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X-ray crystallography

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https://www.readbyqxmd.com/read/28655198/glycosylation-of-igg-fc-a-molecular-perspective
#1
Masato Kiyoshi, Kouhei Tsumoto, Akiko Ishii-Watabe, Jose M M Caaveiro
Antibodies of the IgG class carry a pair of oligosaccharides (N-glycans) in the fragment crystallizable (Fc) region. The importance of the N-glycan is clearly demonstrated by the profound effect it has in the physicochemical and biological properties of antibodies. The term "glycoengineering" has been coined to describe contemporary strategies to improve the performance of therapeutic monoclonal antibodies on the basis of modifications in the structure and composition of the N-glycan. These methodologies have resulted in the approval and commercialization of a new generation of antibodies with improved therapeutic efficacy...
June 26, 2017: International Immunology
https://www.readbyqxmd.com/read/28654325/a-bright-future-for-antibiotics
#2
Donna Matzov, Anat Bashan, Ada Yonath
Multidrug resistance is a global threat as the clinically available potent antibiotic drugs are becoming exceedingly scarce. For example, increasing drug resistance among gram-positive bacteria is responsible for approximately one-third of nosocomial infections. As ribosomes are a major target for these drugs, they may serve as suitable objects for novel development of next-generation antibiotics. Three-dimensional structures of ribosomal particles from Staphylococcus aureus obtained by X-ray crystallography have shed light on fine details of drug binding sites and have revealed unique structural motifs specific for this pathogenic strain, which may be used for the design of novel degradable pathogen-specific, and hence, environmentally friendly drugs...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28654266/unexpected-interactions-between-alkyl-straps-and-pyridine-ligands-in-sulfur-strapped-porphyrin-nanorings
#3
Cecile Roche, Qianfu Luo, Guzman Gil-Ramirez, Hua-Wei Jiang, Daniel R Kohn, Yaoyao Xiong, Amber L Thompson, Harry L Anderson
Strapped - or 'basket-handle' - porphyrins have been investigated previously as hemoglobin mimics and catalysts. The facial selectivity of their interactions with axial ligands is a sensitive test for non-covalent bonding. Here the binding of pyridyl ligands to zinc porphyrins with thioester-linked alkyl straps is investigated in solution by NMR spectroscopy and UV-vis titration, and in the solid state by X-ray crystallography. We expected that coordination of the axial ligand would occur on the less hindered face of the porphyrin, away from the strap...
June 27, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28653703/pitfalls-in-metal-organic-framework-crystallography-towards-more-accurate-crystal-structures
#4
S Øien-Ødegaard, G C Shearer, D S Wragg, K P Lillerud
Single crystal X-ray diffraction (SC-XRD) is the principal method for determining the crystal structures of metal-organic frameworks (MOFs). This tutorial deals with the handling of MOF crystals and analysis of crystallographic data obtained from single-crystal X-ray diffraction, focusing on two features that are particularly important in MOF crystallography and have a large impact on the quality and reliability of the final crystal structures: (1) the treatment of pore-occupying entities (both in the physical crystals and in the crystallographic model) and (2) crystallographic twinning...
June 27, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28653468/chiral-gold-nanoclusters-atomic-level-origins-of-chirality
#5
REVIEW
Chenjie Zeng, Rongchao Jin
Chiral nanomaterials have received wide interest in many areas, but the exact origin of chirality at the atomic level remains elusive in many cases. With recent significant progress in atomically precise gold nanoclusters (e.g., thiolate-protected Aun (SR)m ), several origins of chirality have been unveiled based upon atomic structures determined by using single-crystal X-ray crystallography. The reported chiral Aun (SR)m structures explicitly reveal a predominant origin of chirality that arises from the Au-S chiral patterns at the metal-ligand interface, as opposed to the chiral arrangement of metal atoms in the inner core (i...
June 27, 2017: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/28652603/skeletal-dysplasia-mutations-effect-on-human-filamins-structure-and-mechanosensing
#6
Jonne Seppälä, Rafael C Bernardi, Tatu J K Haataja, Maarit Hellman, Olli T Pentikäinen, Klaus Schulten, Perttu Permi, Jari Ylänne, Ulla Pentikäinen
Cells' ability to sense mechanical cues in their environment is crucial for fundamental cellular processes, leading defects in mechanosensing to be linked to many diseases. The actin cross-linking protein Filamin has an important role in the conversion of mechanical forces into biochemical signals. Here, we reveal how mutations in Filamin genes known to cause Larsen syndrome and Frontometaphyseal dysplasia can affect the structure and therefore function of Filamin domains 16 and 17. Employing X-ray crystallography, the structure of these domains was first solved for the human Filamin B...
June 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28652207/characterizing-the-molecular-architectures-of-chromatin-modifying-complexes
#7
REVIEW
Dheva T Setiaputra, Calvin K Yip
Eukaryotic cells package their genome in the form of a DNA-protein complex known as chromatin. This organization not only condenses the genome to fit within the confines of the nucleus, but also provides a platform for a cell to regulate accessibility to different gene sequences. The basic packaging element of chromatin is the nucleosome, which consists of 146 base pairs of DNA wrapped around histone proteins. One major means that a cell regulates chromatin structure is by depositing post-translational modifications on nucleosomal histone proteins, and thereby altering internucleosomal interactions and/or binding to different chromatin associated factors...
June 23, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28652006/3d-nus-a-web-server-for-automated-modeling-and-visualization-of-non-canonical-3-dimensional-nucleic-acid-structures
#8
L Ponoop Prasad Patro, Abhishek Kumar, Narendar Kolimi, Thenmalarchelvi Rathinavelan
The inherent conformational flexibility of nucleic acids facilitate the formation of a range of conformations such as duplex, triplex, quadruplex etc. that play crucial roles in biological processes. Elucidation about the influence of non-canonical base pair mismatches on DNA/RNA structures at different sequence contexts to understand mismatch repair and misregulation of alternative splicing mechanisms as well as the sequence dependent effect of RNA-DNA hybrid in relevance to antisense strategy demand their three-dimensional structural information...
June 23, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28651169/anticancer-activity-of-hydroxy-and-sulfonamide-azobenzene-platinum-ii-complexes-in-cisplatin-resistant-ovarian-cancer-cells
#9
Katia G Samper, Sierra C Marker, Pau Bayón, Samantha N MacMillan, Ivan Keresztes, Òscar Palacios, Justin J Wilson
The syntheses of three platinum(II) complexes bearing sulfonamide- ( (E)-2-(4-methylphenylsulfonamido)-2',6'-difluoroazobenzene, HL1) and hydroxy-azo-2,6-difluorobenzene ((E)-2-((2,6-difluorophenyl)diazenyl)phenol, HL2) bidentate ligands is described. These complexes, [Pt(L1)(DMSO)Cl] (1), [Pt(L2)(DMSO)Cl] (2), and [Pt(L2)2] (3), were characterized by multinuclear NMR spectroscopy, mass spectrometry, and X-ray crystallography. Despite bearing azobenzene functional groups, none of the three complexes undergo photoisomerization...
June 17, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28650033/chloride-assisted-supramolecular-assembly-of-a-luminescent-gigantic-cluster-ag216s56cl7-c-triple-bond-length-as-m-dash-cph-98-h2o-12-with-pseudo-th-skeleton-and-five-shell-arrangement
#10
Zi-Yi Chen, Dennis Y S Tam, Thomas C W Mak
Using a chloride-assisted supramolecular building-block approach, we have employed the molecular Cl@Agm(C[triple bond, length as m-dash]CPh)n entity in the construction of a gigantic cluster namely [Ag216S56Cl7(C[triple bond, length as m-dash]CPh)98(H2O)12][Ag3(imidazole)(H2O)4](SbF6)2 (1), which contains the largest discrete organometallic cluster investigated by X-ray crystallography. Based on an icosahedral Cl@Ag12 kernel, this spheroidal cluster features an unprecedented five-shell structure Cl@Ag12@S12@Ag32@S44Cl6@Ag172 with idealized Th symmetry...
June 26, 2017: Nanoscale
https://www.readbyqxmd.com/read/28649740/human-vs-robots-in-the-discovery-and-crystallization-of-gigantic-polyoxometalates
#11
Lee Cronin, Vasilios Duros, Jonathan Grizou, Weimin Xuan, Zied Hosni, De-Liang Long, Haralampos Miras
The discovery of new gigantic molecules formed by self-assembly using single crystal X-ray crystallography is a challenging endeavor as it combines two contingent events; first is the formation of a new molecule, and second its crystallization. Herein, we constructed a workflow that can be followed manually or by a robot to probe the envelope of both events and employed it in the chemical space of a new polyoxometalate cluster, namely Na6[Mo120Ce6O366H12(H2O)78]·200H2O (1) which has a trigonal-ring type architecture (yield 4...
June 25, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28645943/the-structure-of-the-tetanus-toxin-reveals-ph-mediated-domain-dynamics
#12
Geoffrey Masuyer, Julian Conrad, Pål Stenmark
The tetanus neurotoxin (TeNT) is a highly potent toxin produced by Clostridium tetani that inhibits neurotransmission of inhibitory interneurons, causing spastic paralysis in the tetanus disease. TeNT differs from the other clostridial neurotoxins by its unique ability to target the central nervous system by retrograde axonal transport. The crystal structure of the tetanus toxin reveals a "closed" domain arrangement stabilised by two disulphide bridges, and the molecular details of the toxin's interaction with its polysaccharide receptor...
June 23, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28644020/the-underestimated-halogen-bonds-forming-with-protein-backbone-in-protein-data-bank
#13
Qian Zhang, Zhijian Xu, Jiye Shi, Weiliang Zhu
Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-Ray crystallography takes into account of XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower...
June 23, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28643783/cdt1-stabilizes-an-open-mcm-ring-for-helicase-loading
#14
Jordi Frigola, Jun He, Kerstin Kinkelin, Valerie E Pye, Ludovic Renault, Max E Douglas, Dirk Remus, Peter Cherepanov, Alessandro Costa, John F X Diffley
ORC, Cdc6 and Cdt1 act together to load hexameric MCM, the motor of the eukaryotic replicative helicase, into double hexamers at replication origins. Here we show that Cdt1 interacts with MCM subunits Mcm2, 4 and 6, which both destabilizes the Mcm2-5 interface and inhibits MCM ATPase activity. Using X-ray crystallography, we show that Cdt1 contains two winged-helix domains in the C-terminal half of the protein and a catalytically inactive dioxygenase-related N-terminal domain, which is important for MCM loading, but not for subsequent replication...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28642465/structural-basis-for-biologically-relevant-mechanical-stiffening-of-a-virus-capsid-by-cavity-creating-or-spacefilling-mutations
#15
Pablo Guerra, Alejandro Valbuena, Jordi Querol-Audí, Cristina Silva, Milagros Castellanos, Alicia Rodríguez-Huete, Damià Garriga, Mauricio G Mateu, Nuria Verdaguer
Recent studies reveal that the mechanical properties of virus particles may have been shaped by evolution to facilitate virus survival. Manipulation of the mechanical behavior of virus capsids is leading to a better understanding of viral infection, and to the development of virus-based nanoparticles with improved mechanical properties for nanotechnological applications. In the minute virus of mice (MVM), deleterious mutations around capsid pores involved in infection-related translocation events invariably increased local mechanical stiffness and interfered with pore-associated dynamics...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28641005/electron-crystallography-reveals-atomic-structures-of-metal-organic-nanoplates-with-m12-%C3%AE-3-o-8-%C3%AE-3-oh-8-%C3%AE-2-oh-6-m-zr-hf-secondary-building-units
#16
Ruihan Dai, Fei Peng, Pengfei Ji, Kuangda Lu, Cheng Wang, Junliang Sun, Wenbin Lin
Nanoscale metal-organic frameworks (nMOFs) have shown tremendous potential in cancer therapy and biomedical imaging. However, their small dimensions present a significant challenge in structure determination by single-crystal X-ray crystallography. We report here the structural determination of nMOFs by rotation electron diffraction (RED). Two isostructural Zr- and Hf-based nMOFs with linear biphenyldicarboxylate (BPDC) or bipyridinedicarboxylate (BPYDC) linkers are stable under intense electron beams to allow the collection of high-quality RED data, which reveal a MOF structure with M12(μ3-O)8(μ3-OH)8(μ2-OH)6 (M = Zr, Hf) secondary building units (SBUs)...
June 22, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28640600/horse-liver-alcohol-dehydrogenase-zinc-coordination-and-catalysis
#17
Bryce V Plapp, Baskar Raj Savarimuthu, Daniel J Ferraro, Jon K Rubach, Eric N Brown, Subramanian Ramaswamy
: During catalysis by liver alcohol dehydrogenase (ADH), a water bound to the catalytic zinc is replaced by the oxygen of the substrates. The mechanism may involve a pentacoordinated zinc or a double displacement reaction with participation by a nearby glutamate residue, as suggested by studies of human ADH3, yeast ADH1 and some other tetrameric ADHs. Zinc coordination and participation of water in the enzyme mechanism were investigated by X-ray crystallography. Apoenzyme and its complex with adenosine 5'-diphosphoribose have an open protein conformation with the catalytic zinc in one position, tetracoordinated by Cys-46, His-67, Cys-174 and a water molecule...
June 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28639360/the-mechanism-of-coupling-between-oxido-reduction-and-proton-translocation-in-respiratory-chain-enzymes
#18
Sergio Papa, Giuseppe Capitanio, Francesco Papa
The respiratory chain of mitochondria and bacteria is made up of a set of membrane-associated enzyme complexes which catalyse sequential, stepwise transfer of reducing equivalents from substrates to oxygen and convert redox energy into a transmembrane protonmotive force (PMF) by proton translocation from a negative (N) to a positive (P) aqueous phase separated by the coupling membrane. There are three basic mechanisms by which a membrane-associated redox enzyme can generate a PMF. These are membrane anisotropic arrangement of the primary redox catalysis with: (i) vectorial electron transfer by redox metal centres from the P to the N side of the membrane; (ii) hydrogen transfer by movement of quinones across the membrane, from a reduction site at the N side to an oxidation site at the P side; (iii) a different type of mechanism based on co-operative allosteric linkage between electron transfer at the metal redox centres and transmembrane electrogenic proton translocation by apoproteins...
June 21, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/28638775/host-guest-complexes-of-c-ethyl-2-methylresorcinarene-and-aromatic-n-n-dioxides
#19
Rakesh Puttreddy, Ngong Kodiah Beyeh, Robin H A Ras, Kari Rissanen
The C-ethyl-2-methylresorcinarene (1) forms 1:1 in-cavity complexes with aromatic N,N'-dioxides, only if each of the aromatic rings has an N-O group. The structurally different C-shaped 2,2'-bipyridine N,N'-dioxide (2,2'-BiPyNO) and the linear rod-shaped 4,4'-bipyridine N,N'-dioxide (4,4'-BiPyNO) both form 1:1 in-cavity complexes with the host resorcinarene in C4v crown and C2v conformations, respectively. In the solid state, the host-guest interactions between the 1,3-bis(4-pyridyl)propane N,N'-dioxide (BiPyPNO) and the host 1 stabilize the unfavorable anti-gauche conformation...
June 2017: ChemistryOpen
https://www.readbyqxmd.com/read/28636340/three-dimensional-modeling-of-quasicrystal-structures-from-x-ray-diffraction-an-icosahedral-al-cu-fe-alloy
#20
Seung-Tae Hong
Quasicrystals (QCs) are well-ordered but aperiodic crystals with classically forbidden symmetries (such as 5-fold). High-dimensional (HD) crystallography is a standard method to locate atom positions explicitly. However, in practice, it is still challenging because of its complexity. Here, we report a new simple approach to three-dimensional (3D) atomic modeling derived from X-ray diffraction data, and apply it to the icosahedral QC Al0.63Cu0.25Fe0.12. Electron density maps were calculated directly from 3D diffraction data indexed with noninteger (fractional) numbers as measured, with proper phases; each of 2(5) = 32 possible phase assignments for the five strongest reflections was used for Fourier synthesis...
June 21, 2017: Inorganic Chemistry
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