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https://www.readbyqxmd.com/read/28731702/drude-polarizable-force-field-for-molecular-dynamics-simulations-of-saturated-and-unsaturated-zwitterionic-lipids
#1
Hui Li, Janamejaya Chowdhary, Lei Huang, Xibing He, Alexander D MacKerell, Benoît Roux
Additive force fields are designed to account for induced electronic polarization in a mean-field average way using effective empirical fixed charges. The limitation of this approximation is cause for serious concerns, particularly in the case of lipid membranes, where the molecular environment undergoes dramatic variations over microscopic length scales. A polarizable force field based on the classical Drude oscillator offers a practical and computationally efficient framework for an improved representation of electrostatic interactions in molecular simulations...
July 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28730431/protocols-for-molecular-dynamics-simulations-of-rna-nanostructures
#2
Taejin Kim, Wojciech K Kasprzak, Bruce A Shapiro
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28728544/cladosporol-a-triggers-apoptosis-sensitivity-by-ros-mediated-autophagic-flux-in-human-breast-cancer-cells
#3
Mytre Koul, Ashok Kumar, Ramesh Deshidi, Vishal Sharma, Rachna D Singh, Jasvinder Singh, Parduman Raj Sharma, Bhawal Ali Shah, Sundeep Jaglan, Shashank Singh
BACKGROUND: Endophytes have proven to be an invaluable resource of chemically diverse secondary metabolites that act as excellent lead compounds for anticancer drug discovery. Here we report the promising cytotoxic effects of Cladosporol A (HPLC purified >98%) isolated from endophytic fungus Cladosporium cladosporioides collected from Datura innoxia. Cladosporol A was subjected to in vitro cytotoxicity assay against NCI60 panel of human cancer cells using MTT assay. We further investigated the molecular mechanism(s) of Cladosporol A induced cell death in human breast (MCF-7) cancer cells...
July 20, 2017: BMC Cell Biology
https://www.readbyqxmd.com/read/28728013/dynamic-and-elastic-shape-transitions-in-curved-escrt-iii-filaments
#4
REVIEW
Nicolas Chiaruttini, Aurélien Roux
The ESCRT-III complex is an evolutionary ancient and conserved complex that catalyzes fission of lipid membranes from the lumen of the neck in many, if not all processes requiring this specific fission reaction. The ESCRT-III membrane remodeling complex is unique as its molecular and polymeric structures do not intuitively suggests how it could deform and break lipid membranes. Here we review the common structural features of the ESCRT-III subunits, and the shape diversity of the various filamentous forms. We propose a simple geometry and elasticity framework that could help to isolate which features of the ESCRT-III filaments are common to all filamentous forms as well as to explain their diversity...
July 17, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28727843/atomistic-modeling-of-alternating-access-of-a-mitochondrial-adp-atp-membrane-transporter-with-molecular-simulations
#5
Koichi Tamura, Shigehiko Hayashi
The mitochondrial ADP/ATP carrier (AAC) is a membrane transporter that exchanges a cytosolic ADP for a matrix ATP. Atomic structures in an outward-facing (OF) form which binds an ADP from the intermembrane space have been solved by X-ray crystallography, and revealed their unique pseudo three-fold symmetry fold which is qualitatively different from pseudo two-fold symmetry of most transporters of which atomic structures have been solved. However, any atomic-level information on an inward-facing (IF) form, which binds an ATP from the matrix side and is fixed by binding of an inhibitor, bongkrekic acid (BA), is not available, and thus its alternating access mechanism for the transport process is unknown...
2017: PloS One
https://www.readbyqxmd.com/read/28725998/membrane-phase-transition-during-heating-and-cooling-molecular-insight-into-reversible-melting
#6
Liping Sun, Rainer A Böckmann
With increasing temperature, lipid bilayers undergo a gel-fluid phase transition, which plays an essential role in many physiological phenomena. In the present work, this first-order phase transition was investigated for variable heating and cooling rates for a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer by means of atomistic molecular dynamics simulations. Alternative methods to track the melting temperature [Formula: see text] are compared. The resulting [Formula: see text] is shown to be independent of the scan rate for small heating rates (0...
July 19, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28724794/apol1-variants-change-c-terminal-conformational-dynamics-and-binding-to-snare-protein-vamp8
#7
Sethu M Madhavan, John F O'Toole, Martha Konieczkowski, Laura Barisoni, David B Thomas, Santhi Ganesan, Leslie A Bruggeman, Matthias Buck, John R Sedor
APOL1 variants in African populations mediate resistance to trypanosomal infection but increase risk for kidney diseases through unknown mechanisms. APOL1 is expressed in glomerular podocytes and does not vary with underlying kidney disease diagnoses or APOL1 genotypes, suggesting that the kidney disease-associated variants dysregulate its function rather than its localization or abundance. Structural homology searches identified vesicle-associated membrane protein 8 (VAMP8) as an APOL1 protein interactor. VAMP8 colocalizes with APOL1 in the podocyte, and the APOL1:VAMP8 interaction was confirmed biochemically and with surface plasmon resonance...
July 20, 2017: JCI Insight
https://www.readbyqxmd.com/read/28723224/high-throughput-automated-preparation-and-simulation-of-membrane-proteins-with-htmd
#8
Stefan Doerr, Toni Giorgino, Gerard Martinez-Rosell, João M Damas, Gianni De Fabritiis
HTMD is a programmable scientific platform intended to facilitate simulation-based research in molecular systems. This paper presents the functionalities of HTMD for the preparation of a molecular dynamics simulation starting from PDB structures, building the system using well-known forcefields and applying standardized protocols for running the simulations. We demonstrate the framework's flexibility for high-throughput molecular simulations by applying a preparation, building and simulation protocol with multiple force-fields on all of the seven hundred eukaryotic membrane proteins resolved to-date from the orientation of proteins in membranes (OPM) database...
July 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28723129/carbon-dioxide-in-a-supported-ionic-liquid-membrane-structural-and-rotational-dynamics-measured-with-2d-ir-and-pump-probe-experiments
#9
Jae Yoon Shin, Steven A Yamada, Michael D Fayer
Supported ionic liquid membranes (SILMs) are porous membranes impregnated with ionic liquids (ILs) and used as advanced carbon capture materials. Here, two-dimensional infrared (2D IR) and IR polarization selective pump-probe (PSPP) spectroscopies were used to investigate CO2 reorientation and spectral diffusion dynamics in SILMs. The SILM contained 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonly)imide in the poly(ether sulfone) membrane with average pore size of ~350 nm. Two ensembles of CO2 were observed in the SILM, one in the IL phase in the membrane pores and the other in the supporting membrane polymer...
July 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28722655/key-steps-in-unconventional-secretion-of-fibroblast-growth-factor-2-reconstituted-with-purified-components
#10
Julia P Steringer, Sascha Lange, Sabína Čujová, Radek Šachl, Chetan Poojari, Fabio Lolicato, Oliver Beutel, Hans-Michael Müller, Sebastian Unger, Ünal Coskun, Alf Honigmann, Ilpo Vattulainen, Martin Hof, Christian Freund, Walter Nickel
FGF2 is secreted from cells by an unconventional secretory pathway. This process is mediated by direct translocation across the plasma membrane. Here, we define the minimal molecular machinery required for FGF2 membrane translocation in a fully reconstituted inside-out vesicle system. FGF2 membrane translocation is thermodynamically driven by PI(4,5)P2-induced membrane insertion of FGF2 oligomers. The latter serve as dynamic translocation intermediates of FGF2 with a subunit number in the range of 8-12 FGF2 molecules...
July 19, 2017: ELife
https://www.readbyqxmd.com/read/28719184/nanoparticle-mediated-mechanical-destruction-of-cell-membranes-a-coarse-grained-molecular-dynamics-study
#11
Liuyang Zhang, Yiping Zhao, Xianqiao Wang
The effects of binding mode, shape, binding strength, and rotational speed of actively rotating nanoparticles on the integrity of cell membranes have been systematically studied using dissipative particle dynamics simulations. With theoretical analyses of lipid density, surface tension, stress distribution, and water permeation, we demonstrate that the rotation of nanoparticles can provide a strong driving force for membrane rupture. The results show that nanoparticles embedded inside a cell membrane via endocytosis are more capable of producing large membrane deformations under active rotation than nanoparticles attached on the cell membrane surface...
July 18, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28718450/dynamics-and-energetics-of-the-mammalian-phosphatidylinositol-transfer-protein-phospholipid-exchange-cycle
#12
Aby Grabon, Adam Orlowski, Ashutosh Tripathi, Joni Vuorio, Matti Javanainen, Tomasz Róg, Max Lönnfors, Mark I McDermott, Garland Siebert, Pentti Somerharju, Ilpo Vattulainen, Vytas A Bankaitis
Phosphatidylinositol-transfer proteins (PITPs) regulate phosphoinositide signaling in eukaryotic cells. The defining feature of PITPs is their ability to exchange phosphatidylinositol (PtdIns) molecules between membranes, and this property is central to PITP-mediated regulation of lipid signaling. Yet, the details of the PITP-mediated lipid exchange cycle remain entirely obscure. Here, all-atom molecular dynamics (MD) simulations of the mammalian StART-like PtdIns/ phosphatidylcholine (PtdCho) transfer protein PITPα, both on membrane bilayers and in solvated systems, informed downstream biochemical analyses that tested key aspects of the hypotheses generated by the MD simulations...
July 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28717993/probing-the-binding-affinities-of-imipenem-and-ertapenem-for-outer-membrane-carboxylate-channel-d1-occd1-from-p-aeruginosa-simulation-studies
#13
Kamolrat Somboon, Jitti Niramitranon, Prapasiri Pongprayoon
Pseudomonas aeruginosa is an important nosocomial human pathogen. The major difficulty in the fight against this pathogen is the relative impermeability of its outer membrane (OM). Only specific substrates can penetrate through the OM of P. aeruginosa via substrate-specific porins, so this has become one of the most problematic drug-resistant pathogens. Carbapenems are the most effective drugs for treating P. aeruginosa infections. One such carbapenem that is applied in cases of P. aeruginosa infection is imipenem (IMI), which uses outer membrane carboxylate channel D1 (OccD1) as a point of entry into the pathogen...
August 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28716648/applications-of-high-speed-atomic-force-microscopy-to-real-time-visualization-of-dynamic-biomolecular-processes
#14
REVIEW
Takayuki Uchihashi, Simon Scheuring
BACKGROUND: Many biological processes in a living cell are consequences of sequential and hierarchical dynamic events of biological macromolecules such as molecular interactions and conformational changes. Hence, knowledge of structures, assembly and dynamics of proteins is the foundation for understanding how biological molecules work. Among several techniques to analyze dynamics of proteins, high-speed atomic force microscopy (HS-AFM) is unique to provide direct information about both structure and dynamics of single proteins at work...
July 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28716627/membrane-proteins-structures-a-review-on-computational-modeling-tools
#15
REVIEW
Jose G Almeida, Antonio J Preto, Panagiotis I Koukos, Alexandre M J J Bonvin, Irina S Moreira
BACKGROUND: Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic organisms' genomes. In humans, their importance is emphasized as they represent 50% of all known drug targets. Nevertheless, experimental determination of their three-dimensional (3D) structure has proven to be both time consuming and rather expensive, which has led to the development of computational algorithms to complement the available experimental methods and provide valuable insights...
July 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28715195/thermomechanical-response-of-self-assembled-nanoparticle-membranes
#16
Yifan Wang, Henry Chan, Badri Narayanan, Sean P McBride, Subramanian K R S Sankaranarayanan, Xiao-Min Lin, Heinrich M Jaeger
Monolayers composed of colloidal nanoparticles, with a thickness of less than 10 nm, have remarkable mechanical moduli and can suspend over micrometer-sized holes to form free-standing membranes. In this paper, we discuss experiments and coarse-grained molecular dynamics simulations characterizing the thermomechanical properties of these self-assembled nanoparticle membranes. These membranes remain strong and resilient up to temperatures much higher than previous simulation predictions and exhibit an unexpected hysteretic behavior during the first heating-cooling cycle...
July 21, 2017: ACS Nano
https://www.readbyqxmd.com/read/28714993/a-two-helix-motif-positions-the-lysophosphatidic-acid-acyltransferase-active-site-for-catalysis-within-the-membrane-bilayer
#17
Rosanna M Robertson, Jiangwei Yao, Stefan Gajewski, Gyanendra Kumar, Erik W Martin, Charles O Rock, Stephen W White
Phosphatidic acid (PA), the central intermediate in membrane phospholipid synthesis, is generated by two acyltransferases in a pathway conserved in all life forms. The second step in this pathway is catalyzed by 1-acyl-sn-glycerol-3-phosphate acyltransferase, called PlsC in bacteria. Here we present the crystal structure of PlsC from Thermotoga maritima, revealing an unusual hydrophobic/aromatic N-terminal two-helix motif linked to an acyltransferase αβ-domain that contains the catalytic HX4D motif. PlsC dictates the acyl chain composition of the 2-position of phospholipids, and the acyl chain selectivity 'ruler' is an appropriately placed and closed hydrophobic tunnel...
July 17, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28713022/resveratrol-inhibits-phorbol-ester-induced-membrane-translocation-of-presynaptic-munc13-1
#18
Satyabrata Pany, Anamitra Ghosh, Youngki You, Nga Nguyen, Joydip Das
BACKGROUND: Resveratrol (1) is a naturally occurring polyphenol that has been implicated in neuroprotection. One of resveratrol's several biological targets is Ca(2+)-sensitive protein kinase C alpha (PKCα). Resveratrol inhibits PKCα by binding to its activator-binding C1 domain. Munc13-1 is a C1 domain-containing Ca(2+)-sensitive SNARE complex protein essential for vesicle priming and neurotransmitter release. METHODS: To test if resveratrol could also bind and inhibit Munc13-1, we studied the interaction of resveratrol and its derivatives, (E)-1,3-dimethoxy-5-(4-methoxystyryl)benzene, (E)-5,5'-(ethene-1,2-diyl)bis(benzene-1,2,3-triol), (E)-1,2-bis(3,4,5-trimethoxyphenyl)ethane, and (E)-5-(4-(hexadecyloxy)-3,5-dihydroxystyryl)benzene-1,2,3-triol with Munc13-1 by studying its membrane translocation from cytosol to plasma membrane in HT22 cells and primary hippocampal neurons...
July 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28712361/plasmodium-knowlesi-a-superb-in-vivo-nonhuman-primate-model-of-antigenic-variation-in-malaria
#19
M R Galinski, S A Lapp, M S Peterson, F Ay, C J Joyner, K G LE Roch, L L Fonseca, E O Voit
Antigenic variation in malaria was discovered in Plasmodium knowlesi studies involving longitudinal infections of rhesus macaques (M. mulatta). The variant proteins, known as the P. knowlesi Schizont Infected Cell Agglutination (SICA) antigens and the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) antigens, expressed by the SICAvar and var multigene families, respectively, have been studied for over 30 years. Expression of the SICA antigens in P. knowlesi requires a splenic component, and specific antibodies are necessary for variant antigen switch events in vivo...
July 17, 2017: Parasitology
https://www.readbyqxmd.com/read/28711675/molecular-dynamics-simulations-of-t-2410-and-t-2429-hiv-fusion-inhibitors-interacting-with-model-membranes-insight-into-peptide-behavior-structure-and-dynamics
#20
I C V C Mavioso, V C R de Andrade, A J Palace Carvalho, A M T Martins do Canto
T-2410 and T-2429 are HIV fusion inhibitor peptides (FI) designed to present a higher efficiency even against HIV strains that developed resistance against other FIs. Similar peptides were shown to interact with model membranes both in the liquid disordered phase and in the liquid ordered state. Those results indicated that such interaction is important to function and could be correlated with their effectiveness. Extensive molecular dynamics simulations were carried out to investigate the interactions between both T-2410 and T-2429 with bilayers of pure 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and a mixture of POPC/cholesterol (Chol) (1:1)...
July 8, 2017: Biophysical Chemistry
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