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https://www.readbyqxmd.com/read/28402873/saxs-oriented-ensemble-refinement-of-flexible-biomolecules
#1
Peng Cheng, Junhui Peng, Zhiyong Zhang
The conformational flexibility of a biomolecule may play a crucial role in its biological function. Small-angle x-ray scattering (SAXS) is a very popular technique for characterizing biomolecule flexibility. It can be used to determine a possible structural ensemble of the biomolecule in solution with the aid of a computer simulation. In this article, we present a tool written in Python, which iteratively runs multiple independent enhanced sampling simulations such as amplified collective motions and accelerated molecular dynamics, and an ensemble optimization method to drive the biomolecule toward an ensemble that fits the SAXS data well...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28371128/intranuclear-actin-structure-modulates-mesenchymal-stem-cell-differentiation
#2
Buer Sen, Gunes Uzer, Rebekah M Samsonraj, Zhihui Xie, Cody McGrath, Maya Styner, Amel Dudakovic, Andre J van Wijnen, Janet Rubin
Actin structure contributes to physiologic events within the nucleus to control mesenchymal stromal cell (MSC) differentiation. Continuous cytochalasin D (Cyto D) disruption of the MSC actin cytoskeleton leads to osteogenic or adipogenic differentiation, both requiring mass transfer of actin into the nucleus. Cyto D remains extranuclear, thus intranuclear actin polymerization is potentiated by actin transfer: we asked whether actin structure affects differentiation. We show that secondary actin filament branching via the Arp2/3 complex is required for osteogenesis and that preventing actin branching stimulates adipogenesis, as shown by expression profiling of osteogenic and adipogenic biomarkers and unbiased RNA-seq analysis...
April 3, 2017: Stem Cells
https://www.readbyqxmd.com/read/28361956/role-for-formin-like-1-dependent-acto-myosin-assembly-in-lipid-droplet-dynamics-and-lipid-storage
#3
Simon G Pfisterer, Gergana Gateva, Peter Horvath, Juho Pirhonen, Veijo T Salo, Leena Karhinen, Markku Varjosalo, Samppa J Ryhänen, Pekka Lappalainen, Elina Ikonen
Lipid droplets (LDs) are cellular organelles specialized in triacylglycerol (TG) storage undergoing homotypic clustering and fusion. In non-adipocytic cells with numerous LDs this is balanced by poorly understood droplet dissociation mechanisms. We identify non-muscle myosin IIa (NMIIa/MYH-9) and formin-like 1 (FMNL1) in the LD proteome. NMIIa and actin filaments concentrate around LDs, and form transient foci between dissociating LDs. NMIIa depletion results in decreased LD dissociations, enlarged LDs, decreased hydrolysis and increased storage of TGs...
March 31, 2017: Nature Communications
https://www.readbyqxmd.com/read/28360928/a-new-kymogram-based-method-reveals-unexpected-effects-of-marker-protein-expression-and-spatial-anisotropy-of-cytoskeletal-dynamics-in-plant-cell-cortex
#4
Fatima Cvrčková, Denisa Oulehlová
BACKGROUND: Cytoskeleton can be observed in live plant cells in situ with high spatial and temporal resolution using a combination of specific fluorescent protein tag expression and advanced microscopy methods such as spinning disc confocal microscopy (SDCM) or variable angle epifluorescence microscopy (VAEM). Existing methods for quantifying cytoskeletal dynamics are often either based on laborious manual structure tracking, or depend on costly commercial software. Current automated methods also do not readily allow separate measurements of structure lifetime, lateral mobility, and spatial anisotropy of these parameters...
2017: Plant Methods
https://www.readbyqxmd.com/read/28348104/non-canonical-activity-of-the-podosomal-formin-fmnl1%C3%AE-supports-immune-cell-migration
#5
Matthew R Miller, Eric W Miller, Scott D Blystone
Having previously localized the formin FMNL1 to macrophage podosomes, we developed an in vivo model to assess the role of FMNL1 in the migration activities of primary macrophages. Deletion of FMNL1 in mice was genetically lethal, however targeted deletion in macrophages was achieved by employing macrophage-specific Cre. Unchallenged FMNL1-deficient mice exhibited an unexpected reduction in tissue resident macrophages despite normal blood monocyte numbers. Upon immune stimulus, the absence of FMNL1 resulted in reduced macrophage recruitment in vivo, decreased migration in 2-dimensional in vitro culture, and a decrease in macrophages exhibiting podosomes...
March 27, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28331069/efficiency-of-lamellipodia-protrusion-is-determined-by-the-extent-of-cytosolic-actin-assembly
#6
Georgi Dimchev, Anika Steffen, Frieda Kage, Vanessa Dimchev, Julien Pernier, Marie-France Carlier, Klemens Rottner
Cell migration and cell-cell communication involves the protrusion of actin-rich cell surface projections such as lamellipodia and filopodia. Lamellipodia are networks of actin filaments generated and turned over by filament branching through Arp2/3 complex. Inhibition of branching is commonly agreed to eliminate formation and maintenance of lamellipodial actin networks, but the regulation of nucleation or elongation of Arp2/3-independent filament populations within the network e.g. by formins or Ena/VASP family members and its impact on the effectivity of protrusion have remained unclear...
March 22, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28329679/mammalian-diaphanous-1-mediates-a-pathway-for-e-cadherin-to-stabilize-epithelial-barriers-through-junctional-contractility
#7
Bipul R Acharya, Selwin K Wu, Zi Zhao Lieu, Robert G Parton, Stephan W Grill, Alexander D Bershadsky, Guillermo A Gomez, Alpha S Yap
Formins are a diverse class of actin regulators that influence filament dynamics and organization. Several formins have been identified at epithelial adherens junctions, but their functional impact remains incompletely understood. Here, we tested the hypothesis that formins might affect epithelial interactions through junctional contractility. We focused on mDia1, which was recruited to the zonula adherens (ZA) of established Caco-2 monolayers in response to E-cadherin and RhoA. mDia1 was necessary for contractility at the ZA, measured by assays that include a FRET-based sensor that reports molecular-level tension across αE-catenin...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28327544/fmnl-formins-boost-lamellipodial-force-generation
#8
Frieda Kage, Moritz Winterhoff, Vanessa Dimchev, Jan Mueller, Tobias Thalheim, Anika Freise, Stefan Brühmann, Jana Kollasser, Jennifer Block, Georgi Dimchev, Matthias Geyer, Hans-Joachim Schnittler, Cord Brakebusch, Theresia E B Stradal, Marie-France Carlier, Michael Sixt, Josef Käs, Jan Faix, Klemens Rottner
Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation...
March 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28298491/cyk-4-regulates-rac-but-not-rho-during-cytokinesis
#9
Yelena Zhuravlev, Sophia M Hirsch, Shawn N Jordan, Julien Dumont, Mimi Shirasu-Hiza, Julie C Canman
Cytokinesis is driven by constriction of an actomyosin contractile ring that is controlled by Rho family small GTPases. Rho, activated by the Guanine-nucleotide Exchange Factor (GEF) ECT-2, is upstream of both myosin-II activation and diaphanous formin-mediated filamentous actin (f-actin) assembly, which drive ring constriction. The role for Rac and its regulators is more controversial but, based on the finding that Rac inactivation can rescue cytokinesis failure when the GTPase Activating Protein (GAP) CYK-4 is disrupted, Rac activity was proposed to be inhibitory to contractile ring constriction and thus specifically inactivated by CYK-4 at the division plane...
March 15, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28263325/genome-wide-mapping-of-long-range-contacts-unveils-clustering-of-dna-double-strand-breaks-at-damaged-active-genes
#10
François Aymard, Marion Aguirrebengoa, Emmanuelle Guillou, Biola M Javierre, Beatrix Bugler, Coline Arnould, Vincent Rocher, Jason S Iacovoni, Anna Biernacka, Magdalena Skrzypczak, Krzysztof Ginalski, Maga Rowicka, Peter Fraser, Gaëlle Legube
The ability of DNA double-strand breaks (DSBs) to cluster in mammalian cells has been a subject of intense debate in recent years. Here we used a high-throughput chromosome conformation capture assay (capture Hi-C) to investigate clustering of DSBs induced at defined loci in the human genome. The results unambiguously demonstrated that DSBs cluster, but only when they are induced within transcriptionally active genes. Clustering of damaged genes occurs primarily during the G1 cell-cycle phase and coincides with delayed repair...
April 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28256237/two-distinct-actin-networks-mediate-traction-oscillations-to-confer-focal-adhesion-mechanosensing
#11
Zhanghan Wu, Sergey V Plotnikov, Abdiwahab Y Moalim, Clare M Waterman, Jian Liu
Focal adhesions (FAs) are integrin-based transmembrane assemblies that connect a cell to its extracellular matrix (ECM). They are mechanosensors through which cells exert actin cytoskeleton-mediated traction forces to sense the ECM stiffness. Interestingly, FAs themselves are dynamic structures that adapt their growth in response to mechanical force. It is unclear how the cell manages the plasticity of the FA structure and the associated traction force to accurately sense ECM stiffness. Strikingly, FA traction forces oscillate in time and space, and govern the cell mechanosensing of ECM stiffness...
February 28, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28255515/microarrays-enabled-hypothesis-generation-the-suspect-role-of-fnbp-1-in-neuropsychiatric-pathogenesis-associated-with-hiv-and-or-hcv-infection
#12
A Katsounas, K R Wilting, R A Lempicki, J F Schlaak, G Gerken
OBJECTIVE: The spectrum of neuropsychiatric illness (NI) associated with the Human Immunodeficiency Virus (HIV) and/or the Hepatitis C Virus (HCV) is far reaching and significantly impacts the clinical presentation and outcome of infected persons; however, the etiological and pathophysiological background remains partially understood. The present work was aimed to investigate the potential significance of formin binding protein 1 (FNBP-1)-dependent pathways in NI-pathogenesis by elaborating on previous microarray-based research in HIV and/or HCV-infected patients receiving interferon-α (IFN-α) immunotherapy via a rigorous data mining procedure...
December 2016: Journal of AIDS & Clinical Research
https://www.readbyqxmd.com/read/28255013/histone-deacetylase-6-regulates-cytokinesis-and-erythrocyte-enucleation-through-deacetylation-of-formin-protein-mdia2
#13
Xuehui Li, Yang Mei, Bowen Yan, Eric Vitriol, Suming Huang, Peng Ji, Yi Qiu
The formin mDia2 plays a critical role in a number of cellular processes through its ability to promote nucleation and elongation of actin filaments. In erythroblasts, this includes control of cytokinesis and enucleation by regulating contractile actin ring formation. Here, we report a novel mechanism of how mDia2 is regulated: through acetylation and deacetylation at lysine 970 in formin homology 2 domain. Ectopic expression of an acetyl-mimic mDia2 mutant in mouse erythroblasts is sufficient to abolish contractile actin ring formation at the cleavage furrow and subsequent erythrocyte cytokinesis and enucleation...
March 2, 2017: Haematologica
https://www.readbyqxmd.com/read/28238662/coordination-by-cdc42-of-actin-contractility-and-adhesion-for-melanoblast-movement-in-mouse-skin
#14
Emma F Woodham, Nikki R Paul, Benjamin Tyrrell, Heather J Spence, Karthic Swaminathan, Michelle R Scribner, Evangelos Giampazolias, Ann Hedley, William Clark, Frieda Kage, Daniel J Marston, Klaus M Hahn, Stephen W G Tait, Lionel Larue, Cord H Brakebusch, Robert H Insall, Laura M Machesky
The individual molecular pathways downstream of Cdc42, Rac, and Rho GTPases are well documented, but we know surprisingly little about how these pathways are coordinated when cells move in a complex environment in vivo. In the developing embryo, melanoblasts originating from the neural crest must traverse the dermis to reach the epidermis of the skin and hair follicles. We previously established that Rac1 signals via Scar/WAVE and Arp2/3 to effect pseudopod extension and migration of melanoblasts in skin...
March 6, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28231467/synaptic-vesicle-endocytosis-occurs-on-multiple-timescales-and-is-mediated-by-formin-dependent-actin-assembly
#15
Tolga Soykan, Natalie Kaempf, Takeshi Sakaba, Dennis Vollweiter, Felix Goerdeler, Dmytro Puchkov, Natalia L Kononenko, Volker Haucke
Neurotransmission is based on the exocytic fusion of synaptic vesicles (SVs) followed by endocytic membrane retrieval and the reformation of SVs. Recent data suggest that at physiological temperature SVs are internalized via clathrin-independent ultrafast endocytosis (UFE) within hundreds of milliseconds, while other studies have postulated a key role for clathrin-mediated endocytosis (CME) of SV proteins on a timescale of seconds to tens of seconds. Here we demonstrate using cultured hippocampal neurons as a model that at physiological temperature SV endocytosis occurs on several timescales from less than a second to several seconds, yet, is largely independent of clathrin...
February 22, 2017: Neuron
https://www.readbyqxmd.com/read/28198387/high-fmnl3-expression-promotes-nasopharyngeal-carcinoma-cell-metastasis-role-in-tgf-%C3%AE-1-induced-epithelia-to-mesenchymal-transition
#16
Yanxia Wu, Zhihua Shen, Keke Wang, Yanping Ha, Hong Lei, Yanan Jia, Ranran Ding, Dongmei Wu, Siyuan Gan, Rujia Li, Botao Luo, Hanguo Jiang, Wei Jie
Formin-like 3 (FMNL3) plays a crucial role in cytoskeletal mediation and is potentially a biomarker for cell migration; however, its role in cancer metastasis remains unknown. In this study, we found elevated FMNL3 protein expression in clinical nasopharyngeal carcinoma (NPC) tissues. FMNL3 expression positively correlated to the clinical stage, T (tumour), N (lymph node metastasis) and M (distant metastasis) classification of NPC patients. Moreover, FMNL3 positively correlated to Vimentin expression and negatively correlated to E-cadherin expression in clinical NPC samples...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28183815/proteomic-screen-for-cellular-targets-of-the-vaccinia-virus-f10-protein-kinase-reveals-that-phosphorylation-of-mdia-regulates-stress-fiber-formation
#17
Matthew D Greseth, Dominique C Carter, Scott S Terhune, Paula Traktman
Vaccinia virus, a complex dsDNA virus, is unusual in replicating exclusively within the cytoplasm of infected cells. Although this prototypic poxvirus encodes >200 proteins utilized during infection, a significant role for host proteins and cellular architecture is increasingly evident. The viral B1 kinase and H1 phosphatase are known to target cellular proteins as well as viral substrates, but little is known about the cellular substrates of the F10 kinase. F10 is essential for virion morphogenesis, beginning with the poorly understood process of diversion of membranes from the ER for the purpose of virion membrane biogenesis...
April 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28183700/2016-atvb-plenary-lecture-receptor-for-advanced-glycation-endproducts-and-implications-for-the-pathogenesis-an-treatment-of-cardiometabolic-disorders-spotlight-on-the-macrophage
#18
REVIEW
Ann Marie Schmidt
The receptor for advanced glycation endproducts (RAGE) interacts with a unique repertoire of ligands that form and collect in the tissues and circulation in diabetes mellitus, aging, inflammation, renal failure, and obesity. RAGE is expressed on multiple cell types linked to tissue perturbation in these settings. This brief review focuses on the role of RAGE in monocytes/macrophages and how RAGE ligand engagement on these cells mediates seminal changes in monocyte/macrophage migration, oxidative stress, cholesterol efflux, and pro- versus anti-inflammatory cues that signal to tissue damage...
April 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28145526/zp3-is-required-for-germinal-vesicle-breakdown-in-mouse-oocyte-meiosis
#19
Lei-Lei Gao, Chun-Xiang Zhou, Xiao-Lan Zhang, Peng Liu, Zhen Jin, Gang-Yi Zhu, Yang Ma, Jing Li, Zhi-Xia Yang, Dong Zhang
ZP3 is a principal component of the zona pellucida (ZP) of mammalian oocytes and is essential for normal fertility, and knockout of ZP3 causes complete infertility. ZP3 promotes fertilization by recognizing sperm binding and activating the acrosome reaction; however, additional cellular roles for ZP3 in mammalian oocytes have not been yet reported. In the current study, we found that ZP3 was strongly expressed in the nucleus during prophase and gradually translocated to the ZP. Knockdown of ZP3 by a specific siRNA dramatically inhibited germinal vesicle breakdown (GVBD) (marking the beginning of meiosis), significantly reducing the percentage of MII oocytes...
February 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28128308/%C3%AE-v-class-integrins-exert-dual-roles-on-%C3%AE-5%C3%AE-1-integrins-to-strengthen-adhesion-to-fibronectin
#20
Mitasha Bharadwaj, Nico Strohmeyer, Georgina P Colo, Jonne Helenius, Niko Beerenwinkel, Herbert B Schiller, Reinhard Fässler, Daniel J Müller
Upon binding to the extracellular matrix protein, fibronectin, αV-class and α5β1 integrins trigger the recruitment of large protein assemblies and strengthen cell adhesion. Both integrin classes have been functionally specified, however their specific roles in immediate phases of cell attachment remain uncharacterized. Here, we quantify the adhesion of αV-class and/or α5β1 integrins expressing fibroblasts initiating attachment to fibronectin (≤120 s) by single-cell force spectroscopy. Our data reveals that αV-class integrins outcompete α5β1 integrins...
January 27, 2017: Nature Communications
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