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https://www.readbyqxmd.com/read/28636907/epr-spectroscopy-targets-structural-changes-in-the-e-%C3%A2-coli-membrane-fusion-cusb-upon-cu-i-binding
#1
Aviv Meir, Ahmad Abdelhai, Yoni Moskovitz, Sharon Ruthstein
Bacterial cells have developed sophisticated systems to deal with the toxicity of metal ions. Escherichia coli CusCFBA is a complex efflux system, responsible for transferring Cu(I) and Ag(I) ions; this system, located in the periplasm, involves four proteins, CusA, CusB, CusC, and CusF. CusA, CusB, and CusC are connected to one another in an oligomerization ratio of 3:6:3 CusA/CusB/CusC to form the CusCBA periplasm membrane transporter. CusB is an adaptor protein that connects the two membrane proteins CusA (inner membrane) and CusC (outer membrane)...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636680/unifying-the-microscopic-picture-of-his-containing-turns-from-gas-phase-model-peptides-to-crystallized-proteins
#2
Woon Yong Sohn, Sana Habka, Eric Gloaguen, Michel Mons
The presence in crystallized proteins of a local anchoring between the side chain of a His residue, located in the central position of a γ- or β-turn, and its local main chain environment, was assessed by the comparison of protein structures with relevant isolated model peptides. Gas phase laser spectroscopy, combined with relevant quantum chemistry methods, was used to characterize the γ- and β-turn structures in these model peptides. A conformer-selective NH stretch infrared study provided evidence for the formation in vacuo of two types of short-range H-bonded motifs, labelled ε-6(δ) and δ-(δ)7/π(H), bridging the His side chain (in its gauche+ rotamer) to the neighbouring NH(i) and CO(i) sites of the backbone; each side chain-backbone motif was found to be specific of the tautomer (ε or δ) adopted by the His side chain in its neutral form...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28636542/niaoduqing-granules-relieve-chronic-kidney-disease-symptoms-by-decreasing-renal-fibrosis-and-anemia
#3
Xu Wang, Suyun Yu, Qi Jia, Lichuan Chen, Jinqiu Zhong, Yanhong Pan, Peiliang Shen, Yin Shen, Siliang Wang, Zhonghong Wei, Yuzhu Cao, Yin Lu
NiaoDuQing (NDQ) granules, a traditional Chinese medicine, has been clinically used in China for over fourteen years to treat chronic kidney disease (CKD). To elucidate the mechanisms underlying the therapeutic benefits of NDQ, we designed an approach incorporating chemoinformatics, bioinformatics, network biology methods, and cellular and molecular biology experiments. A total of 182 active compounds were identified in NDQ granules, and 397 putative targets associated with different diseases were derived through ADME modelling and target prediction tools...
June 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636461/genice-a-novel-framework-for-gene-network-inference-by-clustering-exhaustive-search-and-multivariate-analysis
#4
Ricardo de Souza Jacomini, David Correa Martins-Jr, Felipe Leno da Silva, Anna Helena Reali Costa
Gene network (GN) inference from temporal gene expression data is a crucial and challenging problem in systems biology. Expression data sets usually consist of dozens of temporal samples, while networks consist of thousands of genes, thus rendering many inference methods unfeasible in practice. To improve the scalability of GN inference methods, we propose a novel framework called GeNICE, based on probabilistic GNs; the main novelty is the introduction of a clustering procedure to group genes with related expression profiles and to provide an approximate solution with reduced computational complexity...
June 21, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28636049/neutral-mixed-metal-coordination-polymers-based-on-a-ditopic-acetylacetonate-mg-ii-and-ag-i-syntheses-characterization-and-solvent-dependent-topologies
#5
Qianqian Guo, Ulli Englert
The complex [Mg(acacCN)2(H2O)2] (acacCN = 3-cyanoacetylacetonate) has been synthesized in good yield and fully characterized. It represents a versatile labile precursor for an anionic tris(ligand) complex which is crosslinked with Ag(i) to five different neutral bimetallic networks; all of them are solvates. Four of these extended structures share the same framework stoichiometry Ag[Mg(acacCN)3] and only differ in their solvent content. The co-crystallized solvent molecules decide the topological outcome of the crosslinking: the four compounds can be classified into two isomorphous 3D networks and two non-isomorphous but related 2D layer structures...
June 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28635674/exploring-wound-healing-genomic-machinery-with-a-network-based-approach
#6
Francesca Vitali, Simone Marini, Martina Balli, Hanne Grosemans, Maurilio Sampaolesi, Yves A Lussier, Maria Gabriella Cusella De Angelis, Riccardo Bellazzi
The molecular mechanisms underlying tissue regeneration and wound healing are still poorly understood despite their importance. In this paper we develop a bioinformatics approach, combining biology and network theory to drive experiments for better understanding the genetic underpinnings of wound healing mechanisms and for selecting potential drug targets. We start by selecting literature-relevant genes in murine wound healing, and inferring from them a Protein-Protein Interaction (PPI) network. Then, we analyze the network to rank wound healing-related genes according to their topological properties...
June 21, 2017: Pharmaceuticals
https://www.readbyqxmd.com/read/28635300/pyridine-dinucleotides-from-molecules-to-man
#7
Joshua P Fessel, William M Oldham
SIGNIFICANCE: Pyridine dinucleotides, NAD and NADP, were discovered over 100 years ago as necessary cofactors for fermentation in yeast extracts. Since that time, these molecules have been recognized as fundamental players in a variety of cellular processes, including energy metabolism, redox homeostasis, cellular signaling, and gene transcription, among many others. Given their critical role as mediators of cellular responses to metabolic perturbations, it is unsurprising that dysregulation of NAD and NADP metabolism has been associated with the pathobiology of many chronic human diseases...
June 21, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28634865/dynamics-of-tobacco-dna-topoisomerases-ii-in-cell-cycle-regulation-to-manage-topological-constrains-during-replication-transcription-and-mitotic-chromosome-condensation-and-segregation
#8
Badri Nath Singh, V Mohan Murali Achary, Varakumar Panditi, Sudhir K Sopory, Malireddy K Reddy
The topoisomerase II expression varies as a function of cell proliferation. Maximal topoisomerase II expression was tightly coupled to S phase and G2/M phase via both transcriptional and post-transcriptional regulation. Investigation in meiosis using pollen mother cells also revealed that it is not the major component of meiotic chromosomes, it seems to diffuse out once meiotic chromosomal condensation is completed. Synchronized tobacco BY-2 cell cultures were used to study the role of topoisomerase II in various stages of the cell cycle...
June 20, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28634341/terahertz-circular-airy-vortex-beams
#9
Changming Liu, Jinsong Liu, Liting Niu, Xuli Wei, Kejia Wang, Zhengang Yang
Vortex beams have received considerable research interests both in optical and millimeter-wave domain since its potential to be utilized in the wireless communications and novel imaging systems. Many well-known optical beams have been demonstrated to carry orbital angular momentum (OAM), such as Laguerre-Gaussian beams and high-order Bessel beams. Recently, the radially symmetric Airy beams that exhibit an abruptly autofocusing feature are also demonstrated to be capable of carrying OAM in the optical domain...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634254/widespread-paleopolyploidy-gene-tree-conflict-and-recalcitrant-relationships-among-the-carnivorous-caryophyllales
#10
Joseph F Walker, Ya Yang, Michael J Moore, Jessica Mikenas, Alfonso Timoneda, Samuel F Brockington, Stephen A Smith
PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved. METHODS: To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced 10 transcriptomes, including all the carnivorous genera except those in the rare West African liana family Dioncophyllaceae...
June 20, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28633299/structural-covariance-networks-in-children-with-autism-or-adhd
#11
R A I Bethlehem, R Romero-Garcia, E Mak, E T Bullmore, S Baron-Cohen
Background: While autism and attention-deficit/hyperactivity disorder (ADHD) are considered distinct conditions from a diagnostic perspective, clinically they share some phenotypic features and have high comorbidity. Regardless, most studies have focused on only one condition, with considerable heterogeneity in their results. Taking a dual-condition approach might help elucidate shared and distinct neural characteristics. Method: Graph theory was used to analyse topological properties of structural covariance networks across both conditions and relative to a neurotypical (NT; n = 87) group using data from the ABIDE (autism; n = 62) and ADHD-200 datasets (ADHD; n = 69)...
June 13, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28632985/healable-reconfigurable-reprocessable-thermoset-shape-memory-polymer-with-highly-tunable-topological-rearrangement-kinetics
#12
Zizheng Fang, Ning Zheng, Qian Zhao, Tao Xie
The unique capability of topological rearrangement for dynamic covalent polymer networks has enabled various unusual properties (self-healing, solid-state plasticity, and reprocessability) that are not found in conventional thermosets. Achieving these properties in one network in a synergetic fashion can open up new opportunities for shape memory polymer. To accomplish such a goal, the freedom to tune topological rearrangement kinetics is critical. This is, however, challenging to achieve. In this work, two sets of dynamic bonds (urethane and hindered urea) are incorporated into a hybrid network for synthesizing shape memory poly(urea-urethane)...
June 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28632429/on-stable-states-in-a-topologically-driven-protein-folding-model
#13
Zheng Dai, David Becerra, Jérôme Waldispühl
Theoretical models of protein folding often make simplifying assumptions that allow analysis, yielding interesting theoretical results. In this article, we study models where folding dynamics is primarily driven by local topological features in an iterative manner. We illustrate the merit of the proposed approach through its ability to simulate realistic protein folding processes even when the sequence content information is reduced to just hydrophobic and polar. We then analyze our models and show that under our simple assumptions, certain structures are inherently unstable, and that determining whether structures can be stable is an [Formula: see text]-hard problem...
June 20, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28632333/from-chemical-topology-to-molecular-machines-nobel-lecture
#14
REVIEW
Jean-Pierre Sauvage
To a large extent, the field of "molecular machines" started after several groups were able to prepare, reasonably easily, interlocking ring compounds (named catenanes for compounds consisting of interlocking rings and rotaxanes for rings threaded by molecular filaments or axes). Important families of molecular machines not belonging to the interlocking world were also designed, prepared, and studied but, for most of them, their elaboration was more recent than that of catenanes or rotaxanes. Since the creation of interlocking ring molecules is so important in relation to the molecular machinery area, we will start with this aspect of our work...
June 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28632320/synthesis-optoelectronic-and-self-assembly-properties-of-diazadioxaacene-derivatives
#15
Jinchong Xiao, Huhang Pan, Jingdan Duan, Guixia Zhai, Pengcheng Jin, Xiaohui Zhao, Li Jiang
Two novel diazadioxaacene derivatives (ADOP and ADOQ) have been successfully synthesized and characterized. Their single crystal analyses disclose that molecule ADOP forms a twisted topology configuration, while ADOQ adopts a reclining chair architecture. Both of them emit strong blue fluorescence in organic solvents. Moreover, they can self assemble to form regular nanobelts and nanowires respectively via a simple surfactant-assisted method.
June 20, 2017: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/28632141/phase-transitions-of-the-dimerized-kane-mele-model-with-without-the-strong-interaction
#16
Tao Du, Yue-Xun Li, Yan Li, He-Lin Lu, Hui Zhang
The dimerized Kane-Mele model with/without the strong interaction is studied using analytical methods. The boundary of the topological phase transition of the model without strong interaction is obtained. Our results show that the occurrence of the transition only depends on dimerized parameter α . From the one-particle spectrum, we obtain the completed phase diagram including the quantum spin Hall (QSH) state and the topologically trivial insulator. Then, using different mean-field methods, we investigate the Mott transition and the magnetic transition of the strongly correlated dimerized Kane-Mele model...
June 20, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28631801/morphology-of-elastic-nematic-liquid-crystal-membranes
#17
Pardis Rofouie, Damiano Pasini, Alejandro D Rey
Liquid crystalline phases found in many biological materials, such as actin, DNA, cellulose, and collagen can be responsible for the deformation of cell membranes. In this paper, cell membrane deformation is investigated through the coupling between liquid crystal anisotropy and membrane bending elasticity. The generalized shape equation for anisotropic interfaces, which resort to the Cahn-Hoffman capillarity vector, the Rapini-Papoular anchoring energy, and the Helfrich elastic energy, is applied to gain insight into the deformation of closed liquid crystal membranes...
June 20, 2017: Soft Matter
https://www.readbyqxmd.com/read/28631616/on-the-dynamics-of-perching-manoeuvres-with-low-aspect-ratio-planforms
#18
J N Fernando, D E Rival
The dynamics of a simple perching manoeuvre are investigated using circular and aspect-ratio-two elliptical flat plates, as abstractions of low-aspect-ratio planforms observed in highly-manoeuvrable birds. The perching kinematic investigated in this study involves a pitch-up motion from an angle of attack of [Formula: see text] to [Formula: see text], while simultaneously decelerating. This motion is defined by the shape change number, [Formula: see text], which acts as a measure of the relative contributions of added-mass and circulatory effects...
June 20, 2017: Bioinspiration & Biomimetics
https://www.readbyqxmd.com/read/28631354/cross-population-myelination-covariance-of-human-cerebral-cortex
#19
Zhiwei Ma, Nanyin Zhang
Cross-population covariance of brain morphometric quantities provides a measure of interareal connectivity, as it is believed to be determined by the coordinated neurodevelopment of connected brain regions. Although useful, structural covariance analysis predominantly employed bulky morphological measures with mixed compartments, whereas studies of the structural covariance of any specific subdivisions such as myelin are rare. Characterizing myelination covariance is of interest, as it will reveal connectivity patterns determined by coordinated development of myeloarchitecture between brain regions...
June 20, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28630971/2-thiouracil-intersystem-crossing-photodynamics-studied-by-wavelength-dependent-photoelectron-and-transient-absorption-spectroscopies
#20
José A Sánchez-Rodríguez, Abed Mohamadzade, Sebastian Mai, Brennan Ashwood, Marvin Pollum, Philipp Marquetand, Leticia González, Carlos E Crespo-Hernández, Susanne Ullrich
Single-atom substitution within a natural nucleobase-such as replacing oxygen by sulfur in uracil-can result in drastic changes in the relaxation dynamics after UV excitation. While the photodynamics of natural nucleobases like uracil are dominated by pathways along singlet excited states, the photodynamics of thiobases like 2-thiouracil populate the triplet manifold with near unity quantum yield. In the present study, a synergistic approach based on time-resolved photoelectron spectroscopy (TRPES), time-resolved absorption spectroscopy (TRAS), and ab initio computations has been particularly successful at unraveling the underlying photophysical principles and describing the dissimilarities between the natural and substituted nucleobases...
June 20, 2017: Physical Chemistry Chemical Physics: PCCP
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