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https://www.readbyqxmd.com/read/28346776/proton-exchange-in-a-paramagnetic-chemical-exchange-saturation-transfer-agent-from-experimental-studies-and-ab-initio-metadynamics-simulation
#1
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/28346215/enhanced-optoelectronic-quality-of-perovskite-films-with-excess-ch3nh3i-for-high-efficient-solar-cells-in-ambient-air
#2
Yunhai Zhang, Huiru Lv, Can Cui, Lingbo Xu, Peng Wang, Hao Wang, Xuegong Yu, Jiangsheng Xie, Jiabin Huang, Zeguo Tang, Deren Yang
The solution-processed polycrystalline perovskite film contributes critically to the high photovoltaic performance of perovskite based solar cells (PSCs). The inevitable electronic trap states at grain boundaries and the intrinsic defects such as metallic lead (Pb0) and halide vacancies in perovskite film cause serious carrier recombination loss. Furthermore, the film can easily decompose into PbI2 in moisture atmosphere. Here, we introduce a simple strategy through a small increase in methylammonium iodide (CH3NH3I, MAI) molar proportion (5%) for perovskite fabrication in ambient air with a ~50% relative humidity...
March 27, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28345709/a-study-of-asymmetrical-mixed-valent-mo2-mo2-complexes-in-the-class-iii-regime
#3
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/28342396/high-resolution-cryo-em-the-nuts-and-bolts
#4
REVIEW
Dominika Elmlund, Sarah N Le, Hans Elmlund
Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. Successful high-resolution structure determination by cryo-EM always depends on the quality of the protein sample. While structural heterogeneity remains a key challenge for cryo-EM, it also represents a rare opportunity to study the intrinsic conformational flexibility of macromolecular assemblies...
March 22, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28342286/switching-aurora-a-kinase-on-and-off-at-an-allosteric-site
#5
REVIEW
Richard Bayliss, Selena G Burgess, Patrick J McIntyre
Protein kinases are central players in the regulation of cell cycle and signalling pathways. Their catalytic activities are strictly regulated through post-translational modifications and protein-protein interactions that control switching between inactive and active states. These states have been studied extensively using protein crystallography, although the dynamic nature of protein kinases makes it difficult to capture all relevant states. Here we describe two recent structures of Aurora-A kinase that trap its active and inactive states...
March 25, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28342173/metal-ions-binding-t4-lysozyme-as-an-intramolecular-protein-purification-tag-compatible-with-x-ray-crystallography
#6
Evzen Boura, Adriana Baumlova, Dominika Chalupska, Anna Dubankova, Martin Klima
Phage T4 lysozyme is a well folded and highly soluble protein that is widely used as an insertion tag to improve solubility and crystallization properties of poorly behaved recombinant proteins. It has been used in the fusion protein strategy to facilitate crystallization of various proteins including multiple G protein-coupled receptors, lipid kinases, or sterol binding proteins. Here, we present a structural and biochemical characterization of its novel, metal ions-binding mutant (mbT4L). We demonstrate that mbT4L can be used as a purification tag in the immobilized-metal affinity chromatography and that, in many respects, it is superior to the conventional hexahistidine tag...
March 25, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28341883/conformational-dynamics-play-important-roles-upon-the-function-of-n-acetylglutamate-kinase
#7
REVIEW
Xiaorong Yang
N-acetylglutamate kinase (NAGK) catalyzes the phosphorylation of N-acetylglutamate. In many bacteria, NAGK catalysis is the rate controlling step in the L-arginine biosynthesis pathway from glutamate to L-arginine and is allosterically inhibited by L-arginine. Many data show that conformational dynamics of NAGKs are essential for their function. The demonstration of the conformational mechanism provides a potential way to improve the yield of arginine. Due to the lack of NAGK catalysis step in arginine synthesis route of mammals, the elucidation of the dynamic mechanism can also provide a way to design a new antivirus drug...
March 24, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28340512/activation-mechanisms-of-%C3%AE-v%C3%AE-3-integrin-by-binding-to-fibronectin-a-computational-study
#8
Lingyun Wang, Di Pan, Qi Yan, Yuhua Song
Integrin αVβ3 plays an important role in regulating cellular activities and in human diseases. Although the structure of αVβ3 has been studied by crystallography and electron microscopy, the detailed activation mechanism of integrin αVβ3 induced by fibronectin (Fn) remains unclear. In this study, we investigated the conformational and dynamical motion changes of Mn(2+) -bound integrin αVβ3 by binding to Fn with molecular dynamics simulations. Results showed that Fn binding to integrin αVβ3 caused the changes of the conformational flexibility of αVβ3 domains, the essential mode of motion for the domains of αV subunit and β3 subunit and the degrees of correlated motion of residues between the domains of αV subunit and β3 subunit of integrin αVβ3...
March 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28340354/mechanism-of-substrate-translocation-in-an-alternating-access-transporter
#9
Naomi R Latorraca, Nathan M Fastman, A J Venkatakrishnan, Wolf B Frommer, Ron O Dror, Liang Feng
Transporters shuttle molecules across cell membranes by alternating among distinct conformational states. Fundamental questions remain about how transporters transition between states and how such structural rearrangements regulate substrate translocation. Here, we capture the translocation process by crystallography and unguided molecular dynamics simulations, providing an atomic-level description of alternating access transport. Simulations of a SWEET-family transporter initiated from an outward-open, glucose-bound structure reported here spontaneously adopt occluded and inward-open conformations...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28340337/structural-basis-of-rna-polymerase-i-transcription-initiation
#10
Christoph Engel, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane Oberthuer, Carlo Baejen, Carrie Bernecky, Patrick Cramer
Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28338266/accelerated-oxygen-atom-transfer-and-c-h-bond-oxygenation-by-remote-redox-changes-in-fe3-mn-iodosobenzene-adducts
#11
Graham de Ruiter, Kurtis M Carsch, Sheraz Gul, Ruchira Chatterjee, Niklas B Thompson, Michael K Takase, Junko Yano, Theodor Agapie
We report the synthesis, characterization, and reactivity of [LFe3 (PhPz)3 OMn((s) PhIO)][OTf]x (3: x=2; 4: x=3), where 4 is one of very few examples of iodosobenzene-metal adducts characterized by X-ray crystallography. Access to these rare heterometallic clusters enabled differentiation of the metal centers involved in oxygen atom transfer (Mn) or redox modulation (Fe). Specifically, (57) Fe Mössbauer and X-ray absorption spectroscopy provided unique insights into how changes in oxidation state (Fe(III)2 Fe(II) Mn(II) vs...
March 24, 2017: Angewandte Chemie
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
#12
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/28337982/the-fourth-crystallographic-closest-packing-unveiled-in-the-gold-nanocluster-crystal
#13
Zibao Gan, Jishi Chen, Juan Wang, Chengming Wang, Man-Bo Li, Chuanhao Yao, Shengli Zhuang, An Xu, Lingling Li, Zhikun Wu
Metal nanoclusters have recently attracted extensive interest not only for fundamental scientific research, but also for practical applications. For fundamental scientific research, it is of major importance to explore the internal structure and crystallographic arrangement. Herein, we synthesize a gold nanocluster whose composition is determined to be Au60S6(SCH2Ph)36 by using electrospray ionization mass spectrometry and single crystal X-ray crystallography (SCXC). SCXC also reveals that Au60S6(SCH2Ph)36 consists of a fcc-like Au20 kernel protected by a pair of giant Au20S3(SCH2Ph)18 staple motifs, which contain 6 tetrahedral-coordinate μ4-S atoms not previously reported in the Au-S interface...
March 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28337319/bifunctional-inhibitors-as-a-new-tool-to-reduce-cancer-cell-invasion-by-impairing-mmp-9-homodimerization
#14
Elisa Nuti, Lea Rosalia, Doretta Cuffaro, Caterina Camodeca, Chiara Giacomelli, Eleonora Da Pozzo, Tiziano Tuccinardi, Barbara Costa, Claudia Antoni, Laura Vera, Lidia Ciccone, Elisabetta Orlandini, Susanna Nencetti, Vincent Dive, Claudia Martini, Enrico A Stura, Armando Rossello
Protein homodimers play important roles in physiological and pathological processes, including cancer invasion and metastasis. Recently, MMP-9 natural homodimerization via the PEX domain has been correlated with high migration rates of aggressive cancer cells. Here we propose that bifunctional MMP-9 inhibitors designed to impair natural MMP-9 homodimerization promoted by PEX-PEX interactions might be an effective tool to fight cancer cell invasion. Elaborating a previously described dimeric hydroxamate inhibitor 1, new ligands were synthesized with different linker lengths and branch points...
March 9, 2017: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28336142/novel-11-norbetaenone-isolated-from-an-entomopathogenic-fungus-lecanicillium-antillanum
#15
Chi-Ying Li, I-Wen Lo, Shih-Wei Wang, Tsong-Long Hwang, Yu-Ming Chung, Yuan-Bin Cheng, Sung-Pin Tseng, Yi-Hung Liu, Yu-Ming Hsu, Shu-Rong Chen, Hao-Chun Hu, Fang-Rong Chang, Yang-Chang Wu
A novel nor-betaenone compound, 11-norbetaenone (1), was isolated from the culture broth of an entomopathogenic fungus Lecanicillium antillanum. The structure was determined on the basis of 1D and 2D NMR spectroscopic data. The absolute stereochemistry of 1 was further confirmed by X-ray single crystallography analysis. It is the first secondary metabolite reported from the species Lecanicillium antillanum. And it is also the first time that a betaenone-type compound was isolated from the genus Lecanicillium...
March 11, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28334744/stabilization-of-rna-hairpins-using-non-nucleotide-linkers-and-circularization
#16
Agnieszka Kiliszek, Leszek Blaszczyk, Ryszard Kierzek, Wojciech Rypniewski
An RNA hairpin is an essential structural element of RNA. Hairpins play crucial roles in gene expression and intermolecular recognition but are also involved in the pathogenesis of some congenital diseases. Structural studies of the hairpin motifs are impeded by their thermodynamic instability, as they tend to unfold to form duplexes, especially at high concentrations required for crystallography or nuclear magnetic resonance spectroscopy. We have elaborated techniques to stabilize the RNA hairpins by linking the free ends of the RNA strand at the base of the hairpin stem...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334480/zirconacyclopentadiene-annulated-polycyclic-aromatic-hydrocarbons
#17
Gavin R Kiel, Micah S Ziegler, T Don Tilley
Syntheses of large polycyclic aromatic hydrocarbons (PAHs) and graphene nanostructures demand methods that are capable of selectively and efficiently fusing large numbers of aromatic rings, yet such methods remain scarce. Herein, we report a new approach that is based on the quantitative intramolecular reductive cyclization of an oligo(diyne) with a low-valent zirconocene reagent, which gives a PAH with one or more annulated zirconacyclopentadienes (ZrPAHs). The efficiency of this process is demonstrated by a high-yielding fivefold intramolecular coupling to form a helical ZrPAH with 16 fused rings (from a precursor with no fused rings)...
March 23, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28334201/critical-evaluation-of-bioinformatics-tools-for-the-prediction-of-protein-crystallization-propensity
#18
Huilin Wang, Liubin Feng, Geoffrey I Webb, Lukasz Kurgan, Jiangning Song, Donghai Lin
X-ray crystallography is the main tool for structural determination of proteins. Yet, the underlying crystallization process is costly, has a high attrition rate and involves a series of trial-and-error attempts to obtain diffraction-quality crystals. The Structural Genomics Consortium aims to systematically solve representative structures of major protein-fold classes using primarily high-throughput X-ray crystallography. The attrition rate of these efforts can be improved by selection of proteins that are potentially easier to be crystallized...
February 27, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28333456/calixsmaragdyrin-a-versatile-ligand-for-coordination-complexes
#19
Tamal Chatterjee, Brian Molnar, G G Theophall, Way-Zen Lee, K V Lakshmi, Mangalampalli Ravikanth
The Ru(II) and BF2 complexes of calixsmaragdyrin were prepared under simple reaction conditions and characterized by HR-MS, 1D and 2D NMR spectroscopy, optical spectroscopy, and electrochemistry, and the structure of the Ru(II) complex of calixsmaragdyrin was elucidated by X-ray crystallography. The crystal structure of the Ru(II) complex revealed that the Ru(II) ion is hexacoordinate with the three pyrrole nitrogen ligands from the tripyrrin unit of the calixsmaragdyrin macrocycle, and the remaining coordination sites of Ru(II) ion were occupied by two carbonyl groups and one hydroxyl (-OH) group...
March 23, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28330825/streamlining-workflow-and-automation-to-accelerate-laboratory-scale-protein-production
#20
REVIEW
Jennifer Konczal, Christopher H Gray
Protein production facilities are often required to produce diverse arrays of proteins for demanding methodologies including crystallography, NMR, ITC and other reagent intensive techniques. It is common for these teams to find themselves a bottleneck in the pipeline of ambitious projects. This pressure to deliver has resulted in the evolution of many novel methods to increase capacity and throughput at all stages in the pipeline for generation of recombinant proteins. This review aims to describe current and emerging options to accelerate the success of protein production in Escherichia coli...
March 18, 2017: Protein Expression and Purification
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