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https://www.readbyqxmd.com/read/28340354/mechanism-of-substrate-translocation-in-an-alternating-access-transporter
#1
Naomi R Latorraca, Nathan M Fastman, A J Venkatakrishnan, Wolf B Frommer, Ron O Dror, Liang Feng
Transporters shuttle molecules across cell membranes by alternating among distinct conformational states. Fundamental questions remain about how transporters transition between states and how such structural rearrangements regulate substrate translocation. Here, we capture the translocation process by crystallography and unguided molecular dynamics simulations, providing an atomic-level description of alternating access transport. Simulations of a SWEET-family transporter initiated from an outward-open, glucose-bound structure reported here spontaneously adopt occluded and inward-open conformations...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28329765/structural-insights-into-adiponectin-receptors-suggest-ceramidase-activity
#2
Ieva Vasiliauskaité-Brooks, Remy Sounier, Pascal Rochaix, Gaëtan Bellot, Mathieu Fortier, François Hoh, Luigi De Colibus, Chérine Bechara, Essa M Saied, Christoph Arenz, Cédric Leyrat, Sébastien Granier
Adiponectin receptors (ADIPORs) are integral membrane proteins that control glucose and lipid metabolism by mediating, at least in part, a cellular ceramidase activity that catalyses the hydrolysis of ceramide to produce sphingosine and a free fatty acid (FFA). The crystal structures of the two receptor subtypes, ADIPOR1 and ADIPOR2, show a similar overall seven-transmembrane-domain architecture with large unoccupied cavities and a zinc binding site within the seven transmembrane domain. However, the molecular mechanisms by which ADIPORs function are not known...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28328943/structurally-detailed-coarse-grained-model-for-sec-facilitated-co-translational-protein-translocation-and-membrane-integration
#3
Michiel J M Niesen, Connie Y Wang, Reid C Van Lehn, Thomas F Miller
We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations...
March 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28328746/cross-talk-between-insulin-signaling-and-gpcrs
#4
Qin Fu, Qian Shi, Toni M West, Yang K Xiang
Diabetes is a major risk factor for the development of heart failure. One of the hallmarks of diabetes is insulin resistance associated with hyperinsulinemia. The literature shows that insulin and adrenergic signaling is intimately linked to each other; however, whether and how insulin may modulate cardiac adrenergic signaling and cardiac function remains unknown. Notably, recent studies have revealed that insulin receptor and β2 adrenergic receptor (β2AR) forms a membrane complex in animal hearts, bringing together the direct contact between two receptor signaling systems, and forming an integrated and dynamic network...
March 17, 2017: Journal of Cardiovascular Pharmacology
https://www.readbyqxmd.com/read/28327750/dynamic-studies-of-the-interaction-of-a-ph-responsive-amphiphilic-polymer-with-a-dopc-lipid-membrane
#5
Sivaramakrishnan Ramadurai, Marco Werner, Nigel K H Slater, Aaron Martin, Vladimir A Baulin, Tia E Keyes
Deeper understanding of the molecular interactions between polymeric materials and the lipid membrane is important across a range of applications from permeation for drug delivery to encapsulation for immuno-evasion. Using highly fluidic microcavity supported lipid bilayers, we studied the interactions between amphiphilic polymer PP50 and a DOPC lipid bilayer. As the PP50 polymer is pH responsive the studies were carried out at pH 6.5, 7.05 and 7.5, corresponding to fully, partly protonated (pH = pKa = 7.05) and fully ionized states of the polymer, respectively...
March 22, 2017: Soft Matter
https://www.readbyqxmd.com/read/28325767/cohesive-properties-of-the-caulobacter-crescentus-holdfast-adhesin-are-regulated-by-a-novel-c-di-gmp-effector-protein
#6
Kathrin S Sprecher, Isabelle Hug, Jutta Nesper, Eva Potthoff, Mohamed-Ali Mahi, Matteo Sangermani, Volkhard Kaever, Torsten Schwede, Julia Vorholt, Urs Jenal
When encountering surfaces, many bacteria produce adhesins to facilitate their initial attachment and to irreversibly glue themselves to the solid substrate. A central molecule regulating the processes of this motile-sessile transition is the second messenger c-di-GMP, which stimulates the production of a variety of exopolysaccharide adhesins in different bacterial model organisms. In Caulobacter crescentus, c-di-GMP regulates the synthesis of the polar holdfast adhesin during the cell cycle, yet the molecular and cellular details of this control are currently unknown...
March 21, 2017: MBio
https://www.readbyqxmd.com/read/28325313/a-structural-basis-for-the-amphiphilic-character-of-alginates-implications-for-membrane-fouling
#7
Matthew B Stewart, Darli T Myat, Michael Kuiper, Richard J Manning, Stephen R Gray, John D Orbell
Ostensibly hydrophilic alginates are known to foul hydrophobic membranes, under various conditions. Here, controlled experiments have been conducted at high and low pH on the fouling of a polypropylene membrane by alginate and the results suggest that the observed fouling is due to an intrinsic property of the alginate. Thus quantum chemical calculations on the M and G monomers of alginate reveal that M adopts an equilibrium geometry that is hydrophilic on one face and hydrophobic on the other, i.e. is potentially amphiphilic...
May 15, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28323277/an-alternative-polysaccharide-uptake-mechanism-of-marine-bacteria
#8
Greta Reintjes, Carol Arnosti, Bernhard M Fuchs, Rudolf Amann
Heterotrophic microbial communities process much of the carbon fixed by phytoplankton in the ocean, thus having a critical role in the global carbon cycle. A major fraction of the phytoplankton-derived substrates are high-molecular-weight (HMW) polysaccharides. For bacterial uptake, these substrates must initially be hydrolysed to smaller sizes by extracellular enzymes. We investigated polysaccharide hydrolysis by microbial communities during a transect of the Atlantic Ocean, and serendipitously discovered-using super-resolution structured illumination microscopy-that up to 26% of total cells showed uptake of fluorescently labelled polysaccharides (FLA-PS)...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28319616/dna-probes-for-monitoring-dynamic-and-transient-molecular-encounters-on-live-cell-membranes
#9
Mingxu You, Yifan Lyu, Da Han, Liping Qiu, Qiaoling Liu, Tao Chen, Cuichen Sam Wu, Lu Peng, Liqin Zhang, Gang Bao, Weihong Tan
Cells interact with the extracellular environment through molecules expressed on the membrane. Disruption of these membrane-bound interactions (or encounters) can result in disease progression. Advances in super-resolution microscopy have allowed membrane encounters to be examined, however, these methods cannot image entire membranes and cannot provide information on the dynamic interactions between membrane-bound molecules. Here, we show a novel DNA probe that can transduce transient membrane encounter events into readable cumulative fluorescence signals...
March 20, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28317993/capturing-the-multiscale-dynamics-of-membrane-protein-complexes-with-all-atom-mixed-resolution-and-coarse-grained-models
#10
Chenyi Liao, Xiaochuan Zhao, Jiyuan Liu, Severin T Schneebeli, John C Shelley, Jianing Li
The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28317964/how-does-ytterbium-chloride-interact-with-dmpc-bilayers-a-computational-and-experimental-study
#11
Miguel A Gonzalez, Hanna M G Barriga, Joanna L Richens, Robert V Law, Paul O'Shea, Fernando Bresme
Lanthanide salts have been studied for many years, primarily in Nuclear Magnetic Resonance (NMR) experiments of mixed lipid-protein systems and more recently to study lipid flip-flop in model membrane systems. It is well recognised that lanthanide salts can influence the behaviour of both lipid and protein systems, however a full molecular level description of lipid-lanthanide interactions is still outstanding. Here we present a study of lanthanide-bilayer interactions, using molecular dynamics computer simulations, fluorescence electrostatic potential experiments and nuclear magnetic resonance...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28317948/local-remodeling-of-synthetic-extracellular-matrix-microenvironments-by-co-cultured-endometrial-epithelial-and-stromal-cells-enables-long-term-dynamic-physiological-function
#12
Christi D Cook, Abby S Hill, Margaret Guo, Linda Stockdale, Julia P Papps, Keith B Isaacson, Douglas A Lauffenburger, Linda G Griffith
Mucosal barrier tissues, comprising a layer of tightly-bonded epithelial cells in intimate molecular communication with an underlying matrix-rich stroma containing fibroblasts and immune cells, are prominent targets for drugs against infection, chronic inflammation, and other disease processes. Although human in vitro models of such barriers are needed for mechanistic studies and drug development, differences in extracellular matrix (ECM) needs of epithelial and stromal cells hinder efforts to create such models...
March 20, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28317903/stability-and-dynamics-of-membrane-spanning-dna-nanopores
#13
Vishal Maingi, Jonathan R Burns, Jaakko J Uusitalo, Stefan Howorka, Siewert J Marrink, Mark S P Sansom
Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube...
March 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28315296/annexin-a6-controls-neuronal-membrane-dynamics-throughout-chick-cranial-sensory-gangliogenesis
#14
Ankita Shah, Andrew T Schiffmacher, Lisa A Taneyhill
Cranial sensory ganglia are components of the peripheral nervous system that possess a significant somatosensory role and include neurons within the trigeminal and epibranchial nerve bundles. Although it is well established that these ganglia arise from interactions between neural crest and neurogenic placode cells, the molecular basis of ganglia assembly is still poorly understood. Members of the Annexin protein superfamily play key roles in sensory nervous system development throughout metazoans. Annexin A6 is expressed in chick trigeminal and epibranchial placode cell-derived neuroblasts and neurons, but its function in cranial ganglia formation has not been elucidated...
March 14, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28303813/molecular-typing-of-chlamydia-trachomatis-an-overview
#15
REVIEW
Jyoti Rawre, Deepak Juyal, Benu Dhawan
Urogenital infection due to Chlamydia trachomatis (CT) is one of the most common bacterial sexually transmitted infections (STIs) and is a major public health problem worldwide. Molecular characterisation of CT is important for understanding the pathophysiological mechanisms of chlamydial disease and its transmission dynamics in sexual networks. Traditionally, strain typing of CT was based on serotyping methods characterising the major outer membrane protein (MOMP). With the advent of polymerase chain reaction and sequencing the era of molecular typing began...
January 2017: Indian Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28303107/localization-and-ordering-of-lipids-around-aquaporin-0-protein-and-lipid-mobility-effects
#16
Rodolfo Briones, Camilo Aponte-Santamaría, Bert L de Groot
Hydrophobic matching, lipid sorting, and protein oligomerization are key principles by which lipids and proteins organize in biological membranes. The Aquaporin-0 channel (AQP0), solved by electron crystallography (EC) at cryogenic temperatures, is one of the few protein-lipid complexes of which the structure is available in atomic detail. EC and room-temperature molecular dynamics (MD) of dimyristoylglycerophosphocholine (DMPC) annular lipids around AQP0 show similarities, however, crystal-packing and temperature might affect the protein surface or the lipids distribution...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28302513/expression-purification-and-enzymatic-characterization-of-undecaprenyl-pyrophosphate-phosphatase-from-vibrio-vulnificus
#17
Hsin-Yang Chang, Chia-Cheng Chou, Mao-Lun Wu, Andrew H J Wang
Undecaprenyl pyrophosphate phosphatase (UppP), a cell membrane integral enzyme, catalyzes the dephosphorylation of undecaprenyl pyrophosphate to undecaprenyl phosphate, which is an essential carrier lipid in bacterial cell wall synthesis. We previously purified E. coli UppP and concluded that its catalytic site is likely located in the periplasm. To search for additional natural UppP homologs to elucidate what constitutes a common catalytic mechanism and to gain a better chance of obtaining high-resolution crystal structural information, we expressed and purified recombinant Vibrio vulnificus UppP using E...
March 14, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28302399/elucidation-of-structural-and-functional-integration-of-a-novel-antimicrobial-peptide-from-antheraea-mylitta
#18
Suhrid R Dutta, Samiran S Gauri, Twisa Ghosh, Suman K Halder, Pradeep K DasMohapatra, Keshab C Mondal, Ananta K Ghosh
We report here the amino acid sequence of an antimicrobial peptide of Antheraea mylitta (peptide fraction II) effectively killed urinary tract associated MDR E. coli (Dutta et al., 2016), as Gly-Gly-Gly-Gly-Gly-Gly-His-Leu-Val-Ala. The physicochemical and biological properties of this peptide were evaluated by computational analysis and its isoelectric point, grand average of hydropathicity and Boman index values were found to be 6.74, 0.42 and -1.17kcal/mol, respectively. One valid model of peptide fraction II was constructed, that contains two antiparallel β sheets with a hairpin and appeared as 'U' shaped structure...
March 3, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28301927/molecular-mechanism-underlying-the-action-of-the-influenza-a-virus-fusion-inhibitor-mbx2546
#19
Arnab Basu, Gloria Komazin-Meredith, Courtney McCarthy, Aleksandar Antanasijevic, Steven C Cardinale, Rama K Mishra, Dale L Barnard, Michael Caffrey, Lijun Rong, Terry L Bowlin
Influenza A virus envelop protein, Hemagglutinin (HA), plays important roles in viral entry. We previously have reported that MBX2546, a novel influenza A virus inhibitor, binds to HA and inhibits HA-mediated membrane fusion. In this report, we show that (i) both binding and stabilization of HA by MBX2546 is required for inhibition of viral infection, and (ii) binding of HA by MBX2546 represses the low-pH-induced conformational change of the HA which is a prerequisite for membrane fusion. Mutations in MBX2546-resistant influenza A/PR/8/34 (H1N1) viruses are mapped in the HA stem region near the amino terminus of HA2...
March 16, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/28301740/mitochondrial-machineries-for-protein-import-and-assembly
#20
Nils Wiedemann, Nikolaus Pfanner
Mitochondria are essential organelles with numerous functions in cellular metabolism and homeostasis. Most of the >1,000 different mitochondrial proteins are synthesized as precursors in the cytosol and are imported into mitochondria by five transport pathways. The protein import machineries of the mitochondrial membranes and aqueous compartments reveal a remarkable variability of mechanisms for protein recognition, translocation, and sorting. The protein translocases do not operate as separate entities but are connected to each other and to machineries with functions in energetics, membrane organization, and quality control...
March 15, 2017: Annual Review of Biochemistry
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