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https://www.readbyqxmd.com/read/28731305/the-role-of-lead-ii-in-nucleic-acids
#1
Joana Palou-Mir, Miquel Barceló-Oliver, Roland K O Sigel
Although lead(II) is naturally not associated with nucleic acids, this metal ions has been applied with DNA and RNA in various contexts. Pb2+ is an excellent hydrolytic metal ion for nucleic acids, which is why it is mainly used as probing agent for secondary structure and to determine metal ion binding sites both in vitro and in vivo. A further application of lead(II) is in structural studies, i.e., NMR, but also in X-ray crystallography, mostly using this heavy metal to solve the phase problem in the latter method...
April 10, 2017: Metal Ions in Life Sciences
https://www.readbyqxmd.com/read/28730819/hypervalent-iodine-reagent-mediated-oxidative-heterocyclization-of-aldoximes-with-heterocyclic-alkenes
#2
Akira Yoshimura, Khiem C Nguyen, Gregory T Rohde, Pavel S Postnikov, Mekhman S Yusubov, Viktor V Zhdankin
An efficient cycloaddition of heterocyclic alkenes with nitrile oxides generated in situ from the corresponding aldoximes using organohypervalent iodine(III) reagent, [hydroxy(tosyloxy)iodo]benzene (Koser's reagent), has been developed. The oxidative cyclization of various aldoximes with 1-propene-1,3-sultone affords the respective isoxazoline-ring fused heterobicyclic products in moderate to good yields. Furthermore, the reaction of aldoxime with a cyclic phospholene-oxide under similar conditions produces the corresponding heterobicyclic phospholene oxides in moderate yields...
July 21, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28730437/design-and-crystallography-of-self-assembling-rna-nanostructures
#3
Mark A Boerneke, Thomas Hermann
Biological RNA architectures are composed of autonomously folding modules which can be tailored as building blocks for the construction of RNA nanostructures. Designed base pair interactions allow complex nano-objects to self-assemble from simple RNA motifs. X-ray crystallography plays an important role in both the design and analysis of such RNA nanostructures. Here, we describe methods for the design and X-ray crystallographic structure analysis of an RNA square and two different triangles, which self-assemble from short oligonucleotides and serve as a platform for building functional nano-sized nucleic acid architectures...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730431/protocols-for-molecular-dynamics-simulations-of-rna-nanostructures
#4
Taejin Kim, Wojciech K Kasprzak, Bruce A Shapiro
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28728897/1-3-oxazole-based-selective-picomolar-inhibitors-of-cytosolic-human-carbonic-anhydrase-ii-alleviate-ocular-hypertension-in-rabbits-potency-is-supported-by-x-ray-crystallography-of-two-leads
#5
Marta Ferraroni, Laura Luccarini, Emanuela Masini, Mikhail Korsakov, Andrea Scozzafava, Claudiu T Supuran, Mikhail Krasavin
Two lead 1,3-oxazole-based carbonic anhydrase inhibitors (CAIs) earlier identified as selective, picomolar inhibitors of hCA II (a cytosolic target for treatment of glaucoma) have been investigated further. Firstly, they were found to be conveniently synthesized on multigram scale, which enables further development. These compounds were found to be comparable in efficacy to dorzolamide eye drops when applied in the eye drop form as well. Finally, the reasons for unusually high potency of these compounds became understood from their high-resolution X-ray crystallography structures...
July 11, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28728414/putting-a-new-spin-on-supramolecular-metallacycles-co3-triangle-and-co4-square-bearing-tetrazine-based-radicals-as-bridges
#6
Dimitris I Alexandropoulos, Brian S Dolinar, Kuduva R Vignesh, Kim R Dunbar
The synthesis of two new radical bridged compounds [Co3(bptz)3(dbm)3]∙2toluene (1) and [Co4(bptz)4(dbm)4]∙4MeCN (2) (bptz = 3,6-bis(pyridyl)-1,2,4,5-tetrazine; dbm = 1,3-diphenyl-1,3-propanedione) is reported. The presence of the ligand-centered radical has been confirmed by X-ray crystallography and SQUID magnetometry. These complexes are the first metallacycles bearing nitrogen heterocyclic radicals as bridges. Magnetic studies reveal strong antiferromagnetic metal···radical coupling with coupling constants of J = -67...
July 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28727843/atomistic-modeling-of-alternating-access-of-a-mitochondrial-adp-atp-membrane-transporter-with-molecular-simulations
#7
Koichi Tamura, Shigehiko Hayashi
The mitochondrial ADP/ATP carrier (AAC) is a membrane transporter that exchanges a cytosolic ADP for a matrix ATP. Atomic structures in an outward-facing (OF) form which binds an ADP from the intermembrane space have been solved by X-ray crystallography, and revealed their unique pseudo three-fold symmetry fold which is qualitatively different from pseudo two-fold symmetry of most transporters of which atomic structures have been solved. However, any atomic-level information on an inward-facing (IF) form, which binds an ATP from the matrix side and is fixed by binding of an inhibitor, bongkrekic acid (BA), is not available, and thus its alternating access mechanism for the transport process is unknown...
2017: PloS One
https://www.readbyqxmd.com/read/28726936/dithiolato-and-halogenido-bridged-nickel-iron-complexes-related-to-the-active-site-of-nife-h2ases-preparation-structures-and-electrocatalytic-h2-production
#8
Li-Cheng Song, Xiao-Feng Han, Wei Chen, Jia-Peng Li, Xu-Yong Wang
A new series of the structural and functional models for the active site of [NiFe]-H2ases has been prepared by a simple and convenient synthetic route. Thus, treatment of diphosphines RN(PPh2)2 (1a, R = p-MeC6H4CH2; 1b, R = EtO2CCH2) with an equimolar NiCl2·6H2O, NiBr2·3H2O, and NiI2 in refluxing CH2Cl2/MeOH or EtOH gave the mononuclear Ni complexes RN(PPh2)2NiX2 (2a, R = p-MeC6H4CH2, X = Cl; 2b, R = EtO2CCH2, X = Cl; 3a, R = p-MeC6H4CH2, X = Br; 3b, R = EtO2CCH2, X = Br; 4a, R = p-MeC6H4CH2, X = I; 4b, R = EtO2CCH2, X = I) in 67-97% yields...
July 20, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28724190/testing-limits-of-bophy-platform-preparation-characterization-and-theoretical-modeling-of-bophys-bophys-with-electron-withdrawing-groups-at-b-pyrrolic-and-bridging-positions
#9
Victor N Nemykin, Yuriy V Zatsikha, Dion B Nemez, Rebecca L Davis, Simarpreet Singh, David E Herbert, Alex J King, Christopher J Ziegler
Several BOPHY derivatives with and without ferrocene fragments and with electron-withdrawing carbethoxy groups appended to the -pyrrolic positions have been prepared and characterized by NMR, UV-Vis-NIR, APCI MS, and fluorescence spectroscopy as well as X-ray crystallography. The redox properties of new BOPHYs were probed by electrochemical (CV and DPV) and spectroelectrochemical methods. In attempt for the preparation of the BOPHY derivatives with cyano group at bridging position using similar to recently communicated BODIPY cyanation approach (Chem...
July 19, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28719588/structures-of-carboxylic-acid-reductase-reveal-domain-dynamics-underlying-catalysis
#10
Deepankar Gahloth, Mark S Dunstan, Daniela Quaglia, Evaldas Klumbys, Michael P Lockhart-Cairns, Andrew M Hill, Sasha R Derrington, Nigel S Scrutton, Nicholas J Turner, David Leys
Carboxylic acid reductase (CAR) catalyzes the ATP- and NADPH-dependent reduction of carboxylic acids to the corresponding aldehydes. The enzyme is related to the nonribosomal peptide synthetases, consisting of an adenylation domain fused via a peptidyl carrier protein (PCP) to a reductase termination domain. Crystal structures of the CAR adenylation-PCP didomain demonstrate that large-scale domain motions occur between the adenylation and thiolation states. Crystal structures of the PCP-reductase didomain reveal that phosphopantetheine binding alters the orientation of a key Asp, resulting in a productive orientation of the bound nicotinamide...
July 17, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28716900/structural-insights-into-the-extracellular-recognition-of-the-human-serotonin-2b-receptor-by-an-antibody
#11
Andrii Ishchenko, Daniel Wacker, Mili Kapoor, Ai Zhang, Gye Won Han, Shibom Basu, Nilkanth Patel, Marc Messerschmidt, Uwe Weierstall, Wei Liu, Vsevolod Katritch, Bryan L Roth, Raymond C Stevens, Vadim Cherezov
Monoclonal antibodies provide an attractive alternative to small-molecule therapies for a wide range of diseases. Given the importance of G protein-coupled receptors (GPCRs) as pharmaceutical targets, there has been an immense interest in developing therapeutic monoclonal antibodies that act on GPCRs. Here we present the 3.0-Å resolution structure of a complex between the human 5-hydroxytryptamine 2B (5-HT2B) receptor and an antibody Fab fragment bound to the extracellular side of the receptor, determined by serial femtosecond crystallography with an X-ray free-electron laser...
July 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28715187/charge-density-wave-and-narrow-energy-gap-at-room-temperature-in-2d-pb3-xsb1-xs4te2-%C3%AE-with-square-te-sheets
#12
Haijie Chen, Christos D Malliakas, Awadhesh Narayan, Lei Fang, Duck Young Chung, Lucas K Wagner, Wai-Kwong Kwok, Mercouri G Kanatzidis
We report a new two-dimensional compound Pb3-xSb1+xS4Te2-δ has a charge density wave (CDW) at room temperature. The CDW is incommensurate with q-vector of 0.248(6)a* + 0.246(8)b* + 0.387(9)c* for x = 0.29(2) and δ = 0.37(3) due to positional and occupational long range ordering of Te atoms in the sheets. The modulated structure was refined from the single crystal X-ray diffraction data with a superspace group P-1(αβγ)0 using (3 + 1)-dimensional crystallography. The resistivity increases with decreasing temperature, suggesting semiconducting behavior...
July 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28711020/synthesis-structures-nuclease-activity-cytotoxicity-dft-and-molecular-docking-studies-of-two-nitrato-bridged-homodinuclear-cu-cu-zn-zn-complexes-containing-2-2-bipyridine-and-a-chalcone-derivative
#13
Ruchi Gaur, Diksha Kumari Choubey, Mohammad Usman, Benzamin D Ward, Jagat Kumar Roy, Lallan Mishra
Nitrato briged dinuclear complexes of type [Cu2(L)2(bpy)2(NO3)](NO3)·4H2O, 1 and [Zn2(L)2(bpy)2(NO3)](NO3)·4H2O, 2 (L=deprotonated form of free ligand LH, [1-(2-hydroxyphenyl)-3-(9-anthracenyl) propenone; bpy=2,2'bipyridine] are synthesized and characterized using a battery of physicochemical techniques and X-ray crystallography. A distorted square pyramidal geometry is assigned to them with N2O3 coordination core around the metal ion. The co-ligand L binds the metal ions through its O,O' atoms in anti-syn mode...
July 8, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28707382/neutron-crystallographic-studies-of-t4-lysozyme-at-cryogenic-temperature
#14
Le Li, Shantanu Shukla, Flora Meilleur, Robert F Standaert, Josh Pierce, Dean A A Myles, Matthew J Cuneo
Bacteriophage T4 lysozyme (T4L) has been used as a paradigm for seminal biophysical studies on protein structure, dynamics and stability. Approximately 700 mutants of this protein and their complexes have been characterized by X-ray crystallography; however, despite the high resolution diffraction limits attained in several studies, no hydrogen atoms were reported being visualized in the electron density maps. To address this, a 2.2 Å-resolution neutron data set was collected at 80 K from a crystal of perdeuterated T4L pseudo-wild type...
July 13, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28706325/axsis-exploring-the-frontiers-in-attosecond-x-ray-science-imaging-and-spectroscopy
#15
F X Kärtner, F Ahr, A-L Calendron, H Çankaya, S Carbajo, G Chang, G Cirmi, K Dörner, U Dorda, A Fallahi, A Hartin, M Hemmer, R Hobbs, Y Hua, W R Huang, R Letrun, N Matlis, V Mazalova, O D Mücke, E Nanni, W Putnam, K Ravi, F Reichert, I Sarrou, X Wu, A Yahaghi, H Ye, L Zapata, D Zhang, C Zhou, R J D Miller, K K Berggren, H Graafsma, A Meents, R W Assmann, H N Chapman, P Fromme
X-ray crystallography is one of the main methods to determine atomic-resolution 3D images of the whole spectrum of molecules ranging from small inorganic clusters to large protein complexes consisting of hundred-thousands of atoms that constitute the macromolecular machinery of life. Life is not static, and unravelling the structure and dynamics of the most important reactions in chemistry and biology is essential to uncover their mechanism. Many of these reactions, including photosynthesis which drives our biosphere, are light induced and occur on ultrafast timescales...
September 1, 2016: Nuclear Instruments & Methods in Physics Research. Section A, Accelerators, Spectrometers, Detectors and Associated Equipment
https://www.readbyqxmd.com/read/28705433/recent-advances-in-racemic-protein-crystallography
#16
REVIEW
Bingjia Yan, Linzhi Ye, Weiliang Xu, Lei Liu
Solution of the three-dimensional structures of proteins is a critical step in deciphering the molecular mechanisms of their bioactivities. Among the many approaches for obtaining protein crystals, racemic protein crystallography has been developed as a unique method to solve the structures of an increasing number of proteins. Exploiting unnatural protein enantiomers in crystallization and resolution, racemic protein crystallography manifests two major advantages that are 1) to increase the success rate of protein crystallization, and 2) to obviate the phase problem in X-ray diffraction...
May 10, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28703597/natural-and-semisynthetic-tigliane-diterpenoids-with-new-carbon-skeletons-from-euphorbia-dracunculoides-as-a-wnt-signaling-pathway-inhibitor
#17
Li Wang, Jing Yang, Ling-Mei Kong, Jun Deng, Zijun Xiong, Jianping Huang, Jianying Luo, Yijun Yan, Yikao Hu, Xiao-Nian Li, Yan Li, Yong Zhao, Sheng-Xiong Huang
Euphordraculoates A (1) and B (2), featuring tigliane diterpenoids with two new carbon skeletons, were characterized as metabolites of Euphorbia dracunculoides and semisynthetic products, respectively. Their structures were determined by spectroscopic analyses and X-ray crystallography. The respective biosynthetic and chemical formation mechanisms for 1 and 2 from a known tigliane 3 was proposed. The detailed decarbonization mechanism from 3 to 2 was further explored by (18)O-labeling experiment. Compound 2 could inhibit Wnt pathway in a dose- and time-dependent manner...
July 13, 2017: Organic Letters
https://www.readbyqxmd.com/read/28702572/recent-structural-insights-into-the-function-of-copper-nitrite-reductases
#18
REVIEW
Sam Horrell, Demet Kekilli, Richard W Strange, Michael A Hough
Copper nitrite reductases (CuNiR) carry out the first committed step of the denitrification pathway of the global nitrogen cycle, the reduction of nitrite (NO2(-)) to nitric oxide (NO). As such, they are of major agronomic and environmental importance. CuNiRs occur primarily in denitrifying soil bacteria which carry out the overall reduction of nitrate to dinitrogen. In this article, we review the insights gained into copper nitrite reductase (CuNiR) function from three dimensional structures. We particularly focus on developments over the last decade, including insights from serial femtosecond crystallography using X-ray free electron lasers (XFELs) and from the recently discovered 3-domain CuNiRs...
July 12, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28702564/ru-based-co-releasing-molecules-with-azole-ligands-interaction-with-proteins-and-the-co-release-mechanism-disclosed-by-x-ray-crystallography
#19
Nicola Pontillo, Giarita Ferraro, Luigi Messori, Gabriella Tamasi, Antonello Merlino
fac-[Ru(II)(CO)3Cl2(N(3)-Imidazole)] (Ru(II)IM), fac-[Ru(II)(CO)3Cl2(N(3)-methyl-imidazole)] (Ru(II)MIM) and fac-[Ru(II)(CO)3Cl2(N(3)-methyl-benzimidazole)] (Ru(II)MBI) are three ruthenium based CO releasing molecules (Ru-CORMs) that are cytotoxic towards ovarian and colon carcinoma cell lines. Detailed structural information on the adducts formed upon reaction of Ru(II)IM and Ru(II)MIM with hen egg white lysozyme and of the three Ru-CORMs with bovine pancreatic ribonuclease is provided here by X-ray crystallography...
July 13, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28699533/class-a-gpcrs-structure-function-modeling-and-structure-based-ligand-design
#20
Xiaojing Cong, Jérémie Topin, Jérôme Golebiowski
G protein-coupled receptors (GPCRs), especially the class A, are the most heavily investigated drug targets in the pharmaceutical industry. Tremendous efforts have been made by both industry and academia to understand the molecular structure and function of this large family of transmembrane proteins. Our understanding in GPCR activation has evolved from the classical inactive-active two-state model to a complex view of GPCR conformational ensemble associated with multiple interacting partners such as ligands, allosteric modulators, ions and downstream signaling proteins...
July 10, 2017: Current Pharmaceutical Design
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