigate the constituents of isolated nacre tablets of the gastropod Haliotis glabra in aqueous suspension without additional chemical additives. The obtained particle mixtures were characterized using X-ray crystallography as well as scanning and transmission electron microscopy. Aragonite nanoparticles retained their crystal structure even after 14 h of ball milling. The long-term stability of the particle mixtures varied as a function of the ball-milling duration...
November 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29139153/a-four-step-synthesis-of-substituted-5-11-dicyano-6-12-diaryltetracenes-with-enhanced-stability-and-high-fluorescence-emission
#19
Nicolas Kerisit, Przemyslaw Gawel, Brian Levandowski, Yun-Fang Yang, Víctor García-López, Nils Trapp, Laurent Ruhlmann, Corinne Boudon, Kendall N Houk, François Diederich
A four-step synthesis of substituted 5,11-dicyano-6,12-diaryltetracenes was developed, starting from readily available para-substituted benzophenones. The key step of this straightforward route is the complex cascade reaction between tetraaryl[3]cumulenes and tetracyanoethene (TCNE) resulting in 5,5,11,11-tetracyano-5,11-dihydrotetracenes. The mechanism of this transformation was reinvestigated by means of theoretical calculations. The target tetracenes were obtained by a newly developed decyanation/aromatization reaction catalyzed by Cu(I) or Cu(II) complexes in solution, conditions compatible with a broad range of functional groups...
November 15, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29135057/oxime-ether-radical-cations-stabilized-by-n-heterocyclic-carbene
#20
Youngsuk Kim, Kimoon Kim, Eunsung Lee
N-heterocyclic carbene nitric oxide (NHCNO) radicals, which can be regarded as iminoxyl radicals stabilized by NHCs, were found to react with a series of silyl and alkyl triflates to generate the corresponding oxime ether radical cations. The structures of the resulting oxime ether radical cations were determined by X-ray crystallography, along with EPR and computational analysis. In contrast, lutidinium triflate produced a 1:1 mixture of [NHCNO+][OTf-] and [NHCNHOH+][OTf-] upon the reaction with NHCNO. This study adds an important example of stable singlet carbenes stabilizing main group radicals due to their π-conjugating effect, the synthesis and structures of which have never been elucidated previously...
November 14, 2017: Angewandte Chemie
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