Issue 18, 2017

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

Abstract

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]. The US MD results are in excellent agreement with those obtained previously with the adaptive biasing force (ABF) method. We then utilized the unique features in the US MD method to investigate multi-ion effects in [d(G3T4G4)]2 and discovered that the concerted ion movement is crucial for fully explaining the unusual experimental results on ion movement in this particular G-quadruplex system. We anticipate that these modern free-energy methods will be useful tools in evaluating ion transport properties of other G-quadruplex DNA channels.

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

Supplementary files

Article information

Article type
Paper
Submitted
15 Şub 2017
Accepted
15 Mar 2017
First published
16 Mar 2017

Phys. Chem. Chem. Phys., 2017,19, 11017-11025

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

P. Akhshi and G. Wu, Phys. Chem. Chem. Phys., 2017, 19, 11017 DOI: 10.1039/C7CP01028A

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