Theoretical study on substituent and solvent effects for nanocubes formed with gear-shaped amphiphile molecules

2017 ◽  
Vol 19 (2) ◽  
pp. 1627-1631 ◽  
Author(s):  
T. Mashiko ◽  
S. Hiraoka ◽  
U. Nagashima ◽  
M. Tachikawa
Keyword(s):  
Molecular Dynamic ◽  
Solvent Effects ◽  
Theoretical Study ◽  
Molecular Dynamic Simulations ◽  
Aqueous Methanol ◽  
Dynamic Simulations ◽  
The Stability

We have carried out molecular dynamic simulations to elucidate the stability of hexameric gear-shaped amphiphile nanocube capsules in water, 25% aqueous methanol, and methanol.

scholarly journals Theoretical study of mechanisms for the hydrolytic deamination of cytosine via steered molecular dynamic simulations

RSC Advances ◽  
2018 ◽  
Vol 8 (61) ◽  
pp. 34867-34876 ◽  
Author(s):  
S. Tolosa ◽  
J. A. Sansón ◽  
A. Hidalgo
Keyword(s):  
Free Energy ◽  
Molecular Dynamic ◽  
Theoretical Study ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Cytosine Deamination ◽  
Energy Profiles ◽  
Free Energy Profiles ◽  
Hydrolytic Deamination ◽  
Smd Simulations

Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations.

scholarly journals Identification of the Interactions Interference Between the PH and START Domain of CERT by Limonoid and HPA Inhibitors

2020 ◽  
Vol 7 ◽  
Author(s):  
Mariem Ghoula ◽  
Axelle Le Marec ◽  
Christophe Magnan ◽  
Hervé Le Stunff ◽  
Olivier Taboureau
Keyword(s):  
Molecular Dynamic ◽  
Binding Affinity ◽  
Computational Study ◽  
Md Simulations ◽  
Sphingolipid Metabolism ◽  
Molecular Dynamic Simulations ◽  
Ph Domain ◽  
Dynamic Simulations ◽  
The Difference ◽  
The Stability

The multi domain ceramide transfer protein (CERT) which contains the domains START and PH, is a protein that allows the transport of ceramide from the endoplasmic reticulum to the Golgi and so it plays a major role in sphingolipid metabolism. Recently, the crystal structure of the PH-START complex has been released, suggesting an inhibitory action of START to the binding of the PH domain to the Golgi apparatus and thus limiting the CERT activity. Our study presents a combination of docking and molecular dynamic simulations of N-(3-hydroxy-1-hydroxymethyl-3-phenylpropyl)alkanamides (HPA) analogs and limonoids compounds known to inhibit CERT. Through our computational study, we compared the binding affinity of 14 ligands at both domains (START and PH) and also at the START-PH interface, including several mutations known to play a role in the CERT’s activity. At the difference of HPA compounds, limonoids have a stronger binding affinity for the START-PH interface. Furthermore, 2 inhibitors (HPA-12 and isogedunin) were investigated through molecular dynamic (MD) simulations. 50 ns of molecular dynamic simulations have displayed the stability of isogedunin as well as keys residues in the binding of this molecule at the interface of the PH-START complex. Therefore, this study suggests a novel inhibitory mechanism of CERT for limonoid compounds involving the stabilization of the START-PH interface. This could help to develop new and potentially more selective inhibitors of this transporter, which is a potent target in cancer therapy.

scholarly journals Ranking the Efficiency of Gas Hydrate Anti-agglomerants through Molecular Dynamic Simulations

2021 ◽  
Vol 125 (5) ◽  
pp. 1487-1502
Author(s):  
Stephan Mohr ◽  
Felix Hoevelmann ◽  
Jonathan Wylde ◽  
Natascha Schelero ◽  
Juan Sarria ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Gas Hydrate ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations
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