Analysis of Charged Peptide Loop-Flipping across a Lipid Bilayer Using the String Method with Swarms of Trajectories

2021 ◽  
Author(s):  
Samarthaben J. Patel ◽  
Reid C. Van Lehn
Keyword(s):  
Lipid Bilayer ◽  
String Method

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>

scholarly journals Transmembrane signal transduction by cofactor transport

2021 ◽  
Author(s):  
Istvan Kocsis ◽  
Yudi Ding ◽  
Nicholas H. Williams ◽  
Christopher A. Hunter
Keyword(s):  
Signal Transduction ◽  
Lipid Bilayer ◽  
Metal Ion ◽  
Bilayer Membrane ◽  
Ester Hydrolysis ◽  
Lipid Bilayer Membrane ◽  
Metal Ion Cofactors

Synthetic transducers transport externally added metal ion cofactors across the lipid bilayer membrane of vesicles to trigger catalysis of ester hydrolysis in the inner compartment. Signal transduction activity is modulated by hydrazone formation.

scholarly journals Astaxanthin Prevents Atrophy in Slow Muscle Fibers by Inhibiting Mitochondrial Reactive Oxygen Species via a Mitochondria-Mediated Apoptosis Pathway

Nutrients ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 379
Author(s):  
Luchuanyang Sun ◽  
Nobuyuki Miyaji ◽  
Min Yang ◽  
Edward M. Mills ◽  
Shigeto Taniyama ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Lipid Bilayer ◽  
Muscle Atrophy ◽  
Soleus Muscle ◽  
Reactive Oxygen ◽  
H2o2 Production ◽  
Oxygen Species ◽  
Mitochondrial Reactive Oxygen Species ◽  
Tail Suspension ◽  
Apoptosis Pathway

Astaxanthin (AX) is a carotenoid that exerts potent antioxidant activity and acts in the lipid bilayer. This study aimed to investigate the effects of AX on muscle-atrophy-mediated disturbance of mitochondria, which have a lipid bilayer. Tail suspension was used to establish a muscle-atrophied mouse model. AX diet fed to tail-suspension mice prevented loss of muscle weight, inhibited the decrease of myofiber size, and restrained the increase of hydrogen peroxide (H2O2) production in the soleus muscle. Additionally, AX improved downregulation of mitochondrial respiratory chain complexes I and III in the soleus muscle after tail suspension. Meanwhile, AX promoted mitochondrial biogenesis by upregulating the expressions of adenosine 5′-monophosphate–activated protein kinase (AMPK) α-1, peroxisome proliferator–activated receptor (PPAR)-γ, and creatine kinase in mitochondrial (Ckmt) 2 in the soleus muscle of tail-suspension mice. To confirm the AX phenotype in the soleus muscle, we examined its effects on mitochondria using Sol8 myotubes derived from the soleus muscle. We found that AX was preferentially detected in the mitochondrial fraction; it significantly suppressed mitochondrial reactive oxygen species (ROS) production in Sol8 myotubes. Moreover, AX inhibited the activation of caspase 3 via inhibiting the release of cytochrome c into the cytosol in antimycin A–treated Sol8 myotubes. These results suggested that AX protected the functional stability of mitochondria, alleviated mitochondrial oxidative stress and mitochondria-mediated apoptosis, and thus, prevented muscle atrophy.

The Flexibility of Long Chain Substituents Influences Spin-Crossover in Isomorphous Lipid Bilayer Crystals

2021 ◽  
Author(s):  
Iurii Galadzhun ◽  
Rafal Kulmaczewski ◽  
Namrah Shahid ◽  
Oscar Cespedes ◽  
Mark J Howard ◽  
...  
Keyword(s):  
Lipid Bilayer ◽  
High Spin ◽  
Room Temperature ◽  
Spin Crossover ◽  
Pyridine Derivatives ◽  
Long Chain

[Fe(bpp)2][BF4]2 (bpp = 2,6-di{pyrazol-1-yl}pyridine) derivatives bearing a bent geometry of hexadec-1-ynyl or hexadecyl substituents pyrazole are isomorphous, and high-spin at room temperature. However, only the latter compound undergoes an abrupt,...

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