keyword
MENU ▼
Read by QxMD icon Read
search

Molecular dynamics membrane

keyword
https://www.readbyqxmd.com/read/28812889/influence-of-small-fluorophilic-and-lipophilic-organic-molecules-on-dppc-bilayers
#1
Martin Brehm, Ghulam Saddiq, Tobias Watermann, Daniel Sebastiani
In this study, we investigate the effect of a series of additive molecules with different types of philicities on the structure and dynamics of DPPC bilayers. To this aim, we performed extensive force field molecular dynamics simulations of the systems, using our recently developed perfluoroalkane force field. We found that addition of perfluoro-n-decane and fluorotelomer alcohol at 323 K leads to a phase transition of the membrane from liquid crystalline to gel phase, whereas the addition of n-decane and partially fluorinated n-decane leaves the liquid crystalline phase intact...
August 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28809537/confined-water-structure-dynamics-and-thermodynamics
#2
Sudip Chakraborty, Hemant Kumar, Chandan Dasgupta, Prabal K Maiti
Understanding the properties of strongly confined water is important for a variety of applications such as fast flow and desalination devices, voltage generation, flow sensing, and nanofluidics. Confined water also plays an important role in many biological processes such as flow through ion channels. Water in the bulk exhibits many unusual properties that arise primarily from the presence of a network of hydrogen bonds. Strong confinement in structures such as carbon nanotubes (CNTs) substantially modifies the structural, thermodynamic, and dynamic (both translational and orientational) properties of water by changing the structure of the hydrogen bond network...
August 15, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28809101/a-microsphere-supported-lipid-bilayer-platform-for-dna-reactions-on-a-fluid-surface
#3
Aurora Fabry-Wood, Madalyn Elise Fetrow, Carl W Brown Iii, Nicholas A Baker, Nadiezda Fernandez Oropeza, Andrew P Shreve, Gabriel A Montano, Darko Stefanovic, Matthew R Lakin, Steven W Graves
We report a versatile microsphere-supported lipid bilayer system that can serve as a general-purpose platform for implementing DNA nanotechnologies on a fluid surface. To demonstrate our platform, we implemented both toehold-mediated strand displacement (TMSD) and DNAzyme reactions, which are typically performed in solution and which are the cornerstone of DNA-based molecular logic and dynamic DNA nanotechnology, on the surface. We functionalized microspheres bearing supported lipid bilayers (µSLBs) with membrane-bound nucleic acid components...
August 15, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28808710/interface-nanoparticle-control-of-a-nanometer-water-pump
#4
Jiaye Su, Yunzhen Zhao, Chang Fang, Syed Bilal Ahmed, Yue Shi
Nanoparticles are highly versatile and exhibit broad applications in tuning material properties. Herein, we show through molecular dynamics simulations the possibility of a nanometer water pump, driven by the motion of nanoparticles (NPs) on a membrane surface. Surprisingly, considerable net water flux can be induced through a carbon nanotube (CNT) that is perpendicular to the NP motion. The water transport can occur in a highly controllable fashion, not only by using a single NP with different forces, but also by varying the CNT length or the NP number...
August 15, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28808010/voltage-gated-calcium-flux-mediates-escherichia-coli-mechanosensation
#5
Giancarlo N Bruni, R Andrew Weekley, Benjamin J T Dodd, Joel M Kralj
Electrically excitable cells harness voltage-coupled calcium influx to transmit intracellular signals, typically studied in neurons and cardiomyocytes. Despite intense study in higher organisms, investigations of voltage and calcium signaling in bacteria have lagged due to their small size and a lack of sensitive tools. Only recently were bacteria shown to modulate their membrane potential on the timescale of seconds, and little is known about the downstream effects from this modulation. In this paper, we report on the effects of electrophysiology in individual bacteria...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28808001/two-transmembrane-dimers-of-the-bovine-papillomavirus-e5-oncoprotein-clamp-the-pdgf-%C3%AE-receptor-in-an-active-dimeric-conformation
#6
Alexander G Karabadzhak, Lisa M Petti, Francisco N Barrera, Anne P B Edwards, Andrés Moya-Rodríguez, Yury S Polikanov, J Alfredo Freites, Douglas J Tobias, Donald M Engelman, Daniel DiMaio
The dimeric 44-residue E5 protein of bovine papillomavirus is the smallest known naturally occurring oncoprotein. This transmembrane protein binds to the transmembrane domain (TMD) of the platelet-derived growth factor β receptor (PDGFβR), causing dimerization and activation of the receptor. Here, we use Rosetta membrane modeling and all-atom molecular dynamics simulations in a membrane environment to develop a chemically detailed model of the E5 protein/PDGFβR complex. In this model, an active dimer of the PDGFβR TMD is sandwiched between two dimers of the E5 protein...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28807997/phosphoantigen-induced-conformational-change-of-butyrophilin-3a1-btn3a1-and-its-implication-on-v%C3%AE-9v%C3%AE-2-t-cell-activation
#7
Siyi Gu, Joseph R Sachleben, Christopher T Boughter, Wioletta I Nawrocka, Marta T Borowska, Jeffrey T Tarrasch, Georgios Skiniotis, Benoît Roux, Erin J Adams
Human Vγ9Vδ2 T cells respond to microbial infections as well as certain types of tumors. The key initiators of Vγ9Vδ2 activation are small, pyrophosphate-containing molecules called phosphoantigens (pAgs) that are present in infected cells or accumulate intracellularly in certain tumor cells. Recent studies demonstrate that initiation of the Vγ9Vδ2 T cell response begins with sensing of pAg via the intracellular domain of the butyrophilin 3A1 (BTN3A1) molecule. However, it is unknown how downstream events can ultimately lead to T cell activation...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28807751/a-novel-pmca3-mutation-in-an-ataxic-patient-with-hypomorphic-phosphomannomutase-2-pmm2-heterozygote-mutations-biochemical-characterization-of-the-pump-defect
#8
Mattia Vicario, Tito Calì, Domenico Cieri, Francesca Vallese, Raissa Bortolotto, Raffaele Lopreiato, Francesco Zonta, Marta Nardella, Alessia Micalizzi, Dirk J Lefeber, Enza Maria Valente, Enrico Bertini, Giuseppe Zanotti, Ginevra Zanni, Marisa Brini, Ernesto Carafoli
The neuron-restricted isoform 3 of the plasma membrane Ca(2+) ATPase plays a major role in the regulation of Ca(2+) homeostasis in the brain, where the precise control of Ca(2+) signaling is a necessity. Several function-affecting genetic mutations in the PMCA3 pump associated to X-linked congenital cerebellar ataxias have indeed been described. Interestingly, the presence of co-occurring mutations in additional genes suggest their synergistic action in generating the neurological phenotype as digenic modulators of the role of PMCA3 in the pathologies...
August 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28807151/exocytotic-fusion-pores-as-a-target-for-therapy
#9
REVIEW
Jernej Jorgačevski, Marko Kreft, Robert Zorec
Regulated exocytosis can be split into a sequence of steps ending with the formation and the dilation of a fusion pore, a neck-like connection between the vesicle and the plasma membrane. Each of these steps is precisely controlled to achieve the optimal spatial and temporal profile of the release of signalling molecules. At the level of the fusion pore, tuning of the exocytosis can be achieved by preventing its formation, by stabilizing the unproductive narrow fusion pore, by altering the speed of fusion pore expansion and by completely closing the fusion pore...
September 2017: Cell Calcium
https://www.readbyqxmd.com/read/28806072/modeling-of-the-passive-permeation-of-mercury-and-methylmercury-complexes-through-a-bacterial-cytoplasmic-membrane
#10
Jing Zhou, Micholas Dean Smith, Sarah J Cooper, Xiaolin Cheng, Jeremy C Smith, Jerry M Parks
Cellular uptake and export are important steps in the biotransformation of mercury (Hg) by microorganisms. However, the mechanisms of transport across biological membranes remain unclear. Membrane-bound transporters are known to be relevant, but passive permeation may also be involved. Inorganic Hg(II) and methylmercury ([CH3Hg]+) are commonly complexed with thiolate ligands. Here, we have performed extensive molecular dynamics simulations of the passive permeation of Hg(II) and [CH3Hg]+ complexes with thiolate ligands through a model bacterial cytoplasmic membrane...
August 14, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28805387/polymyxin-binding-to-the-bacterial-outer-membrane-reveals-cation-displacement-and-increasing-membrane-curvature-in-susceptible-but-not-in-resistant-lps-chemotypes
#11
Denys Ewerton da Silva Santos, Laércio Pol-Fachin, Roberto D Lins, Thereza A Soares
Lipid-A is the causative agent of Gram-negative sepsis and responsible for increasingly high mortality rate among hospitalized patients. Compounds that bind Lipid-A can limit this inflammatory process. The cationic antimicrobial peptide polymyxin B (Pmx-B) is one of the simplest molecules capable of selectively bind to Lipid-A, and may serve as a model for further development of Lipid-A binding agents. Gram-negative bacteria resistance to Pmx-B relies on the upregulation of a number of regulatory systems, which promote chemical modifications of the LPS structure, and leads to major changes in the physical-chemical properties of the outer membrane...
August 14, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28801684/structural-properties-of-human-iapp-dimer-in-membrane-environment-studied-by-all-atom-molecular-dynamics-simulations
#12
Na Liu, Mojie Duan, Minghui Yang
The aggregation of human islet amyloid polypeptide (hIAPP) can damage the membrane of the β-cells in the pancreatic islets and induce type 2 diabetes (T2D). Growing evidences indicated that the major toxic species are small oligomers of IAPP. Due to the fast aggregation nature, it is hard to characterize the structures of IAPP oligomers by experiments, especially in the complex membrane environment. On the other side, molecular dynamics simulation can provide atomic details of the structure and dynamics of the aggregation of IAPP...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801600/cav1-3-l-type-ca-2-channel-contributes-to-the-heartbeat-by-generating-a-dihydropyridine-sensitive-persistent-na-current
#13
Futoshi Toyoda, Pietro Mesirca, Stefan Dubel, Wei-Guang Ding, Joerg Striessnig, Matteo E Mangoni, Hiroshi Matsuura
The spontaneous activity of sinoatrial node (SAN) pacemaker cells is generated by a functional interplay between the activity of ionic currents of the plasma membrane and intracellular Ca(2+) dynamics. The molecular correlate of a dihydropyridine (DHP)-sensitive sustained inward Na(+) current (I st), a key player in SAN automaticity, is still unknown. Here we show that I st and the L-type Ca(2+) current (I Ca,L) share CaV1.3 as a common molecular determinant. Patch-clamp recordings of mouse SAN cells showed that I st is activated in the diastolic depolarization range, and displays Na(+) permeability and minimal inactivation and sensitivity to I Ca,L activators and blockers...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801111/luminescence-resonance-energy-transfer-spectroscopy-of-atp-binding-cassette-proteins
#14
REVIEW
Maria E Zoghbi, Guillermo A Altenberg
The ATP-binding cassette (ABC) superfamily includes regulatory and transport proteins. Most human ABC exporters pump substrates out of cells using energy from ATP hydrolysis. Although major advances have been made toward understanding the molecular mechanism of ABC exporters, there are still many issues unresolved. During the last few years, luminescence resonance energy transfer has been used to detect conformational changes in real time, with atomic resolution, in isolated ABC nucleotide binding domains (NBDs) and full-length ABC exporters...
August 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28799584/molecular-determinants-involved-in-differential-behaviour-between-soluble-tissue-factor-and-full-length-tissue-factor-towards-factor-viia
#15
Ramesh Prasad, Prosenjit Sen
During blood-coagulation, the transmembrane protein tissue factor (TF) binds to its ligand, factor (F)VII, activating and allosterically modifying it to form a mature active binary complex (TF-FVIIa). Although the extracellular domain of TF (sTF) can bind to FVII, it fails to activate it. Binding of TF with FVIIa only partially enhances FVIIa proteolytic activity. Our previous kinetic study revealed that sTF has a lower binding capacity with FVIIa compared to membrane bound full-length (fl)TF. The reason behind this incapability of FVII activation and reduced catalytic activity remains unexplored due to the lack of an flTF crystal structure...
August 11, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28799169/mitotic-inheritance-of-the-golgi-complex-and-its-role-in-cell-division
#16
REVIEW
Inmaculada Ayala, Antonino Colanzi
The Golgi apparatus plays essential roles in the processing and sorting of proteins and lipids, but it can also act as a signalling hub and a microtubule-nucleation centre. The Golgi complex of mammalian cells is composed of stacks connected by tubular bridges to form a continuous membranous system. In spite of this structural complexity, the Golgi structure is highly dynamic, and this feature becomes particularly evident during mitosis, when the Golgi complex undergoes a multi-step disassembly process that allows its correct partitioning and inheritance by daughter cells...
August 10, 2017: Biology of the Cell
https://www.readbyqxmd.com/read/28799166/the-molecular-mechanism-underlying-unconventional-secretion-of-fibroblast-growth-factor-2-from-tumor-cells
#17
REVIEW
Julia P Steringer, Walter Nickel
Fibroblast Growth Factor 2 (FGF2) is a potent cell survival factor involved in tumor induced angiogenesis. FGF2 is secreted from cells through an unconventional secretory mechanism based upon direct translocation across the plasma membrane. The molecular mechanism underlying this process depends on a surprisingly small set of trans-acting factors that are physically associated with the plasma membrane. FGF2 membrane translocation is mediated by the ability of FGF2 to oligomerize and to insert into the plasma membrane in a PI(4,5)P2 dependent manner...
August 10, 2017: Biology of the Cell
https://www.readbyqxmd.com/read/28799119/modeling-dmpc-lipid-membranes-with-sirah-force-field
#18
Exequiel E Barrera, Ezequiel N Frigini, Rodolfo D Porasso, Sergio Pantano
Coarse-grained simulation schemes are increasingly gaining popularity in the scientific community because of the significant speed up granted, allowing a considerable expansion of the accessible time and size scales accessible to molecular simulations. However, the number of compatible force fields capable of representing ensembles containing different molecular species (i.e., Protein, DNA, etc) is still limited. Here, we present a set of parameters and simplified representation for lipids compatible with the SIRAH force field for coarse-grained simulations ( http://www...
August 10, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28798393/role-of-water-and-protein-dynamics-in-proton-pumping-by-respiratory-complex-i
#19
Outi Haapanen, Vivek Sharma
Membrane bound respiratory complex I is the key enzyme in the respiratory chains of bacteria and mitochondria, and couples the reduction of quinone to the pumping of protons across the membrane. Recently solved crystal or electron microscopy structures of bacterial and mitochondrial complexes have provided significant insights into the electron and proton transfer pathways. However, due to large spatial separation between the electron and proton transfer routes, the molecular mechanism of coupling remains unclear...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28797162/nanoparticles-of-various-degrees-of-hydrophobicity-interacting-with-lipid-membranes
#20
Chan-Fei Su, Holger Merlitz, Hauke Rabbel, Jens-Uwe Sommer
Using coarse-grained molecular dynamics simulations, we study the passive translocation of nanoparticles with a size of about 1 nm and with tunable degrees of hydrophobicity through lipid bilayer membranes. We observe a window of translocation with a sharp maximum for nanoparticles having a hydrophobicity in between hydrophilic and hydrophobic. Passive translocation can be identified as diffusive motion of individual particles in a free energy landscape. By combining direct sampling with umbrella-sampling techniques we calculate the free energy landscape for nanoparticles covering a wide range of hydrophobicities...
August 16, 2017: Journal of Physical Chemistry Letters
keyword
keyword
78833
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"