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https://www.readbyqxmd.com/read/28817608/data-driven-coarse-graining-of-large-biomolecular-structures
#1
Yi-Ling Chen, Michael Habeck
Advances in experimental and computational techniques allow us to study the structure and dynamics of large biomolecular assemblies at increasingly higher resolution. However, with increasing structural detail it can be challenging to unravel the mechanism underlying the function of molecular machines. One reason is that atomistic simulations become computationally prohibitive. Moreover it is difficult to rationalize the functional mechanism of systems composed of tens of thousands to millions of atoms by following each atom's movements...
2017: PloS One
https://www.readbyqxmd.com/read/28817096/time-resolved-study-of-nanomorphology-and-nanomechanic-change-of-early-stage-mineralized-electrospun-poly-lactic-acid-fiber-by-scanning-electron-microscopy-raman-spectroscopy-and-atomic-force-microscopy
#2
Mengmeng Wang, Yin Cai, Bo Zhao, Peizhi Zhu
In this study, scanning electron microscopy (SEM), Raman spectroscopy and high-resolution atomic force microscopy (AFM) were used to reveal the early-stage change of nanomorphology and nanomechanical properties of poly(lactic acid) (PLA) fibers in a time-resolved manner during the mineralization process. Electrospun PLA nanofibers were soaked in simulated body fluid (SBF) for different periods of time (0, 1, 3, 5, 7 and 21 days) at 10 °C, much lower than the conventional 37 °C, to simulate the slow biomineralization process...
August 17, 2017: Nanomaterials
https://www.readbyqxmd.com/read/28816865/liquid-crystal-spatial-light-modulators-for-simulating-zonal-multifocal-lenses
#3
Yiyu Li, Arthur Bradley, Renfeng Xu, Pete S Kollbaum
SIGNIFICANCE: To maximize efficiency of the normally lengthy and costly multizone lens design and testing process, it is advantageous to evaluate the potential efficacy of a design as thoroughly as possible prior to lens fabrication and on-eye testing. The current work describes an ex vivo approach of optical design testing. PURPOSE: The aim of this study was to describe a system capable of examining the optical characteristics of multizone bifocal and multifocal optics by subaperture stitching using liquid crystal technologies...
August 14, 2017: Optometry and Vision Science: Official Publication of the American Academy of Optometry
https://www.readbyqxmd.com/read/28816592/two-faced-fcab-prevents-polymerization-with-vegf-and-reveals-thermodynamics-and-the-2-15%C3%A2-%C3%A3-crystal-structure-of-the-complex
#4
Elisabeth Lobner, Anne-Sophie Humm, Georg Mlynek, Konstantin Kubinger, Michael Kitzmüller, Michael W Traxlmayr, Kristina Djinović-Carugo, Christian Obinger
Fcabs (Fc domain with antigen-binding sites) are promising novel therapeutics. By engineering of the C-terminal loops of the CH3 domains, two antigen binding sites can be inserted in close proximity. In order to elucidate the binding mode(s) between homodimeric Fcabs and small homodimeric antigens, the interaction between the Fcabs 448 and CT6 (having the AB, CD and EF loops and the C-termini engineered) with homodimeric VEGF was investigated. The crystal structures of these Fcabs, which form polymers with the antigen VEGF in solution, were determined...
August 17, 2017: MAbs
https://www.readbyqxmd.com/read/28816462/-1-h-detected-redor-with-fast-magic-angle-spinning-of-a-deuterated-protein
#5
Manali Ghosh, Chad M Rienstra
Rotational echo double resonance (REDOR) is a highly successful method for heteronuclear distance determination in biological solid-state NMR, and 1H detection methods have emerged in recent years as a powerful approach to improving sensitivity and resolution for small sample quantities by utilizing fast magic-angle spinning (>30 kHz) and deuteration strategies. In theory, involving 1H as one of the spins for measuring REDOR effects can greatly increase the distance measurement range, but few experiments of this type have been reported...
August 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28816437/selective-targeting-by-a-mechanism-based-inactivator-against-plp-dependent-enzymes-mechanisms-of-inactivation-and-alternative-turnover
#6
Romila Mascarenhas, Hoang V Le, Kenneth D Clevenger, Helaina J Lehrer, Dagmar Ringe, Neil L Kelleher, Richard B Silverman, Dali Liu
Potent mechanism-based inactivators can be rationally designed against PLP-dependent drug targets, such as ornithine aminotransferase (OAT) or γ-aminobutyric acid aminotransferase (GABA-AT). An important challenge, however, is the lack of selectivity towards other PLP-dependent off-target enzymes, because of similarities in mechanisms of all PLP-dependent aminotransferase reactions. On the basis of complex crystal structures, we investigate the inactivation mechanism of OAT, a hepatocellular carcinoma (HCC) target, by (1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid (FCP), a known inactivator of GABA-AT...
August 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/28816317/evaluation-of-mapping-schemes-for-systematic-coarse-graining-of-higher-alkanes
#7
Marco Dallavalle, Nico F A van der Vegt
A model is introduced to explore the influence of different coarse-grained (CG) resolutions on the structural and thermodynamic properties of higher alkanes. Four different mapping schemes are considered, for which the potentials are derived using the conditional reversible work (CRW) method. The CRW method is a bottom-up coarse-graining procedure, which derives effective pair potentials between nonbonded chemical groups defined by the mapping scheme from the underlying molecular interactions in a quick, inexpensive way...
August 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28816186/reliability-of-orthopantomography-and-cone-beam-computed-tomography-in-presurgical-implant-planning-a-clinical-study
#8
Jasjit Sahota, Aditya Bhatia, Megha Gupta, Vishal Singh, Juhi Soni, Richa Soni
BACKGROUND: Preoperative diagnosis and treatment planning are fundamental requirements to ensure success rate of implant. Cone-beam computed tomography (CBCT) provides all three dimensions and has been proved as a tool for radiology, especially in the success of implant. This study was conducted to evaluate the reliability of orthopantomography (OPG) and CBCT in presurgical implant planning. MATERIALS AND METHODS: The study was conducted on 110 partially or completely edentulous adult patients (male 50 and female 60)...
August 1, 2017: Journal of Contemporary Dental Practice
https://www.readbyqxmd.com/read/28815647/wildlife-disease-ecology-from-the-individual-to-the-population-insights-from-a-long-term-study-of-a-naturally-infected-european-badger-population
#9
Jenni L McDonald, Andrew Robertson, Matthew J Silk
1. Long-term individual-based datasets on host-pathogen systems are a rare and valuable resource for understanding the infectious disease dynamics in wildlife. A study of European badgers (Meles meles) naturally infected with bovine tuberculosis (bTB) at Woodchester Park in Gloucestershire (UK) has produced a unique dataset, facilitating investigation of a diverse range of epidemiological and ecological questions with implications for disease management. 2. Since the 1970s this badger population has been monitored with a systematic mark-recapture regime yielding a dataset of >15,000 captures of >3000 individuals, providing detailed individual life-history, morphometric, genetic, reproductive and disease data...
August 16, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28815625/association-of-transcallosal-motor-fibres-with-function-of-both-hands-after-unilateral-neonatal-arterial-ischemic-stroke
#10
Samuel Groeschel, Lucie Hertz-Pannier, Matthieu Delion, Sébastien Loustau, Béatrice Husson, Manoelle Kossorotoff, Cyrille Renaud, Sylvie Nguyen The Tich, Stéphane Chabrier, Mickael Dinomais
AIM: The objective of this study was to investigate the involvement of the motor fibres of the corpus callosum after unilateral neonatal arterial ischemic stroke (NAIS) of the middle cerebral artery territory and the relationship to both ipsilesional and contralesional hand function. METHOD: Using high-resolution structural magnetic resonance imaging (MRI), functional MRI, and magnetic resonance diffusion-tractography, we compared the midsagittal area of the motor part of the corpus callosum (defined by the fibres connecting the precentral gyri) between 33 7-year-old children after unilateral NAIS and 31 typically developing 7-year-old children...
August 17, 2017: Developmental Medicine and Child Neurology
https://www.readbyqxmd.com/read/28815458/backbone-and-side-chain-resonance-assignments-of-ca-2-4-calmodulin-bound-to-beta-calcineurin-a-cambd-peptide
#11
C Andrew Fowler, Maria F Núñez Hernandez, Susan E O'Donnell, Liping Yu, Madeline A Shea
Calcineurin (CaN) is a heterodimeric and highly conserved serine/threonine phosphatase (PP2B) that plays a critical role in coupling calcium signals to physiological processes including embryonic cardiac development, NF-AT-regulated gene expression in immune responses, and apoptosis. The catalytic subunit (CaNA) has three isoforms (α, β, and γ,) in humans and seven isoforms in Paramecium. In all eukaryotes, the EF-hand protein calmodulin (CaM) regulates CaN activity in a calcium-dependent manner. The N- and C-domains of CaM (CaMN and CaMC) recognize a CaM-binding domain (CaMBD) within an intrinsically disordered region of CaNA that precedes the auto-inhibitory domain (AID) of CaNA...
August 16, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28814796/crispr-cas9-mediated-labelling-allows-for-single-molecule-imaging-and-resolution
#12
Abdullah O Khan, Victoria A Simms, Jeremy A Pike, Steven G Thomas, Neil V Morgan
Single molecule imaging approaches like dSTORM and PALM resolve structures at 10-20 nm, and allow for unique insights into protein stoichiometry and spatial relationships. However, key obstacles remain in developing highly accurate quantitative single molecule approaches. The genomic tagging of PALM fluorophores through CRISPR-Cas9 offers an excellent opportunity for generating stable cell lines expressing a defined single molecule probe at endogenous levels, without the biological disruption and variability inherent to transfection...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28814668/injury-induced-actin-cytoskeleton-reorganization-in-podocytes-revealed-by-super-resolution-microscopy
#13
Hani Y Suleiman, Robyn Roth, Sanjay Jain, John E Heuser, Andrey S Shaw, Jeffrey H Miner
The architectural integrity of tissues requires complex interactions, both between cells and between cells and the extracellular matrix. Fundamental to cell and tissue homeostasis are the specific mechanical forces conveyed by the actomyosin cytoskeleton. Here we used super-resolution imaging methods to visualize the actin cytoskeleton in the kidney glomerulus, an organized collection of capillaries that filters the blood to make the primary urine. Our analysis of both mouse and human glomeruli reveals a network of myosin IIA-containing contractile actin cables within podocyte cell bodies and major processes at the outer aspects of the glomerular tuft...
August 17, 2017: JCI Insight
https://www.readbyqxmd.com/read/28814404/adaptive-spatiotemporal-changes-in-morphology-anatomy-and-mechanics-during-the-ontogeny-of-subshrubs-with-square-shaped-stems
#14
Ruwen Kaminski, Thomas Speck, Olga Speck
PREMISE OF THE STUDY: Plant stems can be regarded as fiber-reinforced structures characterized by anatomical heterogeneity, mechanical anisotropy, and adaptability to changing internal and external constraints. Our study focused on adaptive spatiotemporal changes in morphology, anatomy, and mechanical properties during the ontogeny of Leonurus cardiaca L. (Lamiaceae) internodes, proving considerable functional adaptability. METHODS: Four-point bending tests and torsional tests were carried out on the same internodes to measure flexural and torsional stiffness...
August 16, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28814181/full-mouth-intraoral-radiographic-survey-in-rabbits
#15
Adriana Regalado, Loïc Legendre
Dental pathologies are highly prevalent in pet rabbit populations, making oral radiography an essential tool in the evaluation of lagomorph dentitions. The unique anatomy of the rabbit's mouth limits the examination of the conscious animal to the rostral portion of it's mouth. In addition, the oral examination of an aradicular hypsodont tooth is restricted to the short coronal fraction of its crown. Erstwhile images obtained by the extraoral technique were once considered the most practical and informative tool in rabbit dentistry; however, limited visualization of the key structures of individual teeth became the major drawback of this technique...
September 2017: Journal of Veterinary Dentistry
https://www.readbyqxmd.com/read/28813668/subnuclear-relocalization-of-structure-specific-endonucleases-in-response-to-dna-damage
#16
Irene Saugar, Alberto Jiménez-Martín, José Antonio Tercero
Structure-specific endonucleases contribute to the maintenance of genome integrity by cleaving DNA intermediates that need to be resolved for faithful DNA repair, replication, or recombination. Despite advances in the understanding of their function and regulation, it is less clear how these proteins respond to genotoxic stress. Here, we show that the structure-specific endonuclease Mus81-Mms4/EME1 relocalizes to subnuclear foci following DNA damage and colocalizes with the endonucleases Rad1-Rad10 (XPF-ERCC1) and Slx1-Slx4...
August 15, 2017: Cell Reports
https://www.readbyqxmd.com/read/28813641/aim2-inflammasome-activation-and-regulation-a-structural-perspective
#17
Bing Wang, Qian Yin
Absent in melanoma 2 (AIM2) inflammasome is a multi-protein platform that recognizes aberrant cytoplasmic dsDNA and induces cytokine maturation, release and pyroptosis. It is composed of AIM2, apoptosis-associated speck-like protein containing a CARD (ASC), and caspase-1. Recent X-ray crystallographic and high resolution cryo-electron microscopic (cryo-EM) studies have revealed a series of structures in AIM2 inflammasome activation and regulation. One prominent feature common in multiple steps is the assembly of high-order structures, especially helical filaments nucleated by upstream molecules, rather than stoichiometric complexes...
August 13, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28813493/mpp10-represents-a-platform-for-the-interaction-of-multiple-factors-within-the-90s-pre-ribosome
#18
Bebiana Sá-Moura, Markus Kornprobst, Satyavati Kharde, Yasar Luqman Ahmed, Gunter Stier, Ruth Kunze, Irmgard Sinning, Ed Hurt
In eukaryotes, ribosome assembly is a highly complex process that involves more than 200 assembly factors that ensure the folding, modification and processing of the different rRNA species as well as the timely association of ribosomal proteins. One of these factors, Mpp10 associates with Imp3 and Imp4 to form a complex that is essential for the normal production of the 18S rRNA. Here we report the crystal structure of a complex between Imp4 and a short helical element of Mpp10 to a resolution of 1.88 Å. Furthermore, we extend the interaction network of Mpp10 and characterize two novel interactions...
2017: PloS One
https://www.readbyqxmd.com/read/28813413/polylox-barcoding-reveals-haematopoietic-stem-cell-fates-realized-in-vivo
#19
Weike Pei, Thorsten B Feyerabend, Jens Rössler, Xi Wang, Daniel Postrach, Katrin Busch, Immanuel Rode, Kay Klapproth, Nikolaus Dietlein, Claudia Quedenau, Wei Chen, Sascha Sauer, Stephan Wolf, Thomas Höfer, Hans-Reimer Rodewald
Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system...
August 16, 2017: Nature
https://www.readbyqxmd.com/read/28813147/synthesis-and-evaluation-of-asymmetric-acyclic-nucleoside-bisphosphonates-as-inhibitors-of-plasmodium-falciparum-and-human-hypoxanthine-guanine-xanthine-phosphoribosyltransferase
#20
Petr Špaček, Dianne T Keough, Marina Chavchich, Martin Dracinsky, Zlatko Janeba, Lieve Naesens, Michael D Edstein, Luke W Guddat, Dana Hocková
Acyclic nucleoside bisphosphonates (ANbPs) have previously been shown to be good inhibitors of human hypoxanthine-guanine phosphoribosyltransferase (HGPRT) and Plasmodium falciparum (Pf) hypoxanthine-guanine-xanthine phosphoribosyltransferase (PfHGXPRT). Based on this scaffold, a new series of ANbPs was synthesized. One of these new ANbPs, [3-(guanine-9-yl)-2-((2-phosphonoethoxy)methyl)propoxy]methylphosphonic acid, exhibited Ki values of 6 and 70 nM for human HGPRT and Pf HGXPRT, respectively. These low Ki values were achieved by inserting an extra carbon atom in the linker connecting the N9 atom of guanine to one of the phosphonate groups...
August 16, 2017: Journal of Medicinal Chemistry
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