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*  Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer. - Oxford Neuroscience
... side chains along the normal to a phosphatidylcholine bilayer were in good agreement with experimental and atomistic simulation ... ranging from their self-assembly to the relation between their structure and function. However, there is a need to evaluate the ... Computer Simulation, Hydrophobic and Hydrophilic Interactions, Ions, Lipid Bilayers, Molecular Conformation, Protein Structure ... ranging from their self-assembly to the relation between their structure and function. However, there is a need to evaluate the ...
  https://www.neuroscience.ox.ac.uk/publications/100612
*  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 ... structure of nAChR embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer and water molecules. A 30-ns CMD simulation ... between the final equilibrated structure of nAChR and the original structure is 1.02 Å. A 30-ns CMD simulation was subsequently ...
  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 ... 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.g005&req=4
*  C60 fullerene promotes lung monolayer collapse | Journal of The Royal Society Interface
Starting structure files, topologies and simulation parameters are available via Figshare (http://dx.doi.org/10.6084/m9. ... 2012 Effects of spherical fullerene nanoparticles on a dipalmitoyl phosphatidylcholine lipid monolayer: a coarse grain ... 2008 Computer simulation study of fullerene translocation through lipid membranes. Nat. Nanotechnol. 3, 363-368. (doi:10.1038/ ... Our simulation system consisted of two lipid monolayers bounding a water slab (figure 1a). The monolayers contained a saturated ...
  http://rsif.royalsocietypublishing.org/content/12/104/20140931
*  Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems
This CRMSα is an average over the last 240 ps of the 60 ns simulation, and the crystal structure is used as a reference point. ... dipalmitoylphosphatidylcholine (DPPC) is represented by four particles in the head group (representing the choline, phosphate ... 1. +. θ. 2. +. ξ. ). θ. i. j. k. 3. +. 1. 2. (. θ. 1. θ. 2. +. θ. 1. ξ. +. θ. 2. ξ. ). θ. i. j. k. 2. −. (. θ. 1. θ. 2. ξ. ). θ ... Structure. 2006;14:1767-1777. [PubMed]. 35. Gibbons MM, Klug WS. Mechanical modeling of viral capsids. J. Matter. Sci. 2007;42: ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2904924/
*  Continuum Approaches to Understanding Ion and Peptide Interactions with the Membrane | SpringerLink
Pandit SA, Bostick D, Berkowitz ML (2003) Molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer with NaCl. ... Kim T, Lee KI, Morris P, Pastor RW, Andersen OS, Im W (2012) Influence of hydrophobic mismatch on structures and dynamics of ... Vepper H, Voth G (2006) Mechanisms of passive ion permeation through lipid bilayers: insights from simulation. J Phys Chem B ... and scalable molecular simulation. J Chem Theory Comput 4(3):435-447. doi: 10.1021/ct700301q CrossRefGoogle Scholar ...
  https://link.springer.com/article/10.1007/s00232-014-9646-z
*  Molecular Dynamic Simulations of Raft Formation and Fullerene Transport in Lipid Membranes
The defects of the bilayer like structures formed in our simulation are likely due to a large size of the simulation box. It is ... The membrane bilayers are modeled using saturated dipalmitoyl phosphatidylcholine (diC 16 PC) lipids, unsaturated dilinoleyl ... Any simulation study typically consists of three steps. The first step is energy minimization Two MD simulation runs are then ... in simulation of aggregate formation due to salt bridges System Composition Duration of simulation Box size Simulation ...
  http://ufdc.ufl.edu/UFE0045619/00001
*  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. ... Membrane protein structures are underrepresented in the Protein Data Bank (PDB) due to difficulties associated with expression ... Membrane protein structures are underrepresented in the Protein Data Bank (PDB) due to difficulties associated with expression ... Recently, there has been substantial progress in the simulation of lipid bilayers and membrane proteins embedded within them. ...
  https://www.neuroscience.ox.ac.uk/publications/503317
*  Cinvestav ::: Centro de Investigaci n y Estudios Avanzados del I.P.N.
De la Peña O., de Coss, R., Heid, R. y Bohnen, K.P.. Effects of Al and C doping on the electronic structure and phonon ... Villanueva J., Anta J.A., Guillén E. y Oskam G.. Numerical Simulation of the Current - Voltage Curve in Dye-Sensitized Solar ... Globulin 11S and its mixture with L-Dipalmitoylphosphatidylcholine at the air/liquid interface.. Journal of Physical Chemistry ... Quijano R., de Coss R. y Singh D.J.. Electronic structure and energetics of the tetragonal distortion for TiH2, ZrH2, and HfH2 ...
  http://www.mda.cinvestav.mx/fa07.php
*  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 ... Membrane structure of the Human Immunodeficiency Virus gp41 fusion domain by molecular dynamics simulation. Biophysical Journal ... Chan, D.C., Fass, D., Berger, J.M. and Kim, P.S. (1997) Core structure of gp41 from the HIV envelope glyco-protein. Cell, 89(2 ... Li, Y., Han, X., Lai, A.L., Bushweller, J.H., Cafiso, D.S. and Tamm, L.K. (2005) Membrane structures of the he-mifusion- ...
  https://www.scirp.org/Journal/PaperInformation.aspx?paperID=1879&JournalID=162
*  Most recent papers with the keyword CL | Read by QxMD
Fine structure of excitons and electron-hole exchange energy in polymorphic CsPbBr 3 single nanocrystals. ... 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 ... Here, high-resolution photoluminescence (PL) spectroscopy of single bromide-based NCs reveals the exciton fine structure in the ...
  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 ... Structure of the oxygen-evolving complex of photosystem II: information on the S(2) state through quantum chemical calculation ... 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=
*  Print - Biology-Online
Membrane Electroporation: A Molecular Dynamics Simulation. Abstract. Membrane Electroporation: A Molecular Dynamics Simulation ... The internal structures of the peptide nanotube assembly and that of the DNA strand are hardly modified under field. For system ... Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and ... where Lz is the size of the simulation box in the direction perpendicular to the applied field. For instance, as we will see ...
  https://www.biology-online.org/kb/print.php?aid=587
*  Nonenzymatic Reactions above Phospholipid Surfaces of Biological Membranes: Reactivity of Phospholipids and Their Oxidation...
J. F. Nagle and S. Tristram-Nagle, "Structure of lipid bilayers," Biochimica et Biophysica Acta-Reviews on Biomembranes, vol. ... 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 ... S. J. Singer and G. L. Nicolson, "The fluid mosaic model of the structure of cell membranes," Science, vol. 175, no. 4023, pp. ...
  https://www.hindawi.com/journals/omcl/2015/319505/
*  Protocols and Video Articles Authored by Andrew S. Mount
... dipalmitoylphosphatidylcholine or DPPC bilayer). The simulation results indicate that, although a pristine C60 molecule can ... affected the membrane structure differently. This study offers a mechanistic explanation of that difference and for the reduced ... In JoVE (1). *Characterization of Calcification Events Using Live Optical and Electron Microscopy Techniques in a Marine ... Chan1, Takashi Toyofuku2, George Wetzel3, Laxmikant Saraf3, Vengatesen Thiyagarajan4, Andrew S. Mount1 1Department of ...
  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) ... first step for understanding the mechanism of cell-permeating peptides and the thermodynamics of membrane protein structure and ... The study found that the Cd in sediments (≤600 mg kg-1 ) was successfully stabilized after 166 d SRB bio-treatment. This was ...
  https://www.readbyqxmd.com/keyword/27697
*  Most recent papers with the keyword Alpha helix mimetic | Read by QxMD
The structure of a third intracellular (i3) loop agonist, pepducin, based on protease-activated receptor-1 (PAR1) was solved by ... Molecular dynamics simulation of human serum paraoxonase 1 in DPPC bilayer reveals a critical role of transmembrane helix H1 ... with a HDL-mimetic dipalmitoylphosphatidylcholine (DPPC) bilayer using homology modeling and molecular dynamics simulations... ... Changes in pH can alter the structure and activity of proteins and may be used by the cell to control molecular function. This ...
  https://www.readbyqxmd.com/keyword/74922
*  Plus it
1998) Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution. Nature 395:347-353. ... 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 ... 2000) Surpassing the lateral resolution by a factor of two using structured illumination microscopy. J Microsc 198:82-87. ...
  http://www.jneurosci.org/content/32/45/15983
*  DiVA - Search result
Experimentally a transition from a stoichiometric cubic structure with disordered vacancies to the ideal B1 structure without ... 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 ... The structures of complexes between polyethylene imine and sodium dodecyl sulfate in D2O: a scattering study2005In: Journal of ...
  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=
*  Scientific Reports Table of Contents e-alert: 25 April 2017
... and electronic structures within highly strained BiFeO3 by transmission electron microscopy and first-principles simulation ▶ ... and Cholinium-Based Ionic Liquids on Vibrio Fischeri Cells and Dipalmitoylphosphatidylcholine Liposomes ▶ ... Crystal and electronic structures of ~380 nm BiFeO3 film grown on LaAlO3 substrate are comprehensively studied using advanced ... Numerous crystal structures of HIV gp120 have been reported, alone or with receptor CD4 and cognate antibodies; however, no ...
  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
Solid-state NMR structure of amantadine-bound M2 proton channel in lipid bilayers. A. Side view showing Ser31, Val27, Gly34, ... 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 ... 5-19F]U23-13C and [5-19F]U23-15N distances were in good agreement with distances obtained from solution-state NMR structures of ... Characterisations of plant material include the structure and dynamics of pectic polysaccharides and the structure of cellulose ...
  https://openmedscience.com/article/nmr-active-nuclei-biological-biomedical-applications/
*  Advanced Materials and Liquid Crystal Institute, Kent State University
The Influence of Monovalent Ions on Dipalmitoylphosphatidyl-choline Bilayer Structure and Packing. Beth A. Cunningham. Leonard ... Quantum Simulation of Polyene Ground States. Stefan Klemm. Michael Lee. Physics. -. 176. 1987. Critical Properties of Phase ... An X-Ray Study of the Crystal Structure and the Smectic E Structure of a Smectogenic Liquid Crystal -- Di-n-Propyl-p-terphenyl- ... Structure and Rheology of Some Bent Core Liquid Crystals. Christopher Bailey. Antal Jakli. Chemical Physics. 27. ...
  https://www.lcinet.kent.edu/facts/dissertation/index.php
*  Lipids, Organization and Aggregation of - CHEMICAL BIOLOGY
... focusing in particular on the fundamental science of biological structures and systems, the use of chemical and biological ... Lipid structure. In: The Structure of Biological Membranes. Yeagle Philip L, ed. 2005. CRC Press, Boca Raton, FL. ... 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 ...
  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 ... Their structure is investigated using molecular dynamics simulations. All-atom models suggest that the lipopeptide is ... [more ... Mycosubtilin was added underneath dipalmitoylphosphatidylcholine or cholesterol monolayers at the air-water interface and ... Their structure is investigated using molecular dynamics simulations. All-atom models suggest that the lipopeptide is flexible ...
  https://orbi.uliege.be/browse?type=author&value=Benichou%2C+Emmanuel
*  SoftSimu - Publications and theses
The influence of lateral and terminal substitution on the structure of a liquid crystal dendrimer: A computer simulation study ... Melatonin directly interacts with cholesterol and alleviates cholesterol effects in dipalmitoylphosphatidylcholine monolayers, ... Coarse-grained simulation studies of a liquid crystal dendrimer: towards computational predictions of nanoscale structure ... Atomic-scale structure and electrostatics of anionic POPG lipid bilayers with Na+ counterions W. Zhao, Tomasz Róg, A.A. ...
  http://softsimu.net/publications.shtml