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https://www.readbyqxmd.com/read/29769721/spatiotemporal-regulation-of-liquid-like-condensates-in-epigenetic-inheritance
#1
Gang Wan, Brandon D Fields, George Spracklin, Aditi Shukla, Carolyn M Phillips, Scott Kennedy
Non-membrane-bound organelles such as nucleoli, processing bodies, Cajal bodies and germ granules form by the spontaneous self-assembly of specific proteins and RNAs. How these biomolecular condensates form and interact is poorly understood. Here we identify two proteins, ZNFX-1 and WAGO-4, that localize to Caenorhabditis elegans germ granules (P granules) in early germline blastomeres. Later in germline development, ZNFX-1 and WAGO-4 separate from P granules to define an independent liquid-like condensate that we term the Z granule...
May 16, 2018: Nature
https://www.readbyqxmd.com/read/29766280/novel-insights-into-nucleoamino-acids-biomolecular-recognition-and-aggregation-studies-of-a-thymine-conjugated-l-phenyl-alanine
#2
Giovanni N Roviello
This article deals with the synthesis in solid phase and characterization of a nucleoamino amide, based on a phenylalaninamide moiety which was N-conjugated to a thymine nucleobase. In analogy to the natural nucleobase-amino acid conjugates, endowed with a wide range of biological properties, the nucleoamino amide interacts with single-stranded nucleic acids as verified in DNA- and RNA-binding assays conducted by CD and UV spectroscopies. These technologies were used to show also that this conjugate binds serum proteins altering significantly their secondary structure, as evidenced by CD and UV using BSA as a model...
May 15, 2018: Amino Acids
https://www.readbyqxmd.com/read/29757605/structural-basis-for-natural-product-selection-and-export-by-bacterial-abc-transporters
#3
Maria Romano, Giuliana Fusco, Hassanul G Choudhury, Shahid Mehmood, Carol V Robinson, Séverine Zirah, Julian D Hegemann, Ewen Lescop, Mohamed A Marahiel, Sylvie Rebuffat, Alfonso De Simone, Konstantinos Beis
Bacteria under stress produce ribosomally synthesized and posttranslationally modified peptides (RiPPs) to target closely related species, such as the lasso peptide microcin J25 (MccJ25). These peptides are also toxic to the producing organisms that utilize dedicated ABC transporters to achieve self-immunity. MccJ25 is exported by the Escherichia coli ABC transporter McjD through a complex mechanism of recognition that has remained elusive. Here, we used biomolecular NMR to study this interaction and identified a region of the toxic peptide that is crucial to its recognition by the ABC transporter...
May 14, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29753223/bioconjugated-nano-bactericidal-complex-for-potent-activity-against-human-and-phytopathogens-with-concern-of-global-drug-resistant-crisis
#4
Baker Syed, M N Nagendra Prasad, K Mohan Kumar, S Satish
The present study emphasizes the need for novel antimicrobial agents to combat the global drug resistant crisis. The development of novel nanomaterials is reported to be of the alternative tool to combat drug resistant pathogens. In present investigation, bioconjugated nano-complex was developed from secondary metabolite secreted from endosymbiont. The endosymbiont capable of secreting antimicrobial metabolite was subjected to fermentation and the culture supernatant was assessed for purification of antimicrobial metabolite via bio-assay guided fraction techniques such as thin layer chromatography (TLC), high performance liquid chromatography (HPLC) and column chromatography...
May 9, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29742900/crowding-stabilizes-dmso-water-hydrogen-bonding-interactions
#5
Kwang-Im Oh, Carlos R Baiz
Up to 40% of intracellular water is confined due to the dense packing of macromolecules, ions, and osmolytes. Despite the large body of work concerning the effect of additives on biomolecular structure and stability, the role of crowding and heterogeneity is not well understood. Here, infrared spectroscopy and molecular dynamics simulations are used to describe the mechanisms by which crowding modulates hydrogen bonding interactions between water and dimethyl sulfoxide (DMSO). Specifically, we use formamide and dimethylformamide (DMF) as molecular crowders and show that S=O hydrogen bond populations in aqueous mixtures are increased by both amides...
May 9, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29741868/self-assembled-n-heterocyclic-carbene-based-carboxymethylated-dextran-monolayers-on-gold-as-a-tunable-platform-for-designing-affinity-capture-biosensor-surfaces
#6
Zhijun Li, Kim A Munro, Mina R Narouz, Andrew Lau, Hongxia Hao, Cathleen M Crudden, J Hugh Horton
Sensor surfaces play a predominant role in the development of optical biosensor technologies for applications analyzing biomolecular interactions. Thiol-based self-assembled monolayers (SAMs) on gold have been widely used as linker layers for sensor surfaces. However, the degradation of the thiol-gold bond can limit the performance and durability of such surfaces, directly impacting their performance and cost effectiveness. To this end, a new family of materials based on N-heterocyclic carbenes (NHCs) have emerged as an alternative anchor for surface modification, capable of self-assembling onto a gold surface with higher affinity and superior stability as compared to the thiol-based systems...
May 9, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29726679/femtomolar-detection-by-nanocoated-fibre-label-free-biosensors
#7
Francesco Chiavaioli, Pablo Zubiate, Ignacio Del Villar, Carlos Ruiz Zamarreño, Ambra Giannetti, Sara Tombelli, Cosimo Trono, Francisco J Arregui, Ignacio R Matias, Francesco Baldini
The advent of optical fibre-based biosensors combined with that of nanotechnologies has provided an opportunity for developing in situ, portable, lightweight, versatile and high-performance optical sensing platforms. We report on the generation of lossy mode resonances by the deposition of nm-thick metal oxide films on optical fibres, which makes it possible to measure precisely and accurately the changes in optical properties of the fibre-surrounding medium with very high sensitivity compared to other technology platforms, such as long period gratings or surface plasmon reso-nances, the gold standard in label-free and real-time biomolecular interaction analysis...
May 4, 2018: ACS Sensors
https://www.readbyqxmd.com/read/29718032/revealing-the-principal-attributes-of-protein-adsorption-on-block-copolymer-surfaces-with-direct-experimental-evidence-at-the-single-protein-level
#8
Tian Xie, Joyjit Chattoraj, Patrick J Mulcahey, Noah P Kelleher, Emanuela Del Gado, Jong-In Hahm
Understanding protein adsorption onto polymer surfaces is of great importance in designing biomaterials, improving bioanalytical devices, and controlling biofouling, to name a few examples. Although steady research efforts have been advancing this field, our knowledge of this ubiquitous and complex phenomenon is still limited. In this study, we elucidate competitive protein adsorption behaviors sequentially occurring onto nanoscale block copolymer (BCP) surfaces via combined experimental and computer simulation approaches...
May 2, 2018: Nanoscale
https://www.readbyqxmd.com/read/29716322/a-tandem-mass-spectrometer-for-crossed-beam-irradiation-of-mass-selected-molecular-systems-by-kev-atomic-ions
#9
Lucas Schwob, Mathieu Lalande, Jean-Yves Chesnel, Alicja Domaracka, Bernd A Huber, Sylvain Maclot, Jean-Christophe Poully, Jimmy Rangama, Patrick Rousseau, Violaine Vizcaino, Lamri Adoui, Alain Méry
In the present paper, we describe a new home-built crossed-beam apparatus devoted to ion-induced ionization and fragmentation of isolated biologically relevant molecular systems. The biomolecular ions are produced by an electrospray ionization source, mass-over-charge selected, accumulated in a 3D ion trap, and then guided to the extraction region of an orthogonal time-of-flight mass spectrometer. Here, the target molecular ions interact with a keV atomic ion beam produced by an electron cyclotron resonance ion source...
April 2018: Review of Scientific Instruments
https://www.readbyqxmd.com/read/29716042/electro-optic-deflectors-deliver-advantages-over-acousto-optical-deflectors-in-a-high-resolution-ultra-fast-force-clamp-optical-trap
#10
Michael S Woody, Marco Capitanio, E Michael Ostap, Yale E Goldman
We characterized experimental artifacts arising from the non-linear response of acousto-optical deflectors (AODs) in an ultra-fast force-clamp optical trap and have shown that using electro-optical deflectors (EODs) instead eliminates these artifacts. We give an example of the effects of these artifacts in our ultra-fast force clamp studies of the interaction of myosin with actin filaments. The experimental setup, based on the concept of Capitanio et al. [Nat. Methods 9, 1013-1019 (2012)] utilizes a bead-actin-bead dumbbell held in two force-clamped optical traps which apply a load to the dumbbell to move it at a constant velocity...
April 30, 2018: Optics Express
https://www.readbyqxmd.com/read/29715005/nanoparticle-enhanced-plasmonic-biosensor-for-digital-biomarker-detection-in-a-microarray
#11
Alexander Belushkin, Filiz Yesilköy, Hatice Altug
Nanoplasmonic devices have become a paradigm for biomolecular detection enabled by enhanced light-matter interactions in the fields from biological and pharmaceutical research to medical diagnostics and global health. In this work, we present a bright-field imaging plasmonic biosensor that allows visualization of single sub-wavelength gold nanoparticles (NPs) on large-area gold nanohole arrays (Au-NHAs). The sensor generates image heatmaps that reveal the locations of single NPs as high-contrast spikes, enabling the detection of individual nanoparticle-labeled molecules...
May 1, 2018: ACS Nano
https://www.readbyqxmd.com/read/29713036/engineering-the-entropy-driven-free-energy-landscape-of-a-dynamic-nanoporous-protein-assembly
#12
Robert Alberstein, Yuta Suzuki, Francesco Paesani, F Akif Tezcan
De novo design and construction of stimuli-responsive protein assemblies that predictably switch between discrete conformational states remains an essential but highly challenging goal in biomolecular design. We previously reported synthetic, two-dimensional protein lattices self-assembled via disulfide bonding interactions, which endows them with a unique capacity to undergo coherent conformational changes without losing crystalline order. Here, we carried out all-atom molecular dynamics simulations to map the free-energy landscape of these lattices, validated this landscape through extensive structural characterization by electron microscopy and established that it is predominantly governed by solvent reorganization entropy...
April 30, 2018: Nature Chemistry
https://www.readbyqxmd.com/read/29704666/resolving-biomolecular-motion-and-interactions-by-r-2-and-r-1%C3%AF-relaxation-dispersion-nmr
#13
REVIEW
Erik Walinda, Daichi Morimoto, Kenji Sugase
Among the tools of structural biology, NMR spectroscopy is unique in that it not only derives a static three-dimensional structure, but also provides an atomic-level description of the local fluctuations and global dynamics around this static structure. A battery of NMR experiments is now available to probe the motions of proteins and nucleic acids over the whole biologically relevant timescale from picoseconds to hours. Here we focus on one of these methods, relaxation dispersion, which resolves dynamics on the micro- to millisecond timescale...
April 25, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29704467/xanthomonas-oryzae-pv-oryzae-tale-proteins-recruit-ostfiia%C3%AE-1-to-compensate-for-the-absence-of-ostfiia%C3%AE-5-in-bacterial-blight-in-rice
#14
Wenxiu Ma, Lifang Zou, Zhiyuan Ji, Xiameng Xu, Zhengyin Xu, Yangyang Yang, James R Alfano, Gongyou Chen
Xanthomonas oryzae pv. oryzae (Xoo), causal agent of bacterial blight (BB) of rice, uses transcription activator-like effectors (TALEs) to interact with the basal transcription factor gama subunit OsTFIIAγ5 (Xa5) and activates transcription of host genes. However, how OsTFIIAγ1, the other OsTFIIAγ protein, functions in the presence of TALEs remains unclear. In this study, we show that OsTFIIAγ1 plays a compensatory role in the absence of Xa5. The expression of OsTFIIAγ1, which is activated by TALE PthXo7, increased the expression of host genes targeted by avirulent and virulent TALEs...
April 28, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29700264/quantitative-mass-imaging-of-single-biological-macromolecules
#15
Gavin Young, Nikolas Hundt, Daniel Cole, Adam Fineberg, Joanna Andrecka, Andrew Tyler, Anna Olerinyova, Ayla Ansari, Erik G Marklund, Miranda P Collier, Shane A Chandler, Olga Tkachenko, Joel Allen, Max Crispin, Neil Billington, Yasuharu Takagi, James R Sellers, Cédric Eichmann, Philipp Selenko, Lukas Frey, Roland Riek, Martin R Galpin, Weston B Struwe, Justin L P Benesch, Philipp Kukura
The cellular processes underpinning life are orchestrated by proteins and their interactions. The associated structural and dynamic heterogeneity, despite being key to function, poses a fundamental challenge to existing analytical and structural methodologies. We used interferometric scattering microscopy to quantify the mass of single biomolecules in solution with 2% sequence mass accuracy, up to 19-kilodalton resolution, and 1-kilodalton precision. We resolved oligomeric distributions at high dynamic range, detected small-molecule binding, and mass-imaged proteins with associated lipids and sugars...
April 27, 2018: Science
https://www.readbyqxmd.com/read/29696086/investigating-the-bioavailability-of-graphene-quantum-dots-in-lung-tissues-via-fourier-transform-infrared-spectroscopy
#16
Tanveer A Tabish, Liangxu Lin, Muhammad Ali, Farhat Jabeen, Muhammad Ali, Rehana Iqbal, David W Horsell, Paul G Winyard, Shaowei Zhang
Biomolecular fractions affect the fate and behaviour of quantum dots (QDs) in living systems but how the interactions between biomolecules and QDs affect the bioavailability of QDs is a major knowledge gap in risk assessment analysis. The transport of QDs after release into a living organism is a complex process. The majority accumulate in the lungs where they can directly affect the inhalation process and lung architecture. Here, we investigate the bioavailability of graphene quantum dots (GQDs) to the lungs of rats by measuring the alterations in macromolecular fractions via Fourier transform infrared spectroscopy (FTIR)...
June 6, 2018: Interface Focus
https://www.readbyqxmd.com/read/29695722/global-profiling-of-protein-dna-and-protein-nucleosome-binding-affinities-using-quantitative-mass-spectrometry
#17
Matthew M Makowski, Cathrin Gräwe, Benjamin M Foster, Nhuong V Nguyen, Till Bartke, Michiel Vermeulen
Interaction proteomics studies have provided fundamental insights into multimeric biomolecular assemblies and cell-scale molecular networks. Significant recent developments in mass spectrometry-based interaction proteomics have been fueled by rapid advances in label-free, isotopic, and isobaric quantitation workflows. Here, we report a quantitative protein-DNA and protein-nucleosome binding assay that uses affinity purifications from nuclear extracts coupled with isobaric chemical labeling and mass spectrometry to quantify apparent binding affinities proteome-wide...
April 25, 2018: Nature Communications
https://www.readbyqxmd.com/read/29688731/molecular-recombination-phenomena-in-palladium-ii-based-self-assembled-complexes
#18
Sudhakar Ganta, Dillip K Chand
A series of self-assembled binuclear complexes (1-4) of Pd2 L'2 L2 composition are prepared by combination of selected cis-protected palladium(II) component cis-PdL' with equimolar amount of the nonchelating bidentate ligand 1,3-bis((pyridine-4-yl)methyl)urea, L. The cis-protecting unit L' crafted in the complexes [Pd2 (L')2 (L)2 ](NO3 )4 , 1-4, are ethylenediamine (en), tetramethylethylenediamine (tmeda), 2,2'-bipyridine (bpy), and 1,10-phenanthroline (phen), respectively. Complexation of palladium(II) with the ligand L, however, resulted in the self-assembled trinuclear complex [Pd3 (L)6 ](NO3 )6 , 5, of Pd3 L6 composition...
April 24, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29688710/hydration-dependent-dynamical-modes-in-xyloglucan-from-molecular-dynamics-simulation-of-13c-nmr-relaxation-times-and-their-distributions
#19
Pan Chen, Camilla Terenzi, Istvan Furo, Lars A Berglund, Jakob Wohlert
Macromolecular dynamics in biological systems, which play a crucial role for biomolecular function and activity at ambient temperature, depend strongly on hydration. Yet, a generally accepted quantitative model of hydration-dependent phenomena based on local relaxation and diffusive dynamics of both polymer and its hydration water is still missing. In this work, atomistic-scale spatial distributions of motional modes are calculated using molecular dynamics (MD) simulations of hydrated xyloglucan (XG). These are shown to reproduce experimental hydration-dependent 13C NMR longitudinal relaxation times (T1) at room temperature, and relevant features of their broad distributions, which are indicative of locally heterogeneous polymer reorientational dynamics...
April 24, 2018: Biomacromolecules
https://www.readbyqxmd.com/read/29687270/computational-solvation-analysis-of-biomolecules-in-aqueous-ionic-liquid-mixtures-from-large-flexible-proteins-to-small-rigid-drugs
#20
REVIEW
Veronika Zeindlhofer, Christian Schröder
Based on their tunable properties, ionic liquids attracted significant interest to replace conventional, organic solvents in biomolecular applications. Following a Gartner cycle, the expectations on this new class of solvents dropped after the initial hype due to the high viscosity, hydrolysis, and toxicity problems as well as their high cost. Since not all possible combinations of cations and anions can be tested experimentally, fundamental knowledge on the interaction of the ionic liquid ions with water and with biomolecules is mandatory to optimize the solvation behavior, the biodegradability, and the costs of the ionic liquid...
April 23, 2018: Biophysical Reviews
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