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Molecular dynamics membrane

Mahar Fatima, Bharat Prajapati, Kanza Saleem, Rina Kumari, Chitra Mohindar Singh Singal, Pankaj Seth
Astroglia are indispensable component of the tripartite synapse ensheathing innumerous soma and synapses. Its proximity to neurons aids the regulation of neuronal functions, health and survival through dynamic neuroglia crosstalk. Susceptibility of astrocyte to HIV-1 infection and subsequent latency culminates in compromised neuronal health. The viral protein HIV-1 transactivator of transcription (Tat) is neurotoxic. HIV-1 Tat is detected in brain of AIDS patients even in cases where viral load is non-detectable due to successful HAART therapy...
October 20, 2016: Glia
Laureano M Alarcón, M de Los Angeles Frías, Marcela A Morini, M Belén Sierra, Gustavo A Appignanesi, E Anibal Disalvo
We employ molecular dynamics simulations to study the hydration properties of Dipalmitoylphosphatidylcholine (DPPC) bilayers, both in the gel and the liquid crystalline states. We show that while the tight hydration centers (PO and CO moieties) are significantly hydrated in both phases, the gel-fluid transition involves significant changes at the second hydration shell, particularly at the buried region between the hydrocarbon tails. Thus, while almost no buried water population exists in the gel state below the carbonyls, this hydrophobic region becomes partially water accesible in the liquid crystalline state...
October 2016: European Physical Journal. E, Soft Matter
Tomasz Róg, Adam Orłowski, Alicia Llorente, Tore Skotland, Tuulia Sylvänne, Dimple Kauhanen, Kim Ekroos, Kirsten Sandvig, Ilpo Vattulainen
In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present in these models are: cholesterol (CHOL), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (POPE), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidyl-ethanolamine (SOPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-D-erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroyl-D-erythro-sphingosyl-phosphatidylcholine (SM24)...
June 2016: Data in Brief
Jelle Hendrix, Tomas Dekens, Waldemar Schrimpf, Don C Lamb
Combining imaging with correlation spectroscopy, as in raster image correlation spectroscopy (RICS), makes it possible to extract molecular translational diffusion constants and absolute concentrations, and determine intermolecular interactions from single-channel or multicolor confocal laser-scanning microscopy (CLSM) images. Region-specific RICS analysis remains very challenging because correlations are always calculated in a square region-of-interest (ROI). In this study, we describe a generalized image correlation spectroscopy algorithm that accepts arbitrarily shaped ROIs...
October 18, 2016: Biophysical Journal
Maite L Ortiz-Suarez, Firdaus Samsudin, Thomas J Piggot, Peter J Bond, Syma Khalid
OmpA is a multidomain protein found in the outer membranes of most Gram-negative bacteria. Despite a wealth of reported structural and biophysical studies, the structure-function relationships of this protein remain unclear. For example, it is still debated whether it functions as a pore, and the precise molecular role it plays in attachment to the peptidoglycan of the periplasm is unknown. The absence of a consensus view is partly due to the lack of a complete structure of the full-length protein. To address this issue, we performed molecular-dynamics simulations of the full-length model of the OmpA dimer proposed by Robinson and co-workers...
October 18, 2016: Biophysical Journal
Priyanka Dutta, Ahnaf Siddiqui, Mohsen Botlani, Sameer Varma
Nipah is an emerging paramyxovirus that is of serious concern to human health. It invades host cells using two of its membrane proteins-G and F. G binds to host ephrins and this stimulates G to activate F. Upon activation, F mediates virus-host membrane fusion. Here we focus on mechanisms that underlie the stimulation of G by ephrins. Experiments show that G interacts with ephrin and F through separate sites located on two different domains, the receptor binding domain (RBD) and the F activation domain (FAD)...
October 18, 2016: Biophysical Journal
Gargi Mahapatra, Ashwathy Varughese, Qinqin Ji, Icksoo Lee, Jenney Liu, Asmita Vaishnav, Christopher Sinkler, Alexandr A Kapralov, Carlos T Moraes, Thomas H Sanderson, Timothy L Stemmler, Lawrence I Grossman, Valerian E Kagan, Joseph S Brunzelle, Arthur R Salomon, Brian F P Edwards, Maik Hüttemann
Mammalian cytochrome c (Cytc) plays a key role in cellular life and death decisions, functioning as an electron carrier in the electron transport chain (ETC) and as a trigger of apoptosis when released from the mitochondria. However, its regulation is not well understood. We show that the major fraction of Cytc isolated from kidneys is phosphorylated on Thr28, leading to a partial inhibition of respiration in the reaction with cytochrome c oxidase. To further study the effect of Cytc phosphorylation in vitro, we generated Thr28Glu phosphomimetic Cytc, revealing superior behavior regarding protein stability and its ability to degrade reactive oxygen species compared to wild-type unphosphorylated Cytc...
October 7, 2016: Journal of Biological Chemistry
Vicente Andreu-Fernandez, Maria J García-Murria, Manuel Bañó-Polo, Juliette Martin, Luca Monticelli, Mar Orzáez, Ismael Mingarro
Changes in the equilibrium of pro- and anti-apoptotic members of the B-cell lymphoma-2 (Bcl-2) protein family in the mitochondrial outer membrane (MOM) induce structural changes that commit cells to apoptosis. Bcl-2 homology-3 (BH3)-only proteins participate in this process by either activating pro-apoptotic effectors or inhibiting anti-apoptotic components and by promoting MOM permeabilization. The association of BH3-only proteins with MOMs is necessary for the activation and amplification of death signals; however, the nature of this association remains controversial, as these proteins lack a canonical transmembrane sequence...
October 7, 2016: Journal of Biological Chemistry
Alexander K Andrianov, Alexander Marin, Thomas R Fuerst
Two macromolecular immunoadjuvants - poly[di(carboxylatophenoxy)phosphazene], PCPP and poly[di(carboxylatoethylphenoxy)phosphazene], PCEP have been investigated for their molecular interactions with model and bio-pharmaceutically important proteins in solutions, as well as for their TLR stimulatory effects and pH-dependent membrane disruptive activity in cellular assays. Solution interactions between polyphosphazenes and proteins, including antigens and soluble immune receptor proteins, have been studied using Asymmetric Flow Field Flow Fractionation (AF4) and Dynamic Light Scattering (DLS) at near physiological conditions - phosphate buffered saline, pH 7...
October 17, 2016: Biomacromolecules
Sang Joon Won, Dahvid Davda, Kristin J Labby, Sin Ye Hwang, Rachel E Pricer, Jaimeen D Majmudar, Kira A Armacost, Laura A Rodriguez, Christina L Rodriguez, Fei San Chong, Kristopher A Torossian, Jasmine Palakurthi, Edward S Hur, Jennifer L Meagher, Charles L Brooks, Jeanne A Stuckey, Brent R Martin
Post-translational S-palmitoylation directs the trafficking and membrane localization of hundreds of cellular proteins, often involving a coordinated palmitoylation cycle that requires both protein acyl transferases (PATs) and acyl protein thioesterases (APTs) to actively re-distribute S-palmitoylated proteins towards different cellular membrane compartments. This process is necessary for the trafficking and oncogenic signaling of S-palmitoylated Ras isoforms, and potentially other peripheral membrane proteins...
October 17, 2016: ACS Chemical Biology
Miguel A Gonzalez-Lozano, Patricia Klemmer, Titia Gebuis, Chopie Hassan, Pim van Nierop, Ronald E van Kesteren, August B Smit, Ka Wan Li
Development of the brain involves the formation and maturation of numerous synapses. This process requires prominent changes of the synaptic proteome and potentially involves thousands of different proteins at every synapse. To date the proteome analysis of synapse development has been studied sparsely. Here, we analyzed the cortical synaptic membrane proteome of juvenile postnatal days 9 (P9), P15, P21, P27, adolescent (P35) and different adult ages P70, P140 and P280 of C57Bl6/J mice. Using a quantitative proteomics workflow we quantified 1560 proteins of which 696 showed statistically significant differences over time...
October 17, 2016: Scientific Reports
Alexandros Koutsioubas
Supported lipid bilayers on planar surfaces constitute an archetypical experimental system for the study of biological membranes. The popularity of these ordered molecular layers in the literature, is on one hand related to the simplicity of their preparation using the method of vesicle fusion and on the other hand to their compatibility with a multitude of surface sensitive experimental probes. Neutron reflectivity has proven as an important experimental method for the investigation of such systems with the ability to provide sub-nanometer structural information perpendicular to the supporting plane...
October 17, 2016: Journal of Physical Chemistry. B
Peter Husen, Ilia A Solov'yov
The homodimeric bc1 protein complex is embedded in membranes of mitochondria and photosynthetic bacteria, where it transports protons across the membrane to maintain an electrostatic potential used to drive ATP synthesis as part of the respiratory or photosynthetic pathways. The reaction cycle of the bc1 complex is driven by series of redox processes involving substrate molecules from the membrane, but occasional side reactions between an intermediate semiquinone substrate and molecular oxygen are suspected to be a source of toxic superoxide, which is believed to be a factor in aging...
October 17, 2016: Journal of Physical Chemistry. B
Xuejuan Liu, Falin Tian, Tongtao Yue, Xianren Zhang, Chongli Zhong
The shape deformation of membrane nanotubes is studied by a combination of theoretical analysis and molecular simulation. First we perform free energy analysis to demonstrate the effects of various factors on two ideal states for the pearling transition, and then we carry out dissipative particle dynamics simulations, through which various types of membrane tube deformation are found, including membrane pearling, buckling, and bulging. Different models for inducing tube deformation, including the osmotic pressure, area difference and spontaneous curvature models, are considered to investigate tubular instabilities...
October 17, 2016: Soft Matter
Ranjeet Kumar, Candan Ariöz, Yaozong Li, Niklas Bosaeus, Sandra Rocha, Pernilla Wittung-Stafshede
After cellular uptake, Copper (Cu) ions are transferred from the chaperone Atox1 to the Wilson disease protein (ATP7B) for incorporation into Cu-dependent enzymes in the secretory pathway. Human ATP7B is a large multi-domain membrane-spanning protein which, in contrast to homologues in other organisms, has six similar cytoplasmic metal-binding domains (MBDs). The reason for multiple MBDs is proposed to be indirect modulation of enzymatic activity and it is thus intriguing that point mutations in MBDs can promote Wilson disease...
October 15, 2016: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
Olivia Gay, Benoît Gilquin, Nicole Assard, Pascal Stuelsatz, Christian Delphin, Joël Lachuer, Xavier Gidrol, Jacques Baudier
Refilins (RefilinA and RefilinB) are members of a novel family of Filamin binding proteins that function as molecular switches to conformationally alter the Actin filament network into bundles. We show here that Refilins are extremely labile proteins. An N-terminal PEST/DSG(X)2-4S motif mediates ubiquitin-independent rapid degradation. A second degradation signal is localized within the C-terminus. Only RefilinB is protected from rapid degradation by an auto-inhibitory domain that masks the PEST/DSG(X)2-4S motif...
October 15, 2016: Biology Open
Hongmei Xia, Yinxiang Xu, Zhiqing Cheng, Yongfeng Cheng
Tetramethylpyrazine (TMP) was extracted from Ligusticum chuanxiong hort. The compound is known to have a variety of medicinal functions; in particular, it is used for the treatment of cerebral ischemic diseases. TMP-loaded hydrogels offer an excellent preparation with the capacity to bypass the blood-brain barrier, allowing treatment of the brain through intranasal administration. We prepared TMP-loaded hydrogels using carbomer 940 and evaluated the release of TMP from the hydrogel. We determined the release rate using Franz-type diffusion cell experiments with a subcutaneous-mucous-membrane model and also by a molecular dynamics (MD) simulation...
October 14, 2016: AAPS PharmSciTech
Benjamin E Brummel, Anthony R Braun, Jonathan N Sachs
Using molecular dynamics simulations, we have explored the effect of asymmetric lipids-specifically those that contain one polyunsaturated (PUFA) and one saturated fatty acid chain-on phase separation in heterogeneous membranes. These lipids are prevalent in neuronal membranes, particularly in synaptic membranes, where the Parkinson's Disease protein α-Synuclein (αS) is found. We have therefore explored the relationship between asymmetric, PUFA-containing lipids, and αS. The simulations show that asymmetric lipids partition to the liquid disordered (Ld) phase of canonical raft mixtures because of the highly disordered PUFA chain...
October 12, 2016: Biochimica et Biophysica Acta
Laura László, Balázs Sarkadi, Tamás Hegedűs
ABCG2/BCRP is a membrane protein, involved in xenobiotic and endobiotic transport in key pharmacological barriers and drug metabolizing organs, in the protection of stem cells, and in multidrug resistance of cancer. Pharmacogenetic studies implicated the role of ABCG2 in response to widely used medicines and anticancer agents, as well as in gout. Its Q141K variant exhibits decreased functional expression thus increased drug accumulation and decreased urate secretion. Still, there has been no reliable molecular model available for this protein, as the published structures of other ABC transporters could not be properly fitted to the ABCG2 topology and experimental data...
2016: PloS One
Panagiotis Angelikopoulos, Lev Sarkisov, Zoe Cournia, Paraskevi Gkeka
Ligand-functionalized nanoparticles (NPs) are a promising platform for imaging and drug delivery applications. A number of recent molecular simulation and theoretical studies explored how these NPs interact with model lipid membranes. However, interactions between ligand-coated NPs leading to possible cooperative effects and association have not been investigated. In this coarse-grained molecular dynamics study, we focus on a specific case of several anionic, ligand-coated NPs embedded in a lipid membrane. Several new effects are observed...
October 14, 2016: Nanoscale
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