title: Is the G-quadruplex an effective nanoconductor for ions?
abstract: We use a stepwise pulling protocol in molecular dynamics simulations to identify how a G-quadruplex selects and conducts Na(+), K(+), and NH4(+) ions. By estimating the minimum free-energy changes of the ions along the central channel via Jarzynski's equality, we find that the G-quadruplex selectively binds the ionic species in the following order: K(+) > Na(+) > NH4(+). This order implies that K(+) optimally fits the channel. However, the features of the free-energy profiles indicate that the channel conducts Na(+) best. These findings are in fair agreement with experiments on G-quadruplexes and reveal a profoundly different behavior from the prototype potassium-ion channel KcsA, which selects and conducts the same ionic species. We further show that the channel can also conduct a single file of water molecules and deform to leak water molecules. We propose a range for the conductance of the G-quadruplex.
authors.affiliation: Department of Physics and Astronomy, University of Southern California , Los Angeles, California 90089, United States.
authors.forename: Van A
authors.initials: VA
authors.lastname: Ngo
authors.forename: Rosa
authors.initials: R
authors.lastname: Di Felice
authors.forename: Stephan
authors.initials: S
authors.lastname: Haas
mesh_terms: D064751:Ammonium Compounds / Q000032:analysis*; D001665:Binding Sites; D054856:G-Quadruplexes; D007477:Ions / Q000032:analysis; D056004:Molecular Dynamics Simulation; D049329:Nanostructures / Q000737:chemistry*; D011188:Potassium / Q000032:analysis*; D012964:Sodium / Q000032:analysis*; D014867:Water / Q000737:chemistry
chemical_list: D064751:Ammonium Compounds; D007477:Ions; D014867:Water; D012964:Sodium; D011188:Potassium