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Molecular dynamics membrane

Baohe Wang, Yan Nie, Jing Ma
Combing molecular dynamics (MD) and Grand Canonical Monte Carlo (GCMC) simulation, the effect of bioadhesive transition layer on the interfacial compatibility of the pervaporation composite membranes, and the pervaporation performance toward penetrant molecules were investigated. In our previous experimental study, the structural stability and permeability selectivity of the composite membranes were considerably enhanced by the introduction of bioadhesive carbopol (CP). In the present study, the interfacial compatibility and the interfacial energies between the chitosan (CS) separation layer, CP transition layer and the support layer were investigated, respectively...
January 5, 2018: Journal of Molecular Graphics & Modelling
Ran Friedman
Biomembranes assemble and operate at the interface with electrolyte solutions. Interactions between ions in solutions and the lipid affect the membrane structure, dynamics and electrostatic potential. In this article, I review some of the experimental and computational methods that are used to study membrane-ions interactions. Experimental methods that account for membrane-ion interactions directly and indirectly are presented first. Then, studies in which molecular dynamics simulations were used to gain an understanding of membrane-ion interactions are surveyed...
January 12, 2018: Journal of Membrane Biology
Talia Zeppelin, Lucy Kate Ladefoged, Steffen Sinning, Xavier Periole, Birgit Schiøtt
Monoamine transporters (MATs) carry out neurotransmitter reuptake from the synaptic cleft, a key step in neurotransmission, which is targeted in the treatment of neurological disorders. Cholesterol (CHOL), a major component of the synaptic plasma membrane, has been shown to exhibit a modulatory effect on MATs. Recent crystal structures of the dopamine transporter (DAT) revealed the presence of two conserved CHOL-like molecules, suggesting a functional protein-CHOL direct interaction. Here, we present extensive atomistic molecular dynamics (MD) simulations of DAT in an outward-facing conformation...
January 12, 2018: PLoS Computational Biology
Taotao Qiu, Xing Shen, Zhen Tian, Riming Huang, Xiangmei Li, Juan Wang, Rong Wang, Yuanming Sun, Yiguo Jiang, Huidong Zhang, Hongtao Lei
Aflatoxin B1 (AFB1) causes hepatotoxic, genotoxic, and immuno¬toxic effects in a variety of species. Although various neutralizing agents of AFB1 toxicity have been studied, the egg yolk immunoglobulins (IgY) detoxification of small molecular toxins and the mechanisms underlying such effects have not yet been reported. In this investigation, anti-AFB1 IgY against AFB1 was successfully raised, and a competitive indirect enzyme-linked immunosorbent assay was established with a sensitive half-maximal inhibitory concentration (IC50, 2...
January 11, 2018: Journal of Agricultural and Food Chemistry
Jun Wang, Daniel Breen, Abraham Akinin, Frederic Broccard, Henry D I Abarbanel, Gert Cauwenberghs
Representing the biophysics of neuronal dynamics and behavior offers a principled analysis-by-synthesis approach toward understanding mechanisms of nervous system functions. We report on a set of procedures assimilating and emulating neurobiological data on a neuromorphic very large scale integrated (VLSI) circuit. The analog VLSI chip, NeuroDyn, features 384 digitally programmable parameters specifying for 4 generalized Hodgkin-Huxley neurons coupled through 12 conductance-based chemical synapses. The parameters also describe reversal potentials, maximal conductances, and spline regressed kinetic functions for ion channel gating variables...
December 2017: IEEE Transactions on Biomedical Circuits and Systems
Taylor E T Hughes, David T Lodowski, Kevin W Huynh, Aysenur Yazici, John Del Rosario, Abhijeet Kapoor, Sandip Basak, Amrita Samanta, Xu Han, Sudha Chakrapani, Z Hong Zhou, Marta Filizola, Tibor Rohacs, Seungil Han, Vera Y Moiseenkova-Bell
The transient receptor potential vanilloid 5 (TRPV5) channel is a member of the transient receptor potential (TRP) channel family, which is highly selective for Ca2+, that is present primarily at the apical membrane of distal tubule epithelial cells in the kidney and plays a key role in Ca2+ reabsorption. Here we present the structure of the full-length rabbit TRPV5 channel as determined using cryo-EM in complex with its inhibitor econazole. This structure reveals that econazole resides in a hydrophobic pocket analogous to that occupied by phosphatidylinositides and vanilloids in TRPV1, thus suggesting conserved mechanisms for ligand recognition and lipid binding among TRPV channels...
January 2018: Nature Structural & Molecular Biology
Li Ding, Yanying Wei, Libo Li, Tao Zhang, Haihui Wang, Jian Xue, Liang-Xin Ding, Suqing Wang, Jürgen Caro, Yury Gogotsi
Molecular sieving membranes with sufficient and uniform nanochannels that break the permeability-selectivity trade-off are desirable for energy-efficient gas separation, and the arising two-dimensional (2D) materials provide new routes for membrane development. However, for 2D lamellar membranes, disordered interlayer nanochannels for mass transport are usually formed between randomly stacked neighboring nanosheets, which is obstructive for highly efficient separation. Therefore, manufacturing lamellar membranes with highly ordered nanochannel structures for fast and precise molecular sieving is still challenging...
January 11, 2018: Nature Communications
Jamal Adiban, Yousef Jamali, Hashem Rafii-Tabar
CaV channels are transmembrane proteins that mediate and regulate ions fluxes across cell membranes, and they are activated in response to action potentials to allow Ca2+ influx. Since ion channels are composed of charge or polar groups, an external alternating electric field may affect the ion-selective membrane transport and the performance of the channel. In this paper, we have investigated the effect of an external GHz electric field on the dynamics of calcium ions in the selectivity filter of the CaV Ab channel...
January 11, 2018: Proteins
Taro Yamada, Ryosuke Matsuzaki
Graphene membranes can be used for nanoscale filtration to remove atoms and are expected to be used for separation. To realize high-permeability and high-filtration performance, we must understand the flow configuration in the nanochannels. In this study, we investigated the applicability of continuum-dynamics laws to water flow through a graphene slit. We calculated the permeability of the flow through a slit using classical molecular dynamics (MD) and compared the MD simulation results for different Knudsen numbers (Kn) to predictions based on the no-slip model and slip model...
January 10, 2018: Scientific Reports
Hiroshi Ueda, Shiori Maeda
Prothymosin alpha (ProTα) has been identified as an anti-necrotic factor from the conditioned medium of primary cultured of rat cortical neurons under the serum-free starving condition. ProTα is released in a non-vesicular manner from neurons or astrocytes by the help of cargo protein S100A13. Thus released ProTα is found to have robustness roles in the brain under the condition of neuronal necrosis or apoptosis. ProTα inhibits necrosis by plasma membrane-translocation of glucose transporters endocytosed by ischemia/starving stress, through an activation of unidentified G protein-coupled receptor and protein kinase Cβ...
2018: Nihon Yakurigaku Zasshi. Folia Pharmacologica Japonica
Tomoko Mizuguchi, Nobuyuki Matubayasi
All-atom molecular dynamics (MD) simulations are performed to examine the stabilities of a variety of binding configurations of alamethicin, a 20-amino-acid amphipathic peptide, in the bilayers of 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC) and 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC). The binding free energy of alamethicin is calculated through a combination of MD simulation and the energy-representation theory of solutions, and it is seen that the transmembrane configuration is stable in both membranes...
January 10, 2018: Journal of Physical Chemistry. B
C D Williams, P Carbone, F R Siperstein
A multi-step molecular dynamics procedure was developed to construct fully flexible atomistic models of graphene oxide (GO) membranes. The method of preparation replicates the experimental synthesis of the material; i.e. the flow-directed self-assembly of individual flakes onto a substrate or filter. A total of 180 GO membrane models were prepared with water contents varying between 0 and 20%, providing an insight into changes in the membrane's interlayer distance with swelling. Membranes with 15% water content have an average interlayer distance (0...
January 10, 2018: Nanoscale
Junghoon Ha, Yu Xu, Takeharu Kawano, Tyler Hendon, Lia Baki, Sumanta Garai, Andreas Papapetropoulos, Ganesh Thakur, Leigh D Plant, Diomedes E Logothetis
Inwardly rectifying potassium (Kir) channels establish and regulate the resting membrane potential of excitable cells in the heart, brain and other peripheral tissues. Phosphatidylinositol 4,5-bisphosphate (PIP2) is a key direct activator of ion channels, including Kir channels. The gasotransmitter carbon monoxide has been shown to regulate Kir channel activity by altering channel-PIP2 interactions.  Here, we tested in two cellular models the effects and mechanism of action of another gasotransmitter, hydrogen sulfide (H2S), thought to play a key role in cellular responses under ischemic conditions...
January 9, 2018: Journal of Biological Chemistry
Maximilien Lopes-Rodrigues, Jordi Triguero, Juan Torras, Eric A Perpète, Catherine Michaux, David Zanuy, Carlos Alemán
Outer-membrane porins are currently being used to prepare bioinspired nanomembranes for selective ion transport by immobilizing them into polymeric matrices. However, the fabrication of these protein-integrated devices has been found to be strongly influenced by the instability of the β-barrel porin structure, which depends on surrounding environment. In this work, molecular dynamics simulations have been used to investigate the structural stability of a representative porin, OmpF, in three different environments: (i) aqueous solution at pH=7; (ii) a solution of neutral detergent in a concentration similar to the critical micelle concentration; and (iii) the protein embedded into a neutral detergent bilayer...
January 2, 2018: Biophysical Chemistry
Zhongwu Li, Yinghua Qiu, Kun Li, Jingjie Sha, Tie Li, Yunfei Chen
Extensive molecular dynamics simulations are employed to optimize nanopore size and surface charge density in order to obtain high ionic selectivity and high water throughput for seawater desalination systems. It is demonstrated that with the help of surface charge exclusion, nanopores with diameter as large as 3.5 nm still have high ionic selectivity. The mechanism of the salt rejection in a surface-charged nanopore is mainly attributed to the ion concentration difference between the cations and anions induced by the surface charges...
January 7, 2018: Journal of Chemical Physics
Anastasiia Golius, Leonid Gorb, Olexander Isayev, Jerzy Leszczynski
Computational studies of the potential biological impact of several energetic compounds were performed. The most commonly used explosives were considered in the present studies: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,4-dinitroanisole (DNAN), and 5-Nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO). The effect of such factors as ionic strength and presence of DMSO in the water solution on the structure of the membrane were considered using the POPC lipid bilayer as an example. Molecular dynamics (MD) simulations revealed that, even on a short-time scale, the influence of those additives is noticeable, and therefore those factors should always be taken into account...
January 4, 2018: Journal of Biomolecular Structure & Dynamics
Huiying Chu, Xiangda Peng, Yan Li, Yuebin Zhang, Guohui Li
In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and following the same framework as Atomic Multipole Optimized Energetics for BiomoleculAr (AMOEBA) simulation, the present effort expands the force field to new anionic lipid models, in which the new lipids contain DMPG and POPS...
December 31, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Alexander C Forse, Miguel I Gonzalez, Rebecca L Siegelman, Velencia J Witherspoon, Sudi Jawahery, Rocio Mercado, Phillip J Milner, Jeffrey D Martell, Berend Smit, Bernhard Blümich, Jeffrey R Long, Jeffrey A Reimer
Metal-organic frameworks are promising materials for energy-efficient gas separations, but little is known about the diffusion of adsorbates in materials featuring one-dimensional porosity at the nanoscale. An understanding of the interplay between framework structure and gas diffusion is crucial for the practical application of these materials as adsorbents or in mixed-matrix membranes, since the rate of gas diffusion within the adsorbent pores impacts the required size (and therefore cost) of the adsorbent column or membrane...
January 4, 2018: Journal of the American Chemical Society
Ning Xiang, Yuan Lyu, Xiao Zhu, Ganesan Narsimhan
Some amyloid related proteins/peptides are involved in aggregation and pore formation in phospholipid membranes (cell membranes), which result in a variety of neurological disorders such as Alzheimer's disease, Parkinson's disease and Huntington disease. In this research, the mechanism of pore formation by β amyloid (Aβ) peptides was investigated using molecular dynamics simulation by simulating the interaction of the Aβ(11-42) peptide, with a lipid membrane and the potential of the mean force of interaction was evaluated...
January 4, 2018: Physical Chemistry Chemical Physics: PCCP
Ewa Stypulkowski, Irfan A Asangani, Eric S Witze
Asymmetric cell division results in two distinctly fated daughter cells. A molecular hallmark of asymmetric division is the unequal partitioning of cell fate determinants. We have previously established that growth factor signaling promotes protein depalmitoylation to foster polarized protein localization, which, in turn, drives migration and metastasis. We report protein palmitoylation as a key mechanism for the asymmetric partitioning of the cell fate determinants Numb and β-catenin through the activity of the depalmitoylating enzyme APT1...
January 2, 2018: Science Signaling
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