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https://www.readbyqxmd.com/read/28214974/interaction-of-scots-pine-defensin-with-model-membrane-by-coarse-grained-molecular-dynamics
#1
Elena Ermakova, Yuriy Zuev
Plant defensins are a part of the innate immune system of plants that acts against a broad range of pathogens. Many plant defensins, including pine defensins, show strong antifungal activity that is associated with their ability to penetrate into the fungal cell membrane. However, the exact molecular mechanism of their action remains poorly defined. To obtain insight into the mechanism of protein-membrane interaction, we applied a coarse-grained molecular dynamics simulation to study the interaction of pine defensin with two model membranes: the first consisted of zwitterion-neutral POPC molecules and the second was composed of combined anionic POPG and POPC...
February 18, 2017: Journal of Membrane Biology
https://www.readbyqxmd.com/read/28214513/molecular-dynamics-simulation-study-of-the-effect-of-glycerol-dialkyl-glycerol-tetraether-hydroxylation-on-membrane-thermostability
#2
Carme Huguet, Susanne Fietz, Antoni Rosell-Melé, Xavier Daura, Lionel Costenaro
Archaeal tetraether membrane lipids span the whole membrane width and present two C40 isoprenoid chains bound by two glycerol groups (or one glycerol and calditol). These lipids confer stability and maintain the membrane fluidity in mesophile to extremophile environments, making them very attractive for biotechnological applications. The isoprenoid lipid composition in archaeal membranes varies with temperature, which has placed these lipids in the focus of paleo-climatological studies for about a decade. Non-hydroxylated isoprenoid archaeal lipids are typically used as paleo-thermometry proxies, but recently identified hydroxylated (OH) derivatives have also been proposed as temperature proxies...
February 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28212178/the-long-journey-through-renal-filtration-new-pieces-in-the-puzzle-of-slit-diaphragm-architecture
#3
Sara Conti, Luca Perico, Florian Grahammer, Tobias B Huber
PURPOSE OF REVIEW: The podocyte slit diaphragm is probably the least understood component of the kidney filtration barrier. In this review, we aim to integrate the most recent findings on the molecular make-up and structural architecture of this specialized cell-cell junction into a current concept of glomerular filtration. RECENT FINDINGS: Analysis of cryopreserved mammalian tissue revealed a bipartite composition of the slit diaphragm. Single NEPH1 molecules span the lower part of the slit close to the glomerular basement membrane whereas NEPHRIN molecules are positioned in the apical part toward Bowman's space...
February 16, 2017: Current Opinion in Nephrology and Hypertension
https://www.readbyqxmd.com/read/28211276/tuning-the-pseudospin-polarization-of-graphene-by-a-pseudo-magnetic-field
#4
Alexander Georgi, Peter Nemes-Incze, Ramon Carrillo-Bastos, Daiara Faria, Silvia Viola Kusminskiy, Dawei Zhai, Martin Schneider, Dinesh Subramaniam, Torge Mashoff, Nils Michael Freitag, Marcus Liebmann, Marco Pratzer, Ludger Wirtz, Colin R Woods, Roman Vladislavovich Gorbachev, Yang Cao, Kostya S Novoselov, Nancy Sandler, Markus Morgenstern
One of the intriguing characteristics of honeycomb lattices is the appearance of a pseudo-magnetic field as a result of mechanical deformation. In the case of graphene, the Landau quantization resulting from this pseudo-magnetic field has been measured using scanning tunneling microscopy. Here we show that a signature of the pseudo-magnetic field is a local sublattice symmetry breaking observable as a redistribution of the local density of states. This can be interpreted as a polarization of graphene's pseudospin due to a strain induced pseudo-magnetic field, in analogy to the alignment of a real spin in a magnetic field...
February 17, 2017: Nano Letters
https://www.readbyqxmd.com/read/28211109/conformational-space-of-a-polyphilic-molecule-with-a-fluorophilic-side-chain-integrated-in-a-dppc-bilayer
#5
Guido F von Rudorff, Tobias Watermann, Xiang-Yang Guo, Daniel Sebastiani
We investigate the conformational space of a polyphilic molecule with hydrophilic, lipophilic and fluorophilic parts inserted as a transmembrane agent into a dipalmitoylphosphatidylcholine bilayer by means of all-atom molecular dynamics simulations. Special focus is put on the competing structural driving forces arising from the hydrophilic, lipophilic and fluorophilic side chains and the aromatic backbone of the polyphile. We observe a significant difference between the lipophilic and the fluorophilic side chains regarding their intramembrane distribution...
April 5, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28209181/de-novo-sequencing-and-comparative-transcriptome-analysis-of-adventitious-root-development-induced-by-exogenous-indole-3-butyric-acid-in-cuttings-of-tetraploid-black-locust
#6
Jine Quan, Seng Meng, Erhui Guo, Sheng Zhang, Zhong Zhao, Xitian Yang
BACKGROUND: Indole-3-butyric acid (IBA) is applied to the cuttings of various plant species to induce formation of adventitious roots (ARs) in commercial settings. Tetraploid black locust is an attractive ornamental tree that is drought resistant, sand tolerant, can prevent sand erosion and has various commercial uses. To further elucidate the mechanisms of AR formation, we used Illumina sequencing to analyze transcriptome dynamics and differential gene expression at four developmental stages in control (CK) and IBA-treated groups...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28207738/testing-the-limits-of-gradient-sensing
#7
Vinal Lakhani, Timothy C Elston
The ability to detect a chemical gradient is fundamental to many cellular processes. In multicellular organisms gradient sensing plays an important role in many physiological processes such as wound healing and development. Unicellular organisms use gradient sensing to move (chemotaxis) or grow (chemotropism) towards a favorable environment. Some cells are capable of detecting extremely shallow gradients, even in the presence of significant molecular-level noise. For example, yeast have been reported to detect pheromone gradients as shallow as 0...
February 16, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28205528/reversed-thermo-switchable-molecular-sieving-membranes-composed-of-two-dimensional-metal-organic-nanosheets-for-gas-separation
#8
Xuerui Wang, Chenglong Chi, Kang Zhang, Yuhong Qian, Krishna M Gupta, Zixi Kang, Jianwen Jiang, Dan Zhao
It is highly desirable to reduce the membrane thickness in order to maximize the throughput and break the trade-off limitation for membrane-based gas separation. Two-dimensional membranes composed of atomic-thick graphene or graphene oxide nanosheets have gas transport pathways that are at least three orders of magnitude higher than the membrane thickness, leading to reduced gas permeation flux and impaired separation throughput. Here we present nm-thick molecular sieving membranes composed of porous two-dimensional metal-organic nanosheets...
February 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28199758/mechanical-trap-surface-enhanced-raman-spectroscopy-for-three-dimensional-surface-molecular-imaging-of-single-live-cells
#9
Qianru Jin, Ming Li, Beril Polat, Santosh K Paidi, Aimee Dai, Amy Zhang, Jayson V Pagaduan, Ishan Barman, David H Gracias
Reported is a new shell-based spectroscopic platform, named mechanical trap surface-enhanced Raman spectroscopy (MTSERS), for simultaneous capture, profiling, and 3D microscopic mapping of the intrinsic molecular signatures on the membrane of single live cells. By leveraging the functionalization of the inner surfaces of the MTs with plasmonic gold nanostars, and conformal contact of the cell membrane, MTSERS permits excellent signal enhancement, reliably detects molecular signatures, and allows non-perturbative, multiplex 3D surface imaging of analytes, such as lipids and proteins on the surface of single cells...
February 15, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28197922/coordination-of-cellular-localization-dependent-effects-of-sumoylation-in-regulating-cardiovascular-and-neurological-diseases
#10
Jun-Ichi Abe, Uday G Sandhu, Nguyet Minh Hoang, Manoj Thangam, Raymundo A Quintana-Quezada, Keigi Fujiwara, Nhat Tu Le
Sumoylation, a reversible post-transcriptional modification process, of proteins are involved in cellular differentiation, growth, and even motility by regulating various protein functions. Sumoylation is not limited to cytosolic proteins as recent evidence shows that nuclear proteins, those associated with membranes, and mitochondrial proteins are also sumoylated. Moreover, it is now known that sumoylation plays an important role in the process of major human ailments such as malignant, cardiovascular and neurological diseases...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28197608/the-dynamic-mechanism-of-rassf5-and-mst-kinase-activation-by-ras
#11
Tsung-Jen Liao, Hyunbum Jang, Chung-Jung Tsai, David Fushman, Ruth Nussinov
As a tumor suppressor, RASSF5 (NORE1A) activates MST1/2 thereby modulating the Hippo pathway. Structurally, activation involves RASSF5 and MST1/2 swapping their SARAH domains to form a SARAH heterodimer. This exposes the MST1/2 kinase domain which homodimerizes, leading to trans-autophosphorylation. The SARAH-SARAH interaction shifts RASSF5 away from its autoinhibited state and relieves MST1/2 autoinhibition. Separate crystal structures are available for the RA (Ras association) domain and SARAH dimer, where SARAH is a long straight α-helix...
February 15, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28197584/nanoscale-tailor-made-membranes-for-precise-and-rapid-molecular-sieve-separation
#12
Jing Wang, Junyong Zhu, Yatao Zhang, Jindun Liu, Bart Van der Bruggen
The precise and rapid separation of different molecules from aqueous, organic solutions and gas mixtures is critical to many technologies in the context of resource-saving and sustainable development. The strength of membrane-based technologies is well recognized and they are extensively applied as cost-effective, highly efficient separation techniques. Currently, empirical-based approaches, lacking an accurate nanoscale control, are used to prepare the most advanced membranes. In contrast, nanoscale control renders the membrane molecular specificity (sub-2 nm) necessary for efficient and rapid molecular separation...
February 15, 2017: Nanoscale
https://www.readbyqxmd.com/read/28193899/structure-of-a-lipid-a-phosphoethanolamine-transferase-suggests-how-conformational-changes-govern-substrate-binding
#13
Anandhi Anandan, Genevieve L Evans, Karmen Condic-Jurkic, Megan L O'Mara, Constance M John, Nancy J Phillips, Gary A Jarvis, Siobhan S Wills, Keith A Stubbs, Isabel Moraes, Charlene M Kahler, Alice Vrielink
Multidrug-resistant (MDR) gram-negative bacteria have increased the prevalence of fatal sepsis in modern times. Colistin is a cationic antimicrobial peptide (CAMP) antibiotic that permeabilizes the bacterial outer membrane (OM) and has been used to treat these infections. The OM outer leaflet is comprised of endotoxin containing lipid A, which can be modified to increase resistance to CAMPs and prevent clearance by the innate immune response. One type of lipid A modification involves the addition of phosphoethanolamine to the 1 and 4' headgroup positions by phosphoethanolamine transferases...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28192423/elucidation-of-molecular-kinetic-schemes-from-macroscopic-traces-using-system-identification
#14
Miguel Fribourg, Diomedes E Logothetis, Javier González-Maeso, Stuart C Sealfon, Belén Galocha-Iragüen, Fernando Las-Heras Andrés, Vladimir Brezina
Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic) processes from the overall (macroscopic) response remains a crucial challenge in the understanding of many aspects of physiology...
February 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28192089/dynamic-phenylalanine-clamp-interactions-define-single-channel-polypeptide-translocation-through-the-anthrax-toxin-protective-antigen-channel
#15
Koyel Ghosal, Jennifer M Colby, Debasis Das, Stephen T Joy, Paramjit S Arora, Bryan A Krantz
Anthrax toxin is an intracellularly acting toxin where sufficient detail is known about the structure of its channel, allowing for molecular investigations of translocation. The toxin is comprised of three proteins, protective antigen (PA), lethal factor (LF), and edema factor (EF). The toxin's translocon, PA, translocates the large enzymes, LF and EF, across the endosomal membrane into the host cell's cytosol. Polypeptide clamps located throughout the PA channel catalyze the translocation of LF and EF. Here we show that the central peptide clamp, the ϕ clamp, is a dynamic site that governs the overall peptide translocation pathway...
February 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28191562/fbpa-iron-storage-and-release-are-governed-by-periplasmic-microenvironments
#16
Ozge Sensoy, Ali Rana Atilgan, Canan Atilgan
Ferric binding protein (FbpA) is part of an elaborate iron piracy mechanism evolved in Gram-negative bacteria, shuttling iron in the periplasmic space, from the outer to the cytoplasmic membrane side. We address how the dissociation process of iron is facilitated, since the binding constant of iron is on the order of 10(18) M(-1) at 6.5 pH and 200 mM ionic strength (IS). We monitor the conformational preferences of FbpA by extensive molecular dynamics (MD) simulations under conditions where IS, charge states of iron coordinating tyrosines and pH are varied, as well as when a mutation is introduced at an allosteric site...
February 13, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28191459/epidermal-growth-factor-signaling-towards-proliferation-modeling-and-logic-inference-using-forward-and-backward-search
#17
Adrián Riesco, Beatriz Santos-Buitrago, Javier De Las Rivas, Merrill Knapp, Gustavo Santos-García, Carolyn Talcott
In biological systems, pathways define complex interaction networks where multiple molecular elements are involved in a series of controlled reactions producing responses to specific biomolecular signals. These biosystems are dynamic and there is a need for mathematical and computational methods able to analyze the symbolic elements and the interactions between them and produce adequate readouts of such systems. In this work, we use rewriting logic to analyze the cellular signaling of epidermal growth factor (EGF) and its cell surface receptor (EGFR) in order to induce cellular proliferation...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28187200/ligand-induced-dynamics-of-heterotrimeric-g-protein-coupled-receptor-like-kinase-complexes
#18
Meral Tunc-Ozdemir, Alan M Jones
BACKGROUND: Arabidopsis, 7-transmembrane Regulator of G signaling protein 1 (AtRGS1) modulates canonical G protein signaling by promoting the inactive state of heterotrimeric G protein complex on the plasma membrane. It is known that plant leucine-rich repeat receptor-like kinases (LRR RLKs) phosphorylate AtRGS1 in vitro but little is known about the in vivo interaction, molecular dynamics, or the cellular consequences of this interaction. METHODS: Therefore, a subset of the known RLKs that phosphorylate AtRGS1 were selected for elucidation, namely, BAK1, BIR1, FLS2...
2017: PloS One
https://www.readbyqxmd.com/read/28186490/atomistic-simulations-indicate-the-c-subunit-ring-of-the-f1fo-atp-synthase-is-not-the-mitochondrial-permeability-transition-pore
#19
Wenchang Zhou, Fabrizio Marinelli, Corrine Nief, José D Faraldo-Gómez
Pathological metabolic conditions such as ischemia induce the rupture of the mitochondrial envelope and the release of pro-apoptotic proteins, leading to cell death. At the onset of this process, the inner mitochondrial membrane becomes depolarized and permeable to osmolytes, due to the opening of a non-selective protein channel of unknown molecular identity. A recent study purports that this channel, referred to as Mitochondrial Permeability Transition Pore (MPTP), is the lumen of the c-subunit ring of the ATP synthase, upon dissociation from the catalytic domain...
February 10, 2017: ELife
https://www.readbyqxmd.com/read/28185927/evidence-of-proteolipid-domain-formation-in-an-inner-mitochondrial-membrane-mimicking-model
#20
Mouhedine Cheniour, Jonathan Brewer, Luis Bagatolli, Olivier Marcillat, Thierry Granjon
BACKGROUND: Mitochondrial Creatine kinase (mtCK) is highly abundant in mitochondria; its quantity is equimolecular to the Adenylic Nucleotide Translocator and represents 1% of the mitochondrial proteins. It is a multitask protein localized in the mitochondria intermembrane space where it binds to the specific cardiolipin (CL) phospholipid. If mtCK was initially thought to be exclusively implicated in energy transfer between mitochondria and cytosol through a mechanism referred to as the phosphocreatine shuttle, several recent studies suggested an additional role in maintaining mitochondria membrane structure...
February 6, 2017: Biochimica et Biophysica Acta
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