Loading...


*  Molecular dynamics simulations of membrane proteins. - Oxford Neuroscience
Recently, there has been substantial progress in the simulation of lipid bilayers and membrane proteins embedded within them. ... In this chapter, we outline practical methods for setting up and running MD simulations of a membrane protein embedded within a ... Initial efforts at simulating membrane proteins embedded within a lipid bilayer were relatively slow and interactive processes ... but recent advances now mean that the setup and running of membrane protein simulations is somewhat more straightforward, ...
  https://www.neuroscience.ox.ac.uk/publications/503317
*  23034757[pmid] - BioMedLib™ search engine
The explanation comprehends from the initial set up of a membrane system to its analysis passing through the simulation itself. ... In the field of lipid membrane research, MD represents a major tool as it grant access to atomic level features of the membrane ... Cell Membrane / chemistry. Cell Membrane / metabolism. Deuterium / chemistry. Diffusion. Molecular Conformation. ... Molecular Dynamics Simulation. *[MeSH-minor] 1,2-Dipalmitoylphosphatidylcholine / chemistry. 1,2-Dipalmitoylphosphatidylcholine ...
  http://bmlsearch.com/?kwr=23034757%5Bpmid%5D&cmpgp0613UwUb=ICD30613TWEitjuoz4&dt02=&dt03=&xpclps3=Matches
*  Schematic Representation of the Simulation System Const | Open-i
Schematic Representation of the Simulation System Constructed on the Basis of the Cryo-EM Structure of nAChR at 4 Å ... structure of nAChR embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer and water molecules. A 30-ns CMD simulation ... Bottom Line: The result confirmed all the motions derived from the CMD simulation and NMA.In addition, the SRMD simulation ... Bottom Line: The result confirmed all the motions derived from the CMD simulation and NMA.In addition, the SRMD simulation ...
  https://openi.nlm.nih.gov/detailedresult.php?img=PMC2211534_pcbi.0040019.g001&req=4
*  Dynamics of the M2 Helices(A) Bending vibrations of the | Open-i
... structure of nAChR embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer and water molecules. A 30-ns CMD simulation ... Bottom Line: The result confirmed all the motions derived from the CMD simulation and NMA.In addition, the SRMD simulation ... Bottom Line: The result confirmed all the motions derived from the CMD simulation and NMA.In addition, the SRMD simulation ... The result confirmed all the motions derived from the CMD simulation and NMA. In addition, the SRMD simulation indicated that ...
  https://openi.nlm.nih.gov/detailedresult.php?img=PMC2211534_pcbi.0040019.g005&req=4
*  C60 fullerene promotes lung monolayer collapse | Journal of The Royal Society Interface
2008 Computer simulation study of fullerene translocation through lipid membranes. Nat. Nanotechnol. 3, 363-368. (doi:10.1038/ ... 2012 Effects of spherical fullerene nanoparticles on a dipalmitoyl phosphatidylcholine lipid monolayer: a coarse grain ... Analogous to cell membranes [6], lung monolayer membranes are laterally heterogeneous, with more rigid domains (consisting ... 2014 Lipid membranes as solvents for carbon nanoparticles. Phys. Rev. Lett. 112, 068102. (doi:10.1103/PhysRevLett.112.068102). ...
  http://rsif.royalsocietypublishing.org/content/12/104/20140931
*  Continuum Approaches to Understanding Ion and Peptide Interactions with the Membrane | SpringerLink
Experimental and computational studies have shown that cellular membranes deform to stabilize the inclusion of transmembrane ( ... Pandit SA, Bostick D, Berkowitz ML (2003) Molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer with NaCl. ... Finally, we show that the energetics of membrane deformation strongly depend on membrane patch size both for ions and peptides ... Membrane bending is critical for the stability of voltage sensor segments in the membrane. J Gen Physiol 140(1):55-68. doi: ...
  https://link.springer.com/article/10.1007/s00232-014-9646-z
*  Molecular Dynamic Simulations of Raft Formation and Fullerene Transport in Lipid Membranes
Mesoscopic simulation of cell membrane damage morphology change and rupture by nonionic surfactants. Biophys. J. 81, 725 736. 7 ... The membrane bilayers are modeled using saturated dipalmitoyl phosphatidylcholine (diC 16 PC) lipids, unsaturated dilinoleyl ... 12 in the membrane (8 ) Therefor e we have explored the likeliness of aggregation surfactant s in a membrane using MD ... Any simulation study typically consists of three steps. The first step is energy minimization Two MD simulation runs are then ...
  http://ufdc.ufl.edu/UFE0045619/00001
*  Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems
Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc. 2006;128:2697-2704. [PMC free article] [PubMed] ... for instance in the case of lipid membranes, dipalmitoylphosphatidylcholine (DPPC) is represented by four particles in the head ... Because all membranes are located in the xy-plane, the membrane normal is chosen to be the z-axis of the system, which is ... consisting mainly of lipid molecules and membrane proteins. How a membrane protein is associated with the lipid membrane ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2904924/
*  Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer. - Oxford Neuroscience
Hence, there is a substantial barrier to membrane insertion for charged amino acids, but the coarse-grained model still ... side chains along the normal to a phosphatidylcholine bilayer were in good agreement with experimental and atomistic simulation ... In particular, coarse-grained simulations have considerable potential for studying many aspects of membrane proteins, ranging ... Hence, there is a substantial barrier to membrane insertion for charged amino acids, but the coarse-grained model still ...
  https://www.neuroscience.ox.ac.uk/publications/100612
*  Molecular dynamics simulation analyses of viral fusion peptides in membranes prone to phase transition: effects on membrane...
... assumed the oblique orientation at the interface between water and the membrane made up of dipalmitoylphosphatidylcholine (DPPC ... palmitic acid (PA), as reported previously for different membranes. Simulations of WT20 embedded in bilayer membranes made up ... Taken together, these results imply that the influenza HA fusion peptide can have substantial effects on the membrane curvature ... Its movability and oblique orientation appear to be associated with its ability to perturb membrane/water interfaces. ...
  https://www.scirp.org/Journal/PaperInformation.aspx?paperID=1879&JournalID=162
*  Brasseur, R., Lorge, P., Goormaghtigh, E., Ruysschaert, J.M., Espion, D. and Burny, A. (1998) The mode of in-sertion of the...
Molecular dynamics simulation analyses of viral fusion peptides in membranes prone to phase transition: effects on membrane ... assumed the oblique orientation at the interface between water and the membrane made up of dipalmitoylphosphatidylcholine (DPPC ... palmitic acid (PA), as reported previously for different membranes. Simulations of WT20 embedded in bilayer membranes made up ... KEYWORDS: Molecular Simulation; Fusion Peptide; Stalk Formation; Lipid Mixing; Hemifusion JOURNAL NAME: Journal of Biophysical ...
  https://www.scirp.org/reference/ReferencesPapers.aspx?ReferenceID=36564
*  Most recent papers with the keyword CL | Read by QxMD
Prior studies have implicated dysfunctional muscarinic signaling from basolateral membranes as the potential perpetrator ... choline chloride mixture containing Cu2+ ions was investigated by electrochemical techniques and molecular dynamics simulation ... Melting of the Dipalmitoylphosphatidylcholine Monolayer.. Lu Xu, Gordon Bosiljevac, Kyle Yu, Yi Y Zuo ... The rate constants of OH radicals with CF3 CF=CCl2 , CF3 CH=CF2 , CF3 CF=CH2 , CF3 CH=CH2 , and (CF3 )2 C=CH2 have been ...
  https://www.readbyqxmd.com/keyword/70530
*  DiVA - Search result
A 0.1 μs MD simulation at T = 50°C of a small lipid bilayer formed by 64 dipalmitoylphosphatidylcholine (DPPC) molecules at the ... The deviation in tilt angle of the PN vector relative to the membrane surface is manifested in the observed 14N NMR quadrupole ... A theoretical spin relaxation and molecular dynamics simulation study of the Gd(H2O)93+ complex2009In: Physical Chemistry, ... A direct simulation of EPR slow-motion spectra of spin labelled phospholipids in liquid crystalline bilayers based on a ...
  http://umu.diva-portal.org/smash/resultList.jsf?af=%5B%5D&aq=%5B%5B%7B%22journalId%22%3A%226370%22%7D%5D%5D&aqe=%5B%5D&aq2=%5B%5B%5D%5D&language=en&query=
*  Nonenzymatic Reactions above Phospholipid Surfaces of Biological Membranes: Reactivity of Phospholipids and Their Oxidation...
J. Weng and W. Wang, "Molecular dynamics simulation of membrane proteins," Advances in Experimental Medicine and Biology, vol. ... PC in its form of dipalmitoylphosphatidylcholine (DPPC) has been considered the benchmark lipid in the study of model bilayers ... The cell membrane surface could also enhance the ability of protons to diffuse promptly along the membrane through hydrogen- ... The vulnerability of membrane phospholipids to be damaged by ROS is related to the physicochemical properties of the membrane ...
  https://www.hindawi.com/journals/omcl/2015/319505/
*  Protocols and Video Articles Authored by Andrew S. Mount
20 across a model cell membrane (dipalmitoylphosphatidylcholine or DPPC bilayer). The simulation results indicate that, ... It was also determined that the two different forms of fullerenes, when adsorbed into/onto the bilayer, affected the membrane ... although a pristine C60 molecule can readily "jump" into the bilayer and translocate the membrane within a few milliseconds, ... In JoVE (1). *Characterization of Calcification Events Using Live Optical and Electron Microscopy Techniques in a Marine ...
  https://www.jove.com/author/Andrew++S._Mount
*  Most recent papers with the keyword Exchanges | Read by QxMD
Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids.. Zanxia Cao, Yunqiang Bian, Guodong Hu, Liling ... to simulate the membrane permeation of all 20 amino acids from water to the center of a dipalmitoylphosphatidylcholine (DPPC) ... www.readbyqxmd.com/read/29547563/bias-exchange-metadynamics-simulation-of-membrane-permeation-of-20-amino-acids ... Herein, the membrane bioreactor system (MBRS) was applied to improve SMX elimination thorough exchanging the cell-free broths ( ...
  https://www.readbyqxmd.com/keyword/27697
*  Membrane-Proximal Tryptophans of Synaptobrevin II Stabilize Priming of Secretory Vesicles | Journal of Neuroscience
7) but not in the MD simulation. This is likely due to the stabilization of the membrane attachment of the JMD by the TMD in ... 1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure ... A, Exemplary recording of cell membrane capacitance (Cm), access resistance (Gs), membrane resistance (Gm), and [Ca2+]i during ... A role of membrane-proximal Trp residues in controlling the position of the JMD and the electrostatic potential at the membrane ...
  http://www.jneurosci.org/content/32/45/15983
*  DiVA - Search result
A Blue-Light-Emitting BODIPY Probe for Lipid Membranes2016In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 32, no 14, p. ... The 100-ns-long molecular dynamics simulation at constant pressure (1 atm) and at a temperature of 50 degrees C of 64 lipid ... Dipalmitoylphosphatidylcholine (DPPC) vesicles were prepared by sonication and their size in sodium chloride solutions ([NaCl ... Here we describe a new BODIPY-based membrane probe (1) that provides an alternative to dialkylcarbocyanine dyes, such as DiI-C, ...
  http://kth.diva-portal.org/smash/resultList.jsf?af=%5B%5D&aq=%5B%5B%7B%22categoryId%22%3A%2211530%22%7D%5D%5D&aqe=%5B%5D&aq2=%5B%5B%5D%5D&language=en&query=
*  Print - Biology-Online
Membrane Electroporation: A Molecular Dynamics Simulation. Abstract. Membrane Electroporation: A Molecular Dynamics Simulation ... Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and ... reporting on membrane/gramicidin stability. The DNA/lipid system simulation was undertaken starting from a well-equilibrated 12 ... Here it is possible to make use of computer simulation to estimate the lateral pressure exerted on a membrane when subject to a ...
  https://www.biology-online.org/kb/print.php?aid=587
*  Scientific Reports Table of Contents e-alert: 25 April 2017
Use of a Visual Aid in addition to a Collector Bag to Evaluate Postpartum Blood loss: A Prospective Simulation Study ▶ ... Mitochondria have a central position in innate immune response via the adaptor protein MAVS in mitochondrial outer membrane to ... and Cholinium-Based Ionic Liquids on Vibrio Fischeri Cells and Dipalmitoylphosphatidylcholine Liposomes ▶ ... In this study, a simulation model was used to assess the epidemiological and economic impacts of the routine vaccination ...
  http://www.healthcareintheuk.co.uk/2017/04/scientific-reports-table-of-contents-e_25.html
*  NMR-Active Nuclei for Biological and Biomedical Applications - Open Medscience
... membranes. Interaction with PE and PS model membranes was described by the presence of two mercury sites, one labile and the ... three carboxyl carbons and their three nearest carbons were used in a seven-spin simulation. Site I: Glu-70 Cδ and Cγ, Asp-90 C ... Shi P, Li D, Chen H, Xiong Y, Wang Y, Tian C. In situ 19F NMR studies of an E. coli membrane protein. Protein Sci. 2012;21(4): ... phase behaviour and dynamics of membranes and elucidate atomic-resolution structure, orientation and dynamics of membrane- ...
  https://openmedscience.com/article/nmr-active-nuclei-biological-biomedical-applications/
*  Advanced Materials and Liquid Crystal Institute, Kent State University
Effects of Anesthetic Membrane Solutes on Orientational Order in Lecithin Bilayer Membranes: An NMR Study. Nason Phonphok. ... Quantum Simulation of Polyene Ground States. Stefan Klemm. Michael Lee. Physics. -. 176. 1987. Critical Properties of Phase ... The Influence of Monovalent Ions on Dipalmitoylphosphatidyl-choline Bilayer Structure and Packing. Beth A. Cunningham. Leonard ... Optical Simulation and Fabrication of Pancharatnam (Geometric) Phase Devices from Liquid Crystals. Kun Gao. Philip Bos. ...
  https://www.lcinet.kent.edu/facts/dissertation/index.php
*  Lipids, Organization and Aggregation of - CHEMICAL BIOLOGY
The lipid membrane provides shelter for membrane proteins to do their functions. However, instead of working alone, membrane ... Atomistic simulation studies of cholesteryl oleates: model for the core of lipoprotein particles. Biophys. J. 2006; 90:2247- ... Hsueh YW, Gilbert K, Trandum C, Zuckermann M, Thewalt J. The effect of ergosterol on dipalmitoylphosphatidylcholine bilayers: a ... and ion transport across the membrane. Understanding ion transport across membranes is especially important, because membranes ...
  http://schoolbag.info/chemistry/chemical_biology/197.html
*  ORBi: Browsing ORBi
To achieve simulation times of several microseconds, a coarse-grained (CG) model based on the MARTINI force field was also used ... Its cell target has been shown to be the cytoplasmic membrane. This tyrosine residue has been previously shown to be essential ... Mycosubtilin was added underneath dipalmitoylphosphatidylcholine or cholesterol monolayers at the air-water interface and ... Modeling of Antimicrobial Lipopeptides in interaction with lipidic membranes. Loison, Claire; Nasir, Mehmet Nail ; Besson, ...
  https://orbi.uliege.be/browse?type=author&value=Benichou%2C+Emmanuel
*  SoftSimu - Publications and theses
Assessment of common simulation protocols for simulations of nanopores, membrane proteins & channels, Jirasak Wong-ekkabut & ... Melatonin directly interacts with cholesterol and alleviates cholesterol effects in dipalmitoylphosphatidylcholine monolayers, ... Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison ... The importance of membrane defects - lessons from simulations, W.F. Bennett and D.P. Tieleman, Acc. Chem. Res. 47, 2244-2251 ( ...
  http://softsimu.net/publications.shtml