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https://www.readbyqxmd.com/read/28646173/transmembrane-interactions-of-full-length-mammalian-bitopic-cytochrome-p450-cytochrome-b5-complex-in-lipid-bilayers-revealed-by-sensitivity-enhanced-dynamic-nuclear-polarization-solid-state-nmr-spectroscopy
#1
Kazutoshi Yamamoto, Marc A Caporini, Sang-Choul Im, Lucy Waskell, Ayyalusamy Ramamoorthy
The dynamic protein-protein and protein-ligand interactions of integral bitopic membrane proteins with a single membrane-spanning helix play a plethora of vital roles in the cellular processes associated with human health and diseases, including signaling and enzymatic catalysis. While an increasing number of high-resolution structural studies of membrane proteins have successfully manifested an in-depth understanding of their biological functions, intact membrane-bound bitopic protein-protein complexes pose tremendous challenges for structural studies by crystallography or solution NMR spectroscopy...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28645943/the-structure-of-the-tetanus-toxin-reveals-ph-mediated-domain-dynamics
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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/28636761/molecular-tools-for-facilitative-carbohydrate-transporters
#10
Marina Tanasova, Joseph R Fedie
Facilitative carbohydrate transporters - Gluts - have received a wide attention over decades due to their essential role in the nutrient uptake and links with various metabolic disorders, including diabetes, obesity, and cancer. Endeavors into understanding mechanisms of Glut-mediated nutrient uptake have resulted in the multidisciplinary research field, branching protein chemistry, chemical biology, organic synthesis, crystallography, and biomolecular modeling. Gluts became attractive targets for cancer research and medicinal chemistry, leading to the development of new approaches to cancer diagnostics and providing avenues for cancer-targeting therapeutics...
June 21, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28636340/three-dimensional-modeling-of-quasicrystal-structures-from-x-ray-diffraction-an-icosahedral-al-cu-fe-alloy
#11
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
https://www.readbyqxmd.com/read/28635955/corrigendum-double-flow-focused-liquid-injector-for-efficient-serial-femtosecond-crystallography
#12
Dominik Oberthuer, Juraj Knoška, Max O Wiedorn, Kenneth R Beyerlein, David A Bushnell, Elena G Kovaleva, Michael Heymann, Lars Gumprecht, Richard A Kirian, Anton Barty, Valerio Mariani, Aleksandra Tolstikova, Luigi Adriano, Salah Awel, Miriam Barthelmess, Katerina Dörner, P Lourdu Xavier, Oleksandr Yefanov, Daniel R James, Garrett Nelson, Dingjie Wang, George Calvey, Yujie Chen, Andrea Schmidt, Michael Szczepek, Stefan Frielingsdorf, Oliver Lenz, Edward Snell, Philip J Robinson, Božidar Šarler, Grega Belšak, Marjan Maček, Fabian Wilde, Andrew Aquila, Sébastien Boutet, Mengning Liang, Mark S Hunter, Patrick Scheerer, John D Lipscomb, Uwe Weierstall, Roger D Kornberg, John C H Spence, Lois Pollack, Henry N Chapman, Saša Bajt
This corrects the article DOI: 10.1038/srep44628.
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634395/seven-membered-lactam-derivatives-of-podophyllotoxins-as-new-pesticidal-agents
#13
Xiaoyan Zhi, Yuanyuan Zhang, Jiulin Huang, Hui Xu
As a continuation of our efforts to discover and develop natural-product-based insecticidal agents, three novel and unusual 7-membered lactam derivatives of podophyllotoxin were prepared by thionyl chloride-mediated ring-expanded Beckmann rearrangement. The steric configurations of 3a-c were unambiguously identified by X-ray crystallography. It demonstrated that the configuration of the picropodophyllotoxin C4-oximes could also be confirmed by the corresponding C-ring expansion products via Beckmann rearrangement...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634233/structural-analyses-of-human-thymidylate-synthase-reveal-a-site-that-may-control-conformational-switching-between-active-and-inactive-states
#14
Dan Chen, Anna Jansson, Daniel Sim, Andreas Larsson, Pär Nordlund
Thymidylate synthase (TS) is the sole enzyme responsible for de novo biosynthesis of thymidylate (TMP) and is essential for cell proliferation and survival. Inhibition of human TS (hTS) has been extensively investigated for cancer chemotherapy, but several aspects of its activity and regulation are still uncertain. In this study, we performed comprehensive structural and biophysical studies of hTS using crystallography and thermal shift assay and provided the first detailed structural information on the conformational changes induced by ligand binding to the hTS active site...
June 20, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28631925/anticancer-activity-of-polyoxometalate-bisphosphonate-complexes-synthesis-characterization-in-vitro-and-in-vivo-results
#15
Amandine Boulmier, Xinxin Feng, Olivier Oms, Pierre Mialane, Eric Rivière, Christopher J Shin, Jiaqi Yao, Tadahiko Kubo, Taisuke Furuta, Eric Oldfield, Anne Dolbecq
We synthesized a series of polyoxometalate-bisphosphonate complexes containing Mo(VI)O6 octahedra, zoledronate, or an N-alkyl (n-C6 or n-C8) zoledronate analogue, and in two cases, Mn as a heterometal. Mo6L2 (L = Zol, ZolC6, ZolC8) and Mo4L2Mn (L = Zol, ZolC8) were characterized by using single-crystal X-ray crystallography and/or IR spectroscopy, elemental and energy dispersive X-ray analysis and (31)P NMR. We found promising activity against human nonsmall cell lung cancer (NCI-H460) cells with IC50 values for growth inhibition of ∼5 μM per bisphosphonate ligand...
June 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28630286/efficient-switching-of-mcherry-fluorescence-using-chemical-caging
#16
Bas M C Cloin, Elke De Zitter, Desiree Salas, Vincent Gielen, Gert E Folkers, Marina Mikhaylova, Maike Bergeler, Bartosz Krajnik, Jeremy Harvey, Casper C Hoogenraad, Luc Van Meervelt, Peter Dedecker, Lukas C Kapitein
Fluorophores with dynamic or controllable fluorescence emission have become essential tools for advanced imaging, such as superresolution imaging. These applications have driven the continuing development of photoactivatable or photoconvertible labels, including genetically encoded fluorescent proteins. These new probes work well but require the introduction of new labels that may interfere with the proper functioning of existing constructs and therefore require extensive functional characterization. In this work we show that the widely used red fluorescent protein mCherry can be brought to a purely chemically induced blue-fluorescent state by incubation with β-mercaptoethanol (βME)...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28628129/high-speed-fixed-target-serial-virus-crystallography
#17
Philip Roedig, Helen M Ginn, Tim Pakendorf, Geoff Sutton, Karl Harlos, Thomas S Walter, Jan Meyer, Pontus Fischer, Ramona Duman, Ismo Vartiainen, Bernd Reime, Martin Warmer, Aaron S Brewster, Iris D Young, Tara Michels-Clark, Nicholas K Sauter, Abhay Kotecha, James Kelly, David J Rowlands, Marcin Sikorsky, Silke Nelson, Daniel S Damiani, Roberto Alonso-Mori, Jingshan Ren, Elizabeth E Fry, Christian David, David I Stuart, Armin Wagner, Alke Meents
We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively...
June 19, 2017: Nature Methods
https://www.readbyqxmd.com/read/28627554/group-2-metal-mg-ca-sr-silylamides-supported-by-a-cyclen-derived-macrocyclic-polyamine
#18
Debabrata Mukherjee, Satoru Shirase, Klaus Beckerle, Thomas P Spaniol, Kazushi Mashima, Jun Okuda
Heteroleptic bis(silyl)amides of magnesium and calcium [(L)M{N(SiMe3)2}] [M = Mg, Ca; LH = 1,4,7-trimethyl-1,4,7,10-tetraazacyclododecane; (Me3TACD)H] were previously synthesized from LH and [M{N(SiMe3)2}2]. Strontium bis(silyl)amides [Sr{N(SiMe3)2}2(thf)2] and [Sr{N(SiHMe2)2}2(thf)2/3] reacted with LH to give different types of products, depending on the presence of the β-SiH function. While the former underwent protonolysis to give the amido-bridged dimer [(L)Sr{N(SiMe3)2}]2 (1), the latter gave the adduct [(LH)Sr{N(SiHMe2)2}2] (2) as a stable solid...
June 19, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28627161/synthesis-and-properties-of-covalently-linked-azabodipy-bodipy-dyads-and-azabodipy-bodipy-2-triads
#19
Sunit Kumar, Kishor Gulab Thorat, Mangalampalli Ravikanth
The azaBODIPYs containing one and two formyl functional groups on the 1, 7-aryl groups present at the azaBODIPY core were synthesized over sequence of steps and characterized by mass, NMR, absorption and electrochemical techniques. The mono-formylated and di-formylated azaBODIPYs are very useful synthons to prepare wide variety of new fluorescent compounds. The mono- and di-formylated azaBODIPYs were treated with pyrrole under mild acidic conditions followed by column chromatographic purification to afford azaBODIPYs appended with one and two dipyrromethanyl groups...
June 19, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28626553/stepwise-crystallographic-visualization-of-dynamic-guest-binding-in-a-nanoporous-framework
#20
Gabriel Brunet, Damir A Safin, Mohammad Z Aghaji, Koen Robeyns, Ilia Korobkov, Tom K Woo, Muralee Murugesu
Binding sites are at the heart of all host-guest systems, whether biological or chemical. When considering binding sites that form covalent bonds with the guest, we generally envision a single, highly specific binding motif. Through single-crystal X-ray crystallography, the dynamic binding of a guest that displays a variety of covalent binding motifs in a single site of adsorption is directly observed for the first time. The stepwise crystallographic visualization of the incorporation of I2 within a porous MOF is presented, wherein the preferred binding motifs throughout the uptake process are identified...
April 1, 2017: Chemical Science
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