Paper Citing NAMD - Abstract
Zhu, Hong; Xiao, Shiyan; Wang, Lei; Liang, Haojun
Communication: Asymmetrical cation movements through G-quadruplex DNA
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 041103, JUL 28 2014
G-quadruplex is a specific DNA structure stabilized by cations dwelling between adjacent G-quartets. The cation which dwelling in the coordination sites can move to the bulk solution through two terminals of G-quadruplex in an asymmetrical manner. In this study, we used molecular dynamics simulations and adaptive biasing force method to investigate the influence of glycosidic bond orientations of guanosines on the moving of cations through the G-quartet. We found that syn glycosidic bond orientation penalizes the escaping of K+ ions, which results in the asymmetrical cation movements through the two terminals of G-quadruplexes. Nonetheless, the syn orientations have slight influence on the energy barrier for Na+ ions penetrating the terminal G-quartets because of its relatively smaller radius. This study contributes to the understanding of the asymmetrical cation displacement in G-quadruplex systems. (C) 2014 AIP Publishing LLC.
