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https://www.readbyqxmd.com/read/29449567/systematic-analysis-of-protein-turnover-in-primary-cells
#1
Toby Mathieson, Holger Franken, Jan Kosinski, Nils Kurzawa, Nico Zinn, Gavain Sweetman, Daniel Poeckel, Vikram S Ratnu, Maike Schramm, Isabelle Becher, Michael Steidel, Kyung-Min Noh, Giovanna Bergamini, Martin Beck, Marcus Bantscheff, Mikhail M Savitski
A better understanding of proteostasis in health and disease requires robust methods to determine protein half-lives. Here we improve the precision and accuracy of peptide ion intensity-based quantification, enabling more accurate protein turnover determination in non-dividing cells by dynamic SILAC-based proteomics. This approach allows exact determination of protein half-lives ranging from 10 to >1000 h. We identified 4000-6000 proteins in several non-dividing cell types, corresponding to 9699 unique protein identifications over the entire data set...
February 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29444946/karyopherin-alpha6-is-required-for-the-replication-of-porcine-reproductive-and-respiratory-syndrome-virus-and-zika-virus
#2
Liping Yang, Rong Wang, Shixing Yang, Zexu Ma, Shaoli Lin, Yuchen Nan, Qisheng Li, Qiyi Tang, Yan-Jin Zhang
Movement of macromolecules between the cytoplasm and the nucleus occurs through the nuclear pore complex (NPC). Karyopherins comprise a family of soluble transport factors facilitating nucleocytoplasmic translocation of proteins through the NPC. In this study, we discovered that karyopherin alpha6 (KPNA6, also known as importin alpha7) was required for the optimal replication of porcine reproductive and respiratory syndrome virus (PRRSV) and Zika virus (ZIKV), which are positive-sense, single-stranded RNA viruses replicating in the cytoplasm...
February 14, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29442997/spatial-structure-of-disordered-proteins-dictates-conductance-and-selectivity-in-nuclear-pore-complex-mimics
#3
Adithya N Ananth, Ankur Mishra, Steffen Frey, Arvind Dwarkasing, Roderick Versloot, Erik van der Giessen, Dirk Görlich, Patrick Onck, Cees Dekker
Nuclear pore complexes (NPCs) lined with intrinsically disordered FG-domains act as selective gatekeepers for molecular transport between the nucleus and the cytoplasm in eukaryotic cells. The underlying physical mechanism of the intriguing selectivity is still under debate. Here, we probe the transport of ions and transport receptors through biomimetic NPCs consisting of Nsp1 domains attached to the inner surface of solid-state nanopores. We examine both wildtype FG-domains and hydrophilic SG-mutants. FG-nanopores showed a clear selectivity as transport receptors can translocate across the pore whereas other proteins cannot...
February 14, 2018: ELife
https://www.readbyqxmd.com/read/29439243/atomic-structures-of-low-complexity-protein-segments-reveal-kinked-%C3%AE-sheets-that-assemble-networks
#4
Michael P Hughes, Michael R Sawaya, David R Boyer, Lukasz Goldschmidt, Jose A Rodriguez, Duilio Cascio, Lisa Chong, Tamir Gonen, David S Eisenberg
Subcellular membraneless assemblies are a reinvigorated area of study in biology, with spirited scientific discussions on the forces between the low-complexity protein domains within these assemblies. To illuminate these forces, we determined the atomic structures of five segments from protein low-complexity domains associated with membraneless assemblies. Their common structural feature is the stacking of segments into kinked β sheets that pair into protofilaments. Unlike steric zippers of amyloid fibrils, the kinked sheets interact weakly through polar atoms and aromatic side chains...
February 9, 2018: Science
https://www.readbyqxmd.com/read/29439116/brr6-and-brl1-locate-to-nuclear-pore-complex-assembly-sites-to-promote-their-biogenesis
#5
Wanlu Zhang, Annett Neuner, Diana Rüthnick, Timo Sachsenheimer, Christian Lüchtenborg, Britta Brügger, Elmar Schiebel
The paralogous Brr6 and Brl1 are conserved integral membrane proteins of the nuclear envelope (NE) with an unclear role in nuclear pore complex (NPC) biogenesis. Here, we analyzed double-degron mutants of Brr6/Brl1 to understand this function. Depletion of Brr6 and Brl1 caused defects in NPC biogenesis, whereas the already assembled NPCs remained unaffected. This NPC biogenesis defect was not accompanied by a change in lipid composition. However, Brl1 interacted with Ndc1 and Nup188 by immunoprecipitation, and with transmembrane and outer and inner ring NPC components by split yellow fluorescent protein analysis, indicating a direct role in NPC biogenesis...
February 9, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29438825/tracing-compartment-exchange-by-nmr-diffusometry-water-in-lithium-exchanged-low-silica-x-zeolites
#6
A Lauerer, R Kurzhals, H Toufar, D Freude, J Kärger
The two-region model for analyzing signal attenuation in pulsed field gradient (PFG) NMR diffusion studies with molecules in compartmented media implies that, on their trajectory, molecules get from one region (one type of compartment) into the other one with a constant (i.e. a time-invariant) probability. This pattern has proved to serve as a good approach for considering guest diffusion in beds of nanoporous host materials, with the two regions ("compartments") identified as the intra- and intercrystalline pore spaces...
February 2, 2018: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/29432180/piezo2-channel-regulates-rhoa-and-actin-cytoskeleton-to-promote-cell-mechanobiological-responses
#7
Carlos Pardo-Pastor, Fanny Rubio-Moscardo, Marina Vogel-González, Selma A Serra, Alexandros Afthinos, Sanela Mrkonjic, Olivier Destaing, Juan F Abenza, José M Fernández-Fernández, Xavier Trepat, Corinne Albiges-Rizo, Konstantinos Konstantopoulos, Miguel A Valverde
Actin polymerization and assembly into stress fibers (SFs) is central to many cellular processes. However, how SFs form in response to the mechanical interaction of cells with their environment is not fully understood. Here we have identified Piezo2 mechanosensitive cationic channel as a transducer of environmental physical cues into mechanobiological responses. Piezo2 is needed by brain metastatic cells from breast cancer (MDA-MB-231-BrM2) to probe their physical environment as they anchor and pull on their surroundings or when confronted with confined migration through narrow pores...
February 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29432143/protein-phosphatases-at-the-nuclear-envelope
#8
REVIEW
Raquel Sales Gil, Ines J de Castro, Jerusalem Berihun, Paola Vagnarelli
The nuclear envelope (NE) is a unique topological structure formed by lipid membranes (Inner and Outer Membrane: IM and OM) interrupted by open channels (Nuclear Pore complexes). Besides its well-established structural role in providing a physical separation between the genome and the cytoplasm and regulating the exchanges between the two cellular compartments, it has become quite evident in recent years that the NE also represents a hub for localized signal transduction. Mechanical, stress, or mitogen signals reach the nucleus and trigger the activation of several pathways, many effectors of which are processed at the NE...
February 6, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29431587/quality-control-of-mrnas-at-the-entry-of-the-nuclear-pore-cooperation-in-a-complex-molecular-system
#9
M Soheilypour, M Mofrad
Despite extensive research on how mRNAs are quality controlled prior to export into the cytoplasm, the exact underlying mechanisms are still under debate. Specifically, it is unclear how quality control proteins at the entry of the nuclear pore complex (NPC) distinguish normal and aberrant mRNAs. While some of the involved components are suggested to act as switches and recruit different factors to normal versus aberrant mRNAs, some experimental and computational evidence suggests that the combined effect of the regulated stochastic interactions between the involved components could potentially achieve an efficient quality control of mRNAs...
February 12, 2018: Nucleus
https://www.readbyqxmd.com/read/29429880/deciphering-the-fuzzy-interaction-of-fg-nucleoporins-and-transport-factors-using-small-angle-neutron-scattering
#10
Samuel Sparks, Deniz B Temel, Michael P Rout, David Cowburn
The largely intrinsically disordered phenylalanine-glycine-rich nucleoporins (FG Nups) underline a selectivity mechanism that enables the rapid translocation of transport factors (TFs) through the nuclear pore complexes (NPCs). Conflicting models of NPC transport have assumed that FG Nups undergo different conformational transitions upon interacting with TFs. To selectively characterize conformational changes in FG Nups induced by TFs we performed small-angle neutron scattering (SANS) with contrast matching...
January 29, 2018: Structure
https://www.readbyqxmd.com/read/29424691/pi-pi-contacts-are-an-overlooked-protein-feature-relevant-to-phase-separation
#11
Robert McCoy Vernon, Paul Andrew Chong, Brian Tsang, Tae Hun Kim, Alaji Bah, Patrick Farber, Hong Lin, Julie Deborah Forman-Kay
Protein phase separation is implicated in formation of membraneless organelles, signaling puncta and the nuclear pore. Multivalent interactions of modular binding domains and their target motifs can drive phase separation. However, forces promoting the more common phase separation of intrinsically disordered regions are less understood, with suggested roles for multivalent cation-pi, pi-pi, and charge interactions and the hydrophobic effect. Known phase-separating proteins are enriched in pi-orbital containing residues and thus we analyzed pi-interactions in folded proteins...
February 9, 2018: ELife
https://www.readbyqxmd.com/read/29423851/estimation-of-gfp-nucleoporin-amount-based-on-fluorescence-microscopy
#12
Haruhiko Asakawa, Yasushi Hiraoka, Tokuko Haraguchi
Cellular structures and biomolecular complexes are not simply assemblies of proteins, but are organized with defined numbers of protein molecules in precise locations. Thus, evaluating the spatial localization and numbers of protein molecules is of fundamental importance in understanding cellular structures and functions. The amounts of proteins of interest have conventionally been determined by biochemical methods. However, biochemical measurements based on the population average have limitations: it is sometimes difficult to determine the amounts of insoluble proteins or low expression proteins localized in small portions of the cell...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29410433/multidimensional-correlation-of-nuclear-relaxation-rates-and-diffusion-tensors-for-model-free-investigations-of-heterogeneous-anisotropic-porous-materials
#13
João P de Almeida Martins, Daniel Topgaard
Despite their widespread use in non-invasive studies of porous materials, conventional MRI methods yield ambiguous results for microscopically heterogeneous materials such as brain tissue. While the forward link between microstructure and MRI observables is well understood, the inverse problem of separating the signal contributions from different microscopic pores is notoriously difficult. Here, we introduce an experimental protocol where heterogeneity is resolved by establishing 6D correlations between the individual values of isotropic diffusivity, diffusion anisotropy, orientation of the diffusion tensor, and relaxation rates of distinct populations...
February 6, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29406728/development-of-a-light-controlled-nanoplatform-for-direct-nuclear-delivery-of-molecular-and-nanoscale-materials
#14
Ya-Xuan Zhu, Hao-Ran Jia, Guang-Yu Pan, Nathan W Ulrich, Zhan Chen, Fu-Gen Wu
Research on nanomedicines has rapidly progressed in the last few years. However, due to the limited size of nuclear pores (9-12 nm), the nuclear membrane remains a difficult barrier to many nucleus-targeting agents. Here, we report the development of a general platform to effectively deliver chemical compounds such as drug molecules or nanomaterials into cell nuclei. This platform consists of a polyamine unit polyhedral oligomeric silsesquioxane (POSS), a hydrophilic polyethylene glycol (PEG) chain, and a photosensitizer rose bengal (RB), which can self-assemble into nanoparticles (denoted as PPR NPs)...
February 6, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29405980/multiscale-nuclear-magnetic-relaxation-dispersion-of-complex-liquids-in-bulk-and-confinement
#15
REVIEW
Jean-Pierre Korb
The nuclear magnetic relaxation dispersion (NMRD) technique consists of measurement of the magnetic-field dependence of the longitudinal nuclear-spin-lattice relaxation rate 1/T1. Usually, the acquisition of the NMRD profiles is made using a fast field cycling (FFC) NMR technique that varies the magnetic field and explores a very large range of Larmor frequencies (10 kHz < ω0/(2π) <40 MHz). This allows extensive explorations of the fluctuations to which nuclear spin relaxation is sensitive...
February 2018: Progress in Nuclear Magnetic Resonance Spectroscopy
https://www.readbyqxmd.com/read/29404398/gene-gating-at-nuclear-pores-prevents-the-formation-of-r-loops
#16
Hélène Gaillard, Francisco García-Benítez, Andrés Aguilera
Transcription is an important source of genetic variability. A large amount of transcription-associated genome variation arises from the unscheduled formation of R loops. We have recently found that physical proximity of chromatin to nuclear pores prevents the formation of pathological R loops during transcription. Our study opens new perspectives to understand genome stability as a function of nuclear location.
2018: Molecular & Cellular Oncology
https://www.readbyqxmd.com/read/29401449/principles-of-systems-biology-no-25
#17
(no author information available yet)
This month: better ways of asking "who's there?" using rRNA sequencing (Albertsen); "humanizing" yeast chromatin (Boeke/Truong); the cargo spectrum of nuclear pores (Mackmull/Beck/Ori); exon-specific mutation rates (Sabarinathan/Gonzalez-Perez/López-Bigas); synthetic virus-like particles (Lajoie/Butterfield); imaging the beating, developing heart (Scherf/Weber/Kohl/Huisken); and RNA-based FRET sensors (Jepsen/Andersen).
January 24, 2018: Cell Systems
https://www.readbyqxmd.com/read/29395481/overexpression-of-the-lamina-proteins-lamin-and-kugelkern-induces-specific-ultrastructural-alterations-in-the-morphology-of-the-nuclear-envelope-of-intestinal-stem-cells-and-enterocytes
#18
Roman Petrovsky, Georg Krohne, Jörg Großhans
The nuclear envelope has a stereotypic morphology consisting of a flat double layer of the inner and outer nuclear membrane, with interspersed nuclear pores. Underlying and tightly linked to the inner nuclear membrane is the nuclear lamina, a proteinous layer of intermediate filament proteins and associated proteins. Physiological, experimental or pathological alterations in the constitution of the lamina lead to changes in nuclear morphology, such as blebs and lobulations. It has so far remained unclear whether the morphological changes depend on the differentiation state and the specific lamina protein...
January 24, 2018: European Journal of Cell Biology
https://www.readbyqxmd.com/read/29378406/uranium-dioxides-and-debris-fragments-released-to-the-environment-with-cesium-rich-microparticles-from-the-fukushima-daiichi-nuclear-power-plant
#19
Asumi Ochiai, Junpei Imoto, Mizuki Suetake, Tatsuki Komiya, Genki Furuki, Ryohei Ikehara, Shinya Yamasaki, Gareth T W Law, Toshihiko Ohnuki, Bernd Grambow, Rodney C Ewing, Satoshi Utsunomiya
Trace U was released from the Fukushima Daiichi Nuclear Power Plant (FDNPP) during the meltdowns, but the speciation of the released components of the nuclear fuel remains unknown. We report, for the first time, the atomic-scale characteristics of nano-fragments of the nuclear fuels that were released from the FDNPP into the environment. Nano-fragments of an intrinsic U-phase were discovered to be closely associated with radioactive cesium-rich microparticles (CsMPs) in paddy soils collected ~4 km from the FDNPP...
January 29, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29376174/rock-the-nucleus-significantly-enhanced-nuclear-membrane-permeability-and-gene-transfection-by-plasmonic-nanobubble-induced-nanomechanical-transduction
#20
Xiuying Li, Peiyuan Kang, Zhuo Chen, Sneha Lal, Li Zhang, Jeremiah J Gassensmith, Zhenpeng Qin
Efficient delivery to the cell nucleus remains a significant challenge for many biomolecules, including anticancer drugs, proteins and DNAs. Despite numerous attempts to improve nuclear import including the use of nuclear localization signal (NLS) peptides and nanoparticle carriers, they are limited by the nanoparticle size, conjugation method, dependence on the functional nuclear import and intracellular trafficking mechanisms. To overcome these limitations, here we report that the nanomechanical force from plasmonic nanobubbles increases nuclear membrane permeability and promotes universal uptake of macromolecules into the nucleus, including macromolecules that are larger than the nuclear pore complex and would otherwise not enter the nucleus...
January 29, 2018: Chemical Communications: Chem Comm
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