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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/28817590/reconstructing-asian-faunal-introductions-to-eastern-africa-from-multi-proxy-biomolecular-and-archaeological-datasets
#2
Mary E Prendergast, Michael Buckley, Alison Crowther, Laurent Frantz, Heidi Eager, Ophélie Lebrasseur, Rainer Hutterer, Ardern Hulme-Beaman, Wim Van Neer, Katerina Douka, Margaret-Ashley Veall, Eriéndira M Quintana Morales, Verena J Schuenemann, Ella Reiter, Richard Allen, Evangelos A Dimopoulos, Richard M Helm, Ceri Shipton, Ogeto Mwebi, Christiane Denys, Mark Horton, Stephanie Wynne-Jones, Jeffrey Fleisher, Chantal Radimilahy, Henry Wright, Jeremy B Searle, Johannes Krause, Greger Larson, Nicole L Boivin
Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species...
2017: PloS One
https://www.readbyqxmd.com/read/28816368/one-pot-self-assembly-of-peptide-based-cage-type-nanostructures-using-orthogonal-ligations
#3
Eline Bartolami, Jérémie Knoops, Yannick Bessin, Mathieu Fossépré, Joseph Chamieh, Pascal Dumy, Mathieu Surin, Sebastien Ulrich
The designed arrangement of biomolecular entities within monodisperse nanostructures is an important challenge toward functional biomaterials. We report herein a method for the formation of water-soluble peptide-based cages using orthogonal ligation reactions - acylhydrazone condensation and thiol-maleimide addition. The results show that using pre-organized cyclic peptides and heterobifunctional spacers as building blocks and a set of orthogonal and chemoselective ligation reactions enable cage formation in one-pot from six components and through eight reactions...
August 17, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28816007/fluorous-phase-directed-peptide-assembly-affords-nano-peptisomes-capable-of-ultrasound-triggered-cellular-delivery
#4
Scott H Medina, Megan S Michie, Stephen E Miller, Martin J Schnermann, Joel P Schneider
Here, we report the design, synthesis and efficacy of a new class of ultrasound (US)-sensitive self-assembled peptide-based nanoparticle. Peptisomes are prepared via templated assembly of a de novo designed peptide at the interface of fluorinated nanodroplets. Utilizing peptide assembly allows for facile particle synthesis, direct incorporation of bioactive sequences displayed from the particle corona, and the ability to easily encapsulate biologics during particle preparation using a mild solvent exchange procedure...
August 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28815771/molstack-interactive-visualization-tool-for-presentation-interpretation-and-validation-of-macromolecules-and-electron-density-maps
#5
Przemyslaw J Porebski, Piotr Sroka, Heping Zheng, David R Cooper, Wladek Minor
Our understanding of the world of biomolecular structures is based upon the interpretation of macromolecular models, of which ∼ 90% are themselves the interpretation of electron density maps. This structural information guides scientific progress and exploration in many biomedical disciplines. The Protein Data Bank's web portals have made these structures available for mass scientific consumption and greatly broaden the scope of information presented in scientific publications. The portals provide numerous quality metrics; however, the portion of the structure that is most vital for interpretation of the function may have the most difficult to interpret electron density and this ambiguity is not reflected by any single metric...
August 17, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28814800/variations-in-biocorona-formation-related-to-defects-in-the-structure-of-single-walled-carbon-nanotubes-and-the-hyperlipidemic-disease-state
#6
Achyut J Raghavendra, Kristofer Fritz, Sherleen Fu, Jared M Brown, Ramakrishna Podila, Jonathan H Shannahan
Ball-milling utilizes mechanical stress to modify properties of carbon nanotubes (CNTs) including size, capping, and functionalization. Ball-milling, however, may introduce structural defects resulting in altered CNT-biomolecule interactions. Nanomaterial-biomolecule interactions result in the formation of the biocorona (BC), which alters nanomaterial properties, function, and biological responses. The formation of the BC is governed by the nanomaterial physicochemical properties and the physiological environment...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28814791/molecular-dynamics-simulations-of-heterogeneous-cell-membranes-in-response-to-uniaxial-membrane-stretches-at-high-loading-rates
#7
Lili Zhang, Zesheng Zhang, John Jasa, Dongli Li, Robin O Cleveland, Mehrdad Negahban, Antoine Jérusalem
The chemobiomechanical signatures of diseased cells are often distinctively different from that of healthy cells. This mainly arises from cellular structural/compositional alterations induced by disease development or therapeutic molecules. Therapeutic shock waves have the potential to mechanically destroy diseased cells and/or increase cell membrane permeability for drug delivery. However, the biomolecular mechanisms by which shock waves interact with diseased and healthy cellular components remain largely unknown...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28814075/nickel-catalyzed-azide-alkyne-cycloaddition-to-access-1-5-disubstituted-1-2-3-triazoles-in-air-and-water
#8
Woo Gyum Kim, Mi Eun Kang, Jae Bin Lee, Min Ho Jeon, Sungmin Lee, Jungha Lee, Bongseo Choi, Pedro M S D Cal, Sebyung Kang, Jung-Min Kee, Gonçalo J L Bernardes, Jan-Uwe Rohde, Wonyoung Choe, Sung You Hong
Transition-metal-catalyzed or metal-free azide-alkyne cycloadditions are versatile and indispensable synthetic methods to access 1,4- or 1,5-disubstituted 1,2,3-triazoles. Although the copper-catalyzed cycloaddition to access 1,4-disubstituted products has been successfully applied to biomolecular reaction systems, the azide-alkyne cycloaddition to access the complementary 1,5-regioisomers under aqueous and ambient conditions remains a formidable challenge due to limited substrate scope or moisture-/air-sensitive catalysts...
August 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28814074/multifunctional-yolk-shell-nanostructure-as-a-superquencher-for-fluorescent-analysis-of-potassium-ion-using-guanine-rich-oligonucleotides
#9
Na Lu, Yanli Wen, Gang Liu, Lei Ding, Caixia Zeng, Ali Aldalbahi, Muhammad Khan, Govindasami Periyasami, Mostafizur Rahaman, Abdulaziz Alrohaili, Jiye Shi, Shiping Song, Lihua Wang, Min Zhang
The excellent performance of biosensor generally depends on the high signal-to-noise ratio, and the superquencher plays dominant role on the fluorescent sensors. Novel nanoquenchers exhibited high quenching efficiency in various fluorescent assays of bio/chemical molecules. Here, we developed a novel nanobiosensor using Fe3O4@C yolk-shell nanoparticles (YSNPs) and studied their quenching effect. We found the Fe3O4@C YSNP was a superquencher and exhibited an ultrastrong quenching ability, up to almost 100% quenching efficiency, toward fluorophores...
August 17, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28814063/icave-an-open-source-tool-for-visualizing-biomolecular-networks-in-3d-stereoscopic-3d-and-immersive-3d
#10
Vaja Liluashvili, Selim Kalayci, Eugene Fluder, Manda Wilson, Aaron Gabow, Zeynep H Gümüs
Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28811262/probe-microscopy-methods-and-applications-in-imaging-of-biological-materials
#11
REVIEW
Alper D Ozkan, Ahmet E Topal, Fatma B Dikecoglu, Mustafa O Guler, Aykutlu Dana, Ayse B Tekinay
Atomic force microscopy is an emerging tool for investigating the biomolecular aspects of cellular interactions; however, cell and tissue analyses must frequently be performed in aqueous environment, over rough surfaces, and on complex adhesive samples that complicate the imaging process and readily facilitate the blunting or fouling of the AFM probe. In addition, the shape and surface chemistry of the probe determine the quality and types of data that can be acquired from biological materials, with certain information becoming available only within a specific range of tip lengths or diameters, or through the assistance of specific chemical or biological functionalization procedures...
August 12, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28810057/crowders-and-cosolvents-major-contributors-to-the-cellular-milieu-and-efficient-means-to-counteract-environmental-stresses
#12
Roland Hermann Alfons Winter, Mimi Gao, Christoph Held, Satyajit Patra, Loana Arns, Gabriele Sadowski
The free energy and conformational landscape of biomolecular systems as well as biochemical reactions depend not only on temperature and pressure, but also only the particular solution conditions. Such conditions include the effects of cosolvents (for example osmolytes) and macromolecular crowding, which are crucial components to understand the energetics and kinetics of biological processes in living system. Such conditions are also important for the understanding of many debilitating diseases, such as those where misfolding and amyloid formation of proteins are involved...
August 15, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28809666/biomolecular-network-controllability-with-drug-binding-information
#13
Lin Wu, Lingkai Tang, Min Li, Jianxin Wang, Fang-Xiang Wu
Complex networks are ubiquitous in nature. In biological systems, biomolecules interact with each other to form so-called biomolecular networks, which determine the cellular behaviors of living organisms. Controlling the cellular behaviors by regulating certain biomolecules in the network is one of the most concerned problems in systems biology. Recently, the connections between biological networks and structural control theory have been explored, uncovering some interesting biological phenomena. Some researchers have paid attentions to the structural controllability of networks in notion of the minimum steering sets (MSSs)...
July 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28809114/boolean-logic-tree-of-label-free-dual-signal-electrochemical-aptasensor-system-for-biosensing-three-state-logic-computation-and-keypad-lock-security-operation
#14
Jiao Yang Lu, Xin Xing Zhang, Wei Tao Huang, Qiu Yan Zhu, Xuezhi Ding, Liqiu Xia, Hong Qun Luo, Nian Bing Li
The most serious and yet unsolved problems of molecular logic computing, consist in how to connect molecular events in complex systems into a usable device with specific functions and how to selectively control branchy logic processes from the cascading logic systems. This report demonstrates that Boolean logic tree is utilized to organize and connect "plug and play" chemical events DNA, nanomaterials, organic dye, biomolecule, and denaturant for developing the dual-signal electrochemical evolution aptasensor system with good resettability for amplification detection of thrombin, controllable and selectable three-state logic computation and keypad lock security operation...
August 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28809082/development-of-a-dual-functional-hydrogel-using-rgd-and-anti-vegf-aptamer
#15
Nan Zhao, Mark R Battig, Ming Xu, Xiuli Wang, Na Xiong, Yong Wang
Synthetic molecular libraries hold great potential to advance the biomaterial development. However, little effort is made to integrate molecules with molecular recognition abilities selected from different libraries into a single biomolecular material. The purpose of this work is to incorporate peptides and nucleic acid aptamers into a porous hydrogel to develop a dual-functional biomaterial. The data show that an anti-integrin peptide can promote the attachment and growth of endothelial cells in a 3D porous poly(ethylene glycol) hydrogel and an antivascular endothelial growth factor aptamer can sequester and release VEGF of high bioactivity...
August 15, 2017: Macromolecular Bioscience
https://www.readbyqxmd.com/read/28808204/safety-immunogenicity-and-cross-species-protection-of-a-plasmid-dna-encoding-plasmodium-falciparum-sera5-polypeptide-microbial-epitopes-and-chemokine-genes-in-mice-and-olive-baboons
#16
Nyamongo Onkoba, Ruth M Mumo, Horace Ochanda, Charles Omwandho, Hastings S Ozwara, Thomas G Egwang
Incorporation of biomolecular epitopes to malarial antigens should be explored in the development of strain-transcending malarial vaccines. The present study sought to determine safety, immunogenicity and cross-species efficacy ofPlasmodium falciparum serine repeat antigen 5 polypeptide co-expressed with epitopes of Bacille-Calmette Guerin (BCG), tetanus toxoid (TT) and a chemokine gene. Olive baboons and BALB/c mice were randomly assigned into vaccine and control groups. The vaccine group animals were primed and boosted twice with pIRES plasmids encoding the SERA5+ BCG+ TT alone, or with either CCL5 or CCL20 and the control group with pIRES plasmid vector backbone...
July 13, 2017: Journal of Biomedical Research
https://www.readbyqxmd.com/read/28806720/exploration-of-acute-genotoxic-effects-and-antigenotoxic-potential-of-gambogic-acid-using-allium-cepa-assay
#17
Abhishek Shetty, Thejaswini Venkatesh, Padmanaban S Suresh, Rie Tsutsumi
The plant derived xanthanoid gambogic acid (GA) is well known for its anticancer activity. To date, biological actions of GA on plant system have not been reported. In the present study, we evaluated the potential acute genotoxic activity of GA, and its antigenotoxic potential against H2O2 induced genetic damage using Allium cepa root chromosomal aberration assay under hydroponic conditions. There was a significant decrease in the percentage of mitotic index/prophase index with the increase in clastogenicity percentage in a dose and time-dependent manner when Allium cepa bulbs were exposed to GA at 0...
August 5, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28805061/a-triple-helix-molecular-switch-electrochemical-ratiometric-biosensor-for-ultrasensitive-detection-of-nucleic-acids
#18
Erhu Xiong, Zhenzhen Li, Xiaohua Zhang, Jiawan Zhou, Xiaoxia Yan, Yunqing Liu, Jinhua Chen
Biomolecular receptors such as nucleic acids that switch between two or more conformations upon binding to a specific target can be used to build specific and sensitive biosensors. In this work, based on the electrochemical dual-signaling ratiometric strategy and triple-helix molecular switch, we developed a selective, reusable, and simple electrochemical DNA (E-DNA) biosensor for target DNA (T-DNA) detection. A hairpin DNA capture probe labeled with methylene blue (MB-DNA) self-assembles on the surface of gold electrode (GE) through Au-S bond, and then a single-strand DNA modified with two ferrocenes (Fc-DNA) on each end to enhance the oxidation signal hybridizes with the MB-DNA to form a triple-helix conformation...
August 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28802890/is-protein-deuteration-beneficial-for-proton-detected-solid-state-nmr-at-and-above-100%C3%A2-khz-magic-angle-spinning
#19
Diane Cala-De Paepe, Jan Stanek, Kristaps Jaudzems, Kaspars Tars, Loren B Andreas, Guido Pintacuda
(1)H-detection in solid-state NMR of proteins has been traditionally combined with deuteration for both resolution and sensitivity reasons, with the optimal level of proton dilution being dependent on MAS rate. Here we present (1)H-detected (15)N and (13)C CP-HSQC spectra on two microcrystalline samples acquired at 60 and 111 kHz MAS and at ultra-high field. We critically compare the benefits of three labeling schemes yielding different levels of proton content in terms of resolution, coherence lifetimes and feasibility of scalar-based 2D correlations under these experimental conditions...
July 25, 2017: Solid State Nuclear Magnetic Resonance
https://www.readbyqxmd.com/read/28801460/multiplexed-silicon-photonic-sensor-arrays-enable-facile-characterization-of-coagulation-protein-binding-to-nanodiscs-with-variable-lipid-content
#20
Ellen M Muehl, Joshua M Gajsiewicz, Sara M Medfisch, Zachary S B Wiersma, James H Morrissey, Ryan C Bailey
Interactions of soluble proteins with the cell membrane are critical within the blood coagulation cascade. Of particular interest are the interactions of γ-carboxyglutamic acid-rich (GLA) domain-containing clotting proteins with lipids. Variability among conventional analytical methods presents challenges for comparing clotting protein-lipid interactions. Most previous studies have investigated only a single clotting protein and lipid composition and have yielded widely different binding constants. Herein, we demonstrate that a combination of lipid bilayer Nanodiscs and a multiplexed silicon photonic analysis technology enables high-throughput probing of many protein-lipid interactions among blood-clotting proteins...
August 11, 2017: Journal of Biological Chemistry
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