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

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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

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Publication details

The article was received on 15 Feb 2017, accepted on 15 Mar 2017 and first published on 16 Mar 2017


Article type: Paper
DOI: 10.1039/C7CP01028A
Citation: Phys. Chem. Chem. Phys., 2017, Advance Article
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    Umbrella sampling molecular dynamics simulations reveal concerted ion movement through G-quadruplex DNA channels

    P. Akhshi and G. Wu, Phys. Chem. Chem. Phys., 2017, Advance Article , DOI: 10.1039/C7CP01028A

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