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Molecular dynamics membrane

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https://www.readbyqxmd.com/read/29784777/structure-of-an-eiic-sugar-transporter-trapped-in-an-inward-facing-conformation
#1
Zhenning Ren, Jumin Lee, Mahdi Muhammad Moosa, Yin Nian, Liya Hu, Zhichun Xu, Jason G McCoy, Allan Chris M Ferreon, Wonpil Im, Ming Zhou
The phosphoenolpyruvate-dependent phosphotransferase system (PTS) transports sugar into bacteria and phosphorylates the sugar for metabolic consumption. The PTS is important for the survival of bacteria and thus a potential target for antibiotics, but its mechanism of sugar uptake and phosphorylation remains unclear. The PTS is composed of multiple proteins, and the membrane-embedded Enzyme IIC (EIIC) component transports sugars across the membrane. Crystal structures of two members of the glucose superfamily of EIICs, bcChbC and bcMalT, were solved in the inward-facing and outward-facing conformations, and the structures suggest that sugar translocation could be achieved by movement of a structured domain that contains the sugar-binding site...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29783744/interplay-between-er-ca-2-binding-proteins-stim1-and-stim2-is-required-for-store-operated-ca-2-entry
#2
Heather A Nelson, Colin A Leech, Richard F Kopp, Michael W Roe
Store-operated calcium entry (SOCE), a fundamentally important homeostatic and Ca2+ signaling pathway in many types of cells, is activated by the direct interaction of stromal interaction molecule 1 (STIM1), an endoplasmic reticulum (ER) Ca2+ -binding protein, with Ca2+ -selective Orai1 channels localized in the plasma membrane. While much is known about the regulation of SOCE by STIM1, the role of stromal interaction molecule 2 (STIM2) in SOCE remains incompletely understood. Here, using clustered regularly interspaced short palindromic repeats -CRISPR associated protein 9 (CRISPR-Cas9) genomic editing and molecular imaging, we investigated the function of STIM2 in NIH 3T3 fibroblast and αT3 cell SOCE...
May 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29780379/point-mutation-of-a-non-elastase-binding-site-in-human-%C3%AE-1-antitrypsin-alters-its-anti-inflammatory-properties
#3
Yotam Lior, Mariana Zaretsky, David E Ochayon, Diana Lotysh, Boris M Baranovski, Ronen Schuster, Ofer Guttman, Amir Aharoni, Eli C Lewis
Introduction: Human α1-antitrypsin (hAAT) is a 394-amino acid long anti-inflammatory, neutrophil elastase inhibitor, which binds elastase via a sequence-specific molecular protrusion (reactive center loop, RCL; positions 357-366). hAAT formulations that lack protease inhibition were shown to maintain their anti-inflammatory activities, suggesting that some attributes of the molecule may reside in extra-RCL segments. Here, we compare the protease-inhibitory and anti-inflammatory profiles of an extra-RCL mutation (cys232pro) and two intra-RCL mutations (pro357cys, pro357ala), to naïve [wild-type (WT)] recombinant hAAT, in vitro , and in vivo ...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29779049/biochemical-and-functional-interplay-between-ion-channels-and-the-components-of-the-dystrophin-associated-glycoprotein-complex
#4
REVIEW
Margarita Leyva-Leyva, Alejandro Sandoval, Ricardo Felix, Ricardo González-Ramírez
Dystrophin is a cytoskeleton-linked membrane protein that binds to a larger multiprotein assembly called the dystrophin-associated glycoprotein complex (DGC). The deficiency of dystrophin or the components of the DGC results in the loss of connection between the cytoskeleton and the extracellular matrix with significant pathophysiological implications in skeletal and cardiac muscle as well as in the nervous system. Although the DGC plays an important role in maintaining membrane stability, it can also be considered as a versatile and flexible molecular complex that contribute to the cellular organization and dynamics of a variety of proteins at specific locations in the plasma membrane...
May 19, 2018: Journal of Membrane Biology
https://www.readbyqxmd.com/read/29778689/network-analysis-of-a-proposed-exit-pathway-for-protons-to-the-p-side-of-cytochrome-c-oxidase
#5
Xiuhong Cai, Kamran Haider, Jianxun Lu, Slaven Radic, Chang Yun Son, Qiang Cui, M R Gunner
Cytochrome c Oxidase (CcO) reduces O2 , the terminal electron acceptor, to water in the aerobic respiration electron transport chain. The energy released by O2 reductions is stored by removing eight protons from the high pH, N-side, of the membrane with four used for chemistry in the active site and four pumped to the low pH, P-side. The proton transfers must occur along controllable proton pathways that prevent energy dissipating movement towards the N-side. The CcO N-side has well established D- and K-channels to deliver protons to the protein interior...
May 17, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29776171/evaluation-of-bending-modulus-of-lipid-bilayers-using-undulation-and-orientation-analysis
#6
Adarsh K Chaurasia, Andrew M Rukangu, Michael K Philen, Gary D Seidel, Eric C Freeman
In the current paper, phospholipid bilayers are modeled using coarse-grained molecular dynamics simulations with the MARTINI force field. The extracted molecular trajectories are analyzed using Fourier analysis of the undulations and orientation vectors to establish the differences between the two approaches for evaluating the bending modulus. The current work evaluates and extends the implementation of the Fourier analysis for molecular trajectories using a weighted horizon-based averaging approach. The effect of numerical parameters in the analysis of these trajectories is explored by conducting parametric studies...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29775570/rapid-non-classical-effects-of-steroids-on-the-membrane-receptor-dynamics-and-downstream-signaling-in-neurons
#7
REVIEW
Klaudia Barabás, Soma Godó, Ferenc Lengyel, Dávid Ernszt, József Pál, István M Ábrahám
Although rapid effects of steroid hormones on membrane receptors and intracellular signaling molecules have been extensively studied in neurons, we are only beginning to understand the molecular mechanisms behind these non-classical steroid actions. Single molecule tracking (SMT) studies on live cells demonstrated that surface trafficking of membrane receptors determines their ligand binding properties and downstream signaling events. Recent findings suggest that one of the underlying mechanisms of non-classical steroid actions is the alteration of receptor movements on the membrane surface...
May 15, 2018: Hormones and Behavior
https://www.readbyqxmd.com/read/29775309/relationship-between-proton-transport-and-morphology-of-perfluorosulfonic-acid-membranes-a-reactive-molecular-dynamics-approach
#8
Takuya Mabuchi, Takashi Tokumasu
A reactive molecular dynamics simulation has been performed for the characterization of the relationship between proton transport and water clustering in polymer electrolyte membranes. We have demonstrated that the anharmonic two-state empirical valence bond ( aTS-EVB) model is capable of describing efficiently excess proton transport through the Grotthuss hopping mechanism within the simplicity of the theoretical framework. In order to explore the long-time diffusion behavior in PFSA membranes with statistical certainty, simulations that are longer than 10 ns are needed...
May 18, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29774203/small-rho-gtpases-and-the-effector-vipa-mediate-the-invasion-of-epithelial-cells-by-filamentous-legionella-pneumophila
#9
Akriti Prashar, María Eugenia Ortiz, Stefanie Lucarelli, Elizabeth Barker, Zohreh Tabatabeiyazdi, Feras Shamoun, Deepa Raju, Costin Antonescu, Cyril Guyard, Mauricio R Terebiznik
Legionella pneumophila (Lp) exhibits different morphologies with varying degrees of virulence. Despite their detection in environmental sources of outbreaks and in respiratory tract secretions and lung autopsies from patients, the filamentous morphotype of Lp remains poorly studied. We previously demonstrated that filamentous Lp invades lung epithelial cells (LECs) and replicates intracellularly in a Legionella containing vacuole. Filamentous Lp activates β1integrin and E-cadherin receptors at the surface of LECs leading to the formation of actin-rich cell membrane structures we termed hooks and membrane wraps...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29774170/liquid-biopsy-of-vitreous-reveals-an-abundant-vesicle-population-consistent-with-the-size-and-morphology-of-exosomes
#10
Yuanjun Zhao, Sarah R Weber, Joshua Lease, Mariano Russo, Christopher A Siedlecki, Li-Chong Xu, Han Chen, Weiwei Wang, Michael Ford, Rafael Simó, Jeffrey M Sundstrom
Purpose: To investigate the molecular components of the vitreous in order to better understand retinal physiology and disease. Methods: Vitreous was acquired from patients undergoing vitrectomy for macular hole and/or epiretinal membrane, postmortem donors, and C57BL/6J mice. Unbiased proteomic analysis was performed via electrospray ionization tandem mass spectrometry (MS/MS). Gene ontology analysis was performed and results were confirmed with transmission electron microscopy, atomic force microscopy, and nanoparticle tracking analysis (NTA)...
May 2018: Translational Vision Science & Technology
https://www.readbyqxmd.com/read/29773865/perlecan-a-heparan-sulfate-proteoglycan-regulates-systemic-metabolism-with-dynamic-changes-in-adipose-tissue-and-skeletal-muscle
#11
Yuri Yamashita, Satoshi Nakada, Toshinori Yoshihara, Takeshi Nara, Norihiko Furuya, Takashi Miida, Nobutaka Hattori, Eri Arikawa-Hirasawa
Perlecan (HSPG2), a heparan sulfate proteoglycan, is a component of basement membranes and participates in a variety of biological activities. Here, we show physiological roles of perlecan in both obesity and the onset of metabolic syndrome. The perinatal lethality-rescued perlecan knockout (Hspg2-/- -Tg) mice showed a smaller mass and cell size of white adipose tissues than control (WT-Tg) mice. Abnormal lipid deposition, such as fatty liver, was not detected in the Hspg2-/- -Tg mice, and those mice also consumed more fat as an energy source, likely due to their activated fatty acid oxidation...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773382/chitosan-polytetrafluoroethylene-composite-membranes-for-separation-of-methanol-and-toluene-by-pervaporation
#12
Siddhartha Moulik, Vani Bukke, S Chandrasekhar Sajja, Sridhar S
Present work reports the synthesis of a novel Chitosan-Polytetrafluoroethylene composite membrane with solvent resistant property for efficient separation of methanol/toluene mixture by pervaporation. The composite was crossed with tetraethyl orthosilicate (TEOS) to prevent or reduce membrane swelling and improve the separation factor. The synthesized membranes were characterized by SEM, FTIR and DSC analysis. Molecular dynamics (MD) simulation and computational fluid dynamics were coupled to predict the structural and diffusive properties besides concentration profile inside the membrane...
August 1, 2018: Carbohydrate Polymers
https://www.readbyqxmd.com/read/29772810/determination-of-the-membrane-environment-of-cd59-in-living-cells
#13
Gergő Fülöp, Mario Brameshuber, Andreas M Arnold, Gerhard J Schütz, Eva Sevcsik
The organization and dynamics of proteins and lipids in the plasma membrane, and their role in membrane functionality, have been subject of a long-lasting debate. Specifically, it is unclear to what extent membrane proteins are affected by their immediate lipid environment and vice versa. Studies on model membranes and plasma membrane vesicles indicated preferences of proteins for lipid phases characterized by different acyl chain order; however, whether such phases do indeed exist in live cells is still not known...
May 17, 2018: Biomolecules
https://www.readbyqxmd.com/read/29771498/structure-and-function-of-the-transmembrane-domain-of-nsas-an-antibiotic-sensing-histidine-kinase-in-s-aureus
#14
Manasi P Bhate, Thomas Lemmin, Georg Kuenze, Bruk Mensa, Soumya Ganguly, Jason Peters, Nathan Schmidt, Jeffrey G Pelton, Carol Gross, Jens Meiler, William F DeGrado
NsaS is one of four intramembrane histidine kinases (HKs) in Staphylococcus aureus that mediate the pathogen's response to membrane active antimicrobials and human innate immunity. We describe the first integrative structural study of NsaS using a combination of solution state NMR spectroscopy, chemical-crosslinking, molecular modeling and dynamics. Three key structural features emerge: First, NsaS has a short N-terminal amphiphilic helix that anchors its transmembrane (TM) bundle into the inner leaflet of the membrane such that it might sense neighboring proteins or membrane deformations...
May 17, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29769724/structural-basis-for-gating-pore-current-in-periodic-paralysis
#15
Daohua Jiang, Tamer M Gamal El-Din, Christopher Ing, Peilong Lu, Régis Pomès, Ning Zheng, William A Catterall
Potassium-sensitive hypokalaemic and normokalaemic periodic paralysis are inherited skeletal muscle diseases characterized by episodes of flaccid muscle weakness1,2 . They are caused by single mutations in positively charged residues ('gating charges') in the S4 transmembrane segment of the voltage sensor of the voltage-gated sodium channel Nav 1.4 or the calcium channel Cav 1.11,2 . Mutations of the outermost gating charges (R1 and R2) cause hypokalaemic periodic paralysis1,2 by creating a pathogenic gating pore in the voltage sensor through which cations leak in the resting state3,4 ...
May 16, 2018: Nature
https://www.readbyqxmd.com/read/29769303/how-alternative-splicing-affects-membrane-trafficking-dynamics
#16
REVIEW
R Eric Blue, Ennessa G Curry, Nichlas M Engels, Eunice Y Lee, Jimena Giudice
The cell biology field has outstanding working knowledge of the fundamentals of membrane-trafficking pathways, which are of critical importance in health and disease. Current challenges include understanding how trafficking pathways are fine-tuned for specialized tissue functions in vivo and during development. In parallel, the ENCODE project and numerous genetic studies have revealed that alternative splicing regulates gene expression in tissues and throughout development at a post-transcriptional level. This Review summarizes recent discoveries demonstrating that alternative splicing affects tissue specialization and membrane-trafficking proteins during development, and examines how this regulation is altered in human disease...
May 16, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29767757/the-contribution-of-organelles-to-plant-intracellular-calcium-signalling
#17
Alex Costa, Lorella Navazio, Ildiko Szabo
Calcium (Ca2+) is among the most important intracellular messengers in living organisms. Understanding of the players and dynamics of Ca2+ signalling pathways in plants may help to unravel the molecular basis of their exceptional flexibility to respond and to adapt to different stimuli. In the present review we focus on new tools that have recently revolutionized our view of organellar Ca2+ signalling as well as on the current knowledge regarding the pathways mediating Ca2+ fluxes across intracellular membranes...
May 15, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29767519/molecular-structure-and-permeability-at-the-interface-between-phase-separated-membrane-domains
#18
Rodrigo Maghdissian Cordeiro
Phase-separated membrane domains, also known as lipid rafts, are believed to play an important role in cell function. Although most rafts are sterol-enriched membrane regions, evidence suggests that living cells may also contain gel-like rafts. Interactions between gel and fluid domains have a large impact on membrane properties, as is the case with permeability. The membrane permeability may reach a peak at the main phase transition temperature, by far exceeding the values recorded at the fluid phase. It has been proposed that gel-fluid interfaces are leaky, but the effect has not yet been demonstrated at the molecular level...
May 16, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29767453/optimizing-antimicrobial-peptide-dendrimers-in-chemical-space
#19
Thissa Siriwardena, Alice Capecchi, Bee-Ha Gan, Xian Jin, Runze He, Dengwen Wei, Lan Ma, Thilo Köhler, Christian van Delden, Sacha Javor, Jean-Louis Reymond
Here we used nearest neighbor searches in chemical space to improve the activity of antimicrobial peptide dendrimer (AMPD) G3KL and identified dendrimer T7 with an expanded activity range against Gram-negative pathogenic bacteria including Klebsiellae pneumoniae, increased serum stability and promising activity in an in vivo infection model against a multidrug resistant strain of Acinetobacter baumannii. Imaging, spectroscopic studies and a structural model from molecular dynamics simulations suggest that T7 acts by membrane disruption...
May 16, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29760097/the-glycolipid-gm1-reshapes-asymmetric-biomembranes-and-giant-vesicles-by-curvature-generation
#20
Raktim Dasgupta, Markus S Miettinen, Nico Fricke, Reinhard Lipowsky, Rumiana Dimova
The ganglioside GM1 is present in neuronal membranes at elevated concentrations with an asymmetric spatial distribution. It is known to generate curvature and can be expected to strongly influence the neuron morphology. To elucidate these effects, we prepared giant vesicles with GM1 predominantly present in one leaflet of the membrane, mimicking the asymmetric GM1 distribution in neuronal membranes. Based on pulling inward and outward tubes, we developed a technique that allowed the direct measurement of the membrane spontaneous curvature...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
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