Observation of self-spreading lipid bilayer on hydrophilic surface with a periodic array of metallic nano-gate

2008 ◽  
Vol 53 (21) ◽  
pp. 6278-6283 ◽  
Author(s):  
H. Nabika ◽  
B. Takimoto ◽  
N. Iijima ◽  
K. Murakoshi
Keyword(s):  
Lipid Bilayer ◽  
Periodic Array ◽  
Hydrophilic Surface

Controlling Molecular Diffusion in Self-Spreading Lipid Bilayer Using Periodic Array of Ultra-Small Metallic Architecture on Solid Surface

2005 ◽  
Vol 127 (48) ◽  
pp. 16786-16787 ◽  
Author(s):  
Hideki Nabika ◽  
Atsushi Sasaki ◽  
Baku Takimoto ◽  
Yoshitaka Sawai ◽  
Shengtai He ◽  
...  
Keyword(s):  
Lipid Bilayer ◽  
Solid Surface ◽  
Molecular Diffusion ◽  
Periodic Array

Nano-pore Lipid Bilayer Formed by Self-spreading Method

2019 ◽  
Vol 139 (10) ◽  
pp. 1146-1152
Author(s):  
Zugui Peng ◽  
Kenta Shimba ◽  
Yoshitaka Miyamoto ◽  
Tohru Yagi
Keyword(s):  
Lipid Bilayer

Spotting Differences in Molecular Dynamic Simulations of Influenza A M2 Protein-Ligand Complexes by Varying M2 construct, Lipid Bilayer and Force Field

2019 ◽  
Author(s):  
Dimitrios Kolokouris ◽  
Iris Kalenderoglou ◽  
Panagiotis Lagarias ◽  
Antonios Kolocouris
Keyword(s):  
Molecular Dynamic ◽  
Lipid Bilayer ◽  
Influenza A ◽  
Md Simulations ◽  
Membrane Curvature ◽  
Buffer Size ◽  
M2 Protein ◽  
Dynamic Simulations ◽  
Amphipathic Helices ◽  
Drug Protein Binding

<p>We studied by molecular dynamic (MD) simulations systems including the inward<sub>closed</sub> state of influenza A M2 protein in complex with aminoadamantane drugs in membrane bilayers. We varied the M2 construct and performed MD simulations in M2TM or M2TM with amphipathic helices (M2AH). We also varied the lipid bilayer by changing either the lipid, DMPC or POPC, POPE or POPC/cholesterol (chol), or the lipids buffer size, 10x10 Å<sup>2 </sup>or 20x20 Å<sup>2</sup>. We aimed to suggest optimal system conditions for the computational description of this ion channel and related systems. Measures performed include quantities that are available experimentally and include: (a) the position of ligand, waters and chlorine anion inside the M2 pore, (b) the passage of waters from the outward Val27 gate of M2 S31N in complex with an aminoadamantane-aryl head blocker, (c) M2 orientation, (d) the AHs conformation and structure which is affected from interactions with lipids and chol and is important for membrane curvature and virus budding. In several cases we tested OPLS2005, which is routinely applied to describe drug-protein binding, and CHARMM36 which describes reliably protein conformation. We found that for the description of the ligands position inside the M2 pore, a 10x10 Å<sup>2</sup> lipids buffer in DMPC is needed when M2TM is used but 20x20 Å<sup>2</sup> lipids buffer of the softer POPC; when M2AH is used all 10x10 Å<sup>2</sup> lipid buffers with any of the tested lipids can be used. For the passage of waters at least M2AH with a 10x10 Å<sup>2</sup> lipid buffer is needed. The folding conformation of AHs which is defined from hydrogen bonding interactions with the bilayer and the complex with chol is described well with a 10x10 Å<sup>2</sup> lipids buffer and CHARMM36. </p>

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