Molecular Dynamics Simulations to Provide New Insights into the Asymmetrical Ammonium Ion Movement Inside of the [d(G3T4G4)]2 G-Quadruplex DNA Structure

2012 ◽  
Vol 116 (31) ◽  
pp. 9363-9370 ◽  
Author(s):  
Parisa Akhshi ◽  
Gregory Acton ◽  
Gang Wu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dna Structure ◽  
Ammonium Ion ◽  
Quadruplex Dna ◽  
Ion Movement ◽  
G Quadruplex ◽  
Dynamics Simulations

Umbrella sampling molecular dynamics simulations reveal concerted ion movement through G-quadruplex DNA channels

2017 ◽  
Vol 19 (18) ◽  
pp. 11017-11025 ◽  
Author(s):  
Parisa Akhshi ◽  
Gang Wu
Keyword(s):  
Molecular Dynamics ◽  
Ion Transport ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Umbrella Sampling ◽  
Potential Of Mean Force ◽  
Quadruplex Dna ◽  
Ion Movement ◽  
G Quadruplex ◽  
Dynamics Simulations

We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion transport through three representative G-quadruplex DNA channels: [d(TG4T)]4, [d(G3T4G4)]2, and d[G4(T4G4)3].

scholarly journals Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands

2021 ◽  
Author(s):  
Michael P. O'Hagan ◽  
Susanta Haldar ◽  
Juan C. Morales ◽  
Adrian J. Mulholland ◽  
M. Carmen Galan
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Solution Phase ◽  
Enhanced Sampling ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Dynamics Simulations

Enhanced sampling molecular dynamics simulations and solution-phase experiments come together to demonstrate the diverse effects of G4-interactive small molecules.

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