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Single molecule localization

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https://www.readbyqxmd.com/read/28821864/nanomechanics-of-multidomain-neuronal-cell-adhesion-protein-contactin-revealed-by-single-molecule-afm-and-smd
#1
K Mikulska-Ruminska, A J Kulik, C Benadiba, I Bahar, G Dietler, W Nowak
Contactin-4 (CNTN4) is a complex cell adhesion molecule (CAM) localized at neuronal membranes, playing a key role in maintaining the mechanical integrity and signaling properties of the synapse. CNTN4 consists of six immunoglobulin C2 type (IgC2) domains and four fibronectin type III (FnIII) domains that are shared with many other CAMs. Mutations in CNTN4 gene have been linked to various psychiatric disorders. Toward elucidating the response of this modular protein to mechanical stress, we studied its force-induced unfolding using single molecule atomic force microscopy (smAFM) and steered molecular dynamics (SMD) simulations...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28820941/a-photoactivatable-probe-for-super-resolution-imaging-of-enzymatic-activity-in-live-cells
#2
Elias A Halabi, Zacharias Thiel, Nils Trapp, Dorothea Pinotsi, Pablo Rivera-Fuentes
A dual-activatable, fluorogenic probe was developed to sense esterase activity with single-molecule resolution. Without enzymatic pre-activation, the diazoindanone-based probe has an electron poor core and, upon irradiation, undergoes Wolff rearrangement to give a ring-expanded xanthene core that is non-emissive. If the probe is pre-activated by carboxylesterases, the tricyclic core becomes electron-rich and the photoinduced Wolff rearrangement produces a highly emissive rhodol dye. Live-cell and solution studies confirmed the selectivity of the probe and revealed that the photoactivated dye does not diffuse away from the original location of activation because the intermediate ketene forms a covalent bond with surrounding macromolecules...
August 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28819924/dynamic-imaging-of-mitochondrial-membrane-proteins-in-specific-sub-organelle-membrane-locations
#3
REVIEW
Timo Appelhans, Karin B Busch
Mitochondria are cellular organelles with multifaceted tasks and thus composed of different sub-compartments. The inner mitochondrial membrane especially has a complex nano-architecture with cristae protruding into the matrix. Related to their function, the localization of mitochondrial membrane proteins is more or less restricted to specific sub-compartments. In contrast, it can be assumed that membrane proteins per se diffuse unimpeded through continuous membranes. Fluorescence recovery after photobleaching is a versatile technology used in mobility analyses to determine the mobile fraction of proteins, but it cannot provide data on subpopulations or on confined diffusion behavior...
August 17, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28819646/a-molecular-quantum-spin-network-controlled-by-a-single-qubit
#4
Lukas Schlipf, Thomas Oeckinghaus, Kebiao Xu, Durga Bhaktavatsala Rao Dasari, Andrea Zappe, Felipe Fávaro de Oliveira, Bastian Kern, Mykhailo Azarkh, Malte Drescher, Markus Ternes, Klaus Kern, Jörg Wrachtrup, Amit Finkler
Scalable quantum technologies require an unprecedented combination of precision and complexity for designing stable structures of well-controllable quantum systems on the nanoscale. It is a challenging task to find a suitable elementary building block, of which a quantum network can be comprised in a scalable way. We present the working principle of such a basic unit, engineered using molecular chemistry, whose collective control and readout are executed using a nitrogen vacancy (NV) center in diamond. The basic unit we investigate is a synthetic polyproline with electron spins localized on attached molecular side groups separated by a few nanometers...
August 2017: Science Advances
https://www.readbyqxmd.com/read/28817257/cation-anion-arrangement-patterns-in-self-assembled-pd2l4-and-pd4l8-coordination-cages
#5
Guido H Clever, Philip Punt
Compounds featuring one-dimensional regular arrangements of stacked metal complexes and alternating [cation-anion]∞ sequences have raised considerable interest owing to their peculiar electronic and optical properties as well as guest inclusion capabilities. While traditional ways to realize these structural motifs rely on crystalline compounds, exclusively existing in the solid state, recent progress in the area of metal-mediated supramolecular self-assembly allows for the rational synthesis of structurally well-defined short stretches of stacked metal complexes and cation-anion arrangements...
August 17, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28814796/crispr-cas9-mediated-labelling-allows-for-single-molecule-imaging-and-resolution
#6
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/28809559/on-the-influence-of-the-bridge-on-triplet-state-delocalization-in-linear-porphyrin-oligomers
#7
Sabine Richert, Bart Limburg, Harry L Anderson, Christiane R Timmel
The extent of triplet state delocalization is investigated in rigid linear zinc porphyrin oligomers as a function of interporphyrin bonding characteristics, specifically in meso-meso singly linked and β,meso,β fused structures, using electron paramagnetic resonance techniques. The results are compared with those of earlier measurements on porphyrin oligomers with alkyne linkers exhibiting different preferred conformations. It is shown that dihedral angles near 90° between the porphyrin planes in directly meso-to-meso linked porphyrin oligomers lead to localization of the photoexcited triplet state on a single porphyrin unit, whereas previous work demonstrated even delocalization over two units in meso-to-meso ethyne or butadiyne-bridged oligomers, where the preferred dihedral angles amount to roughly 30° and 0°, respectively...
August 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28809537/confined-water-structure-dynamics-and-thermodynamics
#8
Sudip Chakraborty, Hemant Kumar, Chandan Dasgupta, Prabal K Maiti
Understanding the properties of strongly confined water is important for a variety of applications such as fast flow and desalination devices, voltage generation, flow sensing, and nanofluidics. Confined water also plays an important role in many biological processes such as flow through ion channels. Water in the bulk exhibits many unusual properties that arise primarily from the presence of a network of hydrogen bonds. Strong confinement in structures such as carbon nanotubes (CNTs) substantially modifies the structural, thermodynamic, and dynamic (both translational and orientational) properties of water by changing the structure of the hydrogen bond network...
August 15, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28805817/room-temperature-current-blockade-in-atomically-defined-single-cluster-junctions
#9
Giacomo Lovat, Bonnie Choi, Daniel W Paley, Michael L Steigerwald, Latha Venkataraman, Xavier Roy
Fabricating nanoscopic devices capable of manipulating and processing single units of charge is an essential step towards creating functional devices where quantum effects dominate transport characteristics. The archetypal single-electron transistor comprises a small conducting or semiconducting island separated from two metallic reservoirs by insulating barriers. By enabling the transfer of a well-defined number of charge carriers between the island and the reservoirs, such a device may enable discrete single-electron operations...
August 14, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28805223/the-effect-of-defects-on-the-catalytic-activity-of-single-au-atom-supported-carbon-nanotubes-and-reaction-mechanism-for-co-oxidation
#10
Sajjad Ali, Tian Fu Liu, Zan Lian, Bo Li, Dang Sheng Su
The mechanism of CO oxidation by O2 on a single Au atom supported on pristine, mono atom vacancy (m), di atom vacancy (di) and the Stone Wales defect (SW) on single walled carbon nanotube (SWCNT) surface is systematically investigated theoretically using density functional theory. We determine that single Au atoms can be trapped effectively by the defects on SWCNTs. The defects on SWCNTs can enhance both the binding strength and catalytic activity of the supported single Au atom. Fundamental aspects such as adsorption energy and charge transfer are elucidated to analyze the adsorption properties of CO and O2 and co-adsorption of CO and O2 molecules...
August 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28802172/interaction-of-phenazinium-based-photosensitizers-with-the-n-and-b-isoforms-of-human-serum-albumin-effect-of-methyl-substitution
#11
Swagata Sen, Riya Sett, Bijan K Paul, Nikhil Guchhait
The present work is focused on exploring the interaction of two phenazinium-based biological photosensitizers, phenosafranin (PSF) and safranin-O (SO), with human serum albumin (HSA), with particular emphasis on the physiologically significant NB conformational transition of the protein on the dye:HSA interaction. In addition, the presence of methyl substitution on the planar phenazinium ring in SO paves way for looking into the effect of simple chemical manipulation (that is, methyl substitution on the dye nucleus) on the dye:protein interaction behavior as a function of various (pH-induced) isoforms of HSA...
August 3, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28799587/unravelling-hydrogen-bonding-interactions-of-tryptamine-water-dimer-from-neutral-to-cation
#12
Zongyuan Liu, Carl O Trindle, Quanli Gu, Wei Wu, Peifeng Su
The neutral and cationic forms of tryptamine-water dimer present a variety of noncovalent interactions. To characterize these interactions, a series of complementary methods, including the quantum theory of atoms in molecules, noncovalent interaction plots, natural bond orbital analysis, and energy decomposition analysis, were used. For the first time, the existence of the three intermolecular H-bonds in the conformer-locked tryptamine-water dimer A-H2O are identified, highlighting a single water's role as one proton donor and two proton acceptors as it binds to tryptamine...
August 11, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28798045/global-mrna-polarization-regulates-translation-efficiency-in-the-intestinal-epithelium
#13
Andreas E Moor, Matan Golan, Efi E Massasa, Doron Lemze, Tomer Weizman, Rom Shenhav, Shaked Baydatch, Orel Mizrahi, Roni Winkler, Ofra Golani, Noam Stern-Ginossar, Shalev Itzkovitz
Asymmetric mRNA localization facilitates efficient translation in cells such as neurons and fibroblasts. However, the extent and significance of mRNA polarization in epithelial tissues are unclear. Here, we used single molecule transcript imaging and subcellular transcriptomics to uncover global apical-basal intracellular polarization of mRNA in the mouse intestinal epithelium. The localization of mRNAs did not generally overlap protein localization. Instead, ribosomes were more abundant on the apical sides, and apical transcripts were consequently more efficiently translated...
August 10, 2017: Science
https://www.readbyqxmd.com/read/28793768/computational-evaluation-of-mixtures-of-hydrofluorocarbons-and-deep-eutectic-solvents-for-absorption-refrigeration-systems
#14
Rubaiyet Abedin, Sharareh Heidarian, John C Flake, Francisco R Hung
We used computational tools to evaluate three working fluid mixtures for single-effect absorption refrigeration systems, where the generator (desorber) is powered by waste or solar heat. The mixtures studied here resulted from combining a widely used hydrofluorocarbon (HFC) refrigerant, R134a, with three common deep eutectic solvents (DESs) formed by mixing choline chloride (hydrogen bond acceptor, HBA) with either urea, glycerol or ethylene glycol as the hydrogen bond donor (HBD) species. The COSMOtherm/TmoleX software package was used in combination with refrigerant data from NIST/REFPROP, to perform a thermodynamic evaluation of absorption refrigeration cycles using the proposed working fluid mixtures...
August 9, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28792742/sequential-release-of-proteins-from-structured-multishell-microcapsules
#15
Ulyana Shimanovich, Thomas C T Michaels, Erwin J de Genst, Dijana Matak-Vinkovic, Christopher M Dobson, Tuomas P J Knowles
In nature, a wide range of functional materials is based on proteins. Increasing attention is also turning to the use of proteins as artificial biomaterials in the form of films, gels, particles and fibrils that offer great potential for applications in areas ranging from molecular medicine to materials science. To date, however, most such applications have been limited to single component materials despite the fact that their natural analogues are composed of multiple types of proteins with a variety of functionalities that are co-assembled in a highly organized manner on the micron scale, a process which is currently challenging to achieve in the laboratory...
August 9, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28790428/an-unusual-role-for-the-phytyl-chains-in-the-photoprotection-of-the-chlorophylls-bound-to-water-soluble-chlorophyll-binding-proteins
#16
Alessandro Agostini, Daniel M Palm, Franz-Josef Schmitt, Marco Albertini, Marilena Di Valentin, Harald Paulsen, Donatella Carbonera
Water-Soluble Chlorophyll Proteins (WSCPs) from Brassicaceae are non-photosynthetic proteins which tetramerize upon binding four chlorophyll (Chl) molecules. The bound Chls are highly photostable, despite the lack of bound carotenoids known, in Chl-containing photosynthetic proteins, to act as singlet oxygen and Chl triplet ((3)Chl) quenchers. Although the physiological function of WSCPs is still unclear, it is likely to be related to their biochemical stability and their resistance to photodegradation. To get insight into the origin of this photostability, the properties of the (3)Chl generated in WSCPs upon illumination were investigated...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28789536/computational-simulations-of-solvation-force-and-squeezing-out-of-dodecane-chain-molecules-in-an-atomic-force-microscope
#17
Rong-Guang Xu, Yuan Xiang, Yongsheng Leng
Understanding the squeeze out behaviors of liquid films at nanometer scale in an atomic force microscope (AFM) has been a significant interest since the 1990s. We carry out all-atom static-mode AFM simulations in a liquid-vapor molecular dynamics ensemble to investigate the solvation force oscillation and squeeze out mechanisms of a confined linear dodecane fluid between a gold AFM tip and a mica substrate. Solvation force oscillations are found to be associated with the layering transition of the liquid film and unstable jumps of the AFM tip...
August 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28783324/a-noncanonical-binding-site-in-the-evh1-domain-of-vasp-regulates-its-interactions-with-the-proline-rich-region-of-zyxin
#18
Lucila Andrea Acevedo, Alexander Ian Greenwood, Linda K Nicholson
Vasodilator-Stimulated Phosphoprotein, VASP, is a processive actin polymerase with roles in the control of cell shape and cell migration. Through interaction with the cytoskeletal adaptor protein Zyxin, VASP can localize to damaged stress fibers where it serves to repair and reinforce these structures. VASP localization is mediated by its N-terminal Ena/VASP Homology domain (EVH1), which binds to the motif (W/F)PxφP (most commonly occurring as FPPPP) found in cytoskeletal proteins such as vinculin, lamellipodin, and Zyxin...
August 7, 2017: Biochemistry
https://www.readbyqxmd.com/read/28783303/single-walled-carbon-nanotube-reactor-for-redox-transformation-of-mercury-dichloride
#19
Yuliya V Fedoseeva, Andrey S Orekhov, Galina N Chekhova, Victor O Koroteev, Mikhail A Kanygin, Boris V Senkovskiy, Andrey Chuvilin, Daniele Pontiroli, Mauro Riccò, Lyubov G Bulusheva, Alexander V Okotrub
Single-walled carbon nanotubes (SWCNTs) possessing a confined inner space protected by chemically resistant shells are promising for delivery, storage, and desorption of various compounds, as well as carrying out specific reactions. Here, we show that SWCNTs interact with molten mercury dichloride (HgCl2) and guide its transformation into dimercury dichloride (Hg2Cl2) in the cavity. The chemical state of host SWCNTs remains almost unchanged except for a small p-doping from the guest Hg2Cl2 nanocrystals. The density functional theory calculations reveal that the encapsulated HgCl2 molecules become negatively charged and start interacting via chlorine bridges when local concentration increases...
August 14, 2017: ACS Nano
https://www.readbyqxmd.com/read/28782953/revealing-the-local-proton-network-through-three-dimensional-13-c-1-h-double-quantum-1-h-single-quantum-and-1-h-double-quantum-13-c-1-h-single-quantum-correlations-fast-mas-solid-state-nmr-spectroscopy-at-natural-abundance
#20
Michal Malon, Manoj Kumar Pandey, Yusuke Nishiyama
1H double quantum (DQ)/1H single quantum (SQ) correlation solid-state NMR spectroscopy is widely used to obtain internuclear 1H-1H proximities, especially at fast magic angle spinning (MAS) rate > 60 kHz. However, 1H signals are not well-resolved due to intense 1H-1H homonuclear dipolar interactions even at the attainable maximum MAS frequencies of ~100 kHz to date and/or under 1H-1H homonuclear dipolar decoupling irradiations. Here we introduce novel three-dimensional (3D) experiments to resolve the 1H DQ/1H SQ correlation peaks using the additional 13C dimension...
August 7, 2017: Journal of Physical Chemistry. B
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