Paper Citing NAMD - Abstract
Yan, Xiliang; Fan, Jianfen; Yu, Yi; Xu, Jian; Zhang, Mingming
Transport Behavior of a Single Ca2+, K+, and Na+ in a Water-Filled Transmembrane Cyclic Peptide Nanotube
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:998-1011, MAY 2015
Molecular dynamics simulations have been performed to investigate the transport properties of a single Ca2+, K+, and Na+ in a, water-filled transmembrane cyclic peptide nanotube (CPNT). Two transmembrane CPNTs, i.e., 8x(WL)(n=4,5)/POPE (with uniform lengths but various radii), were applied to clarify the dependence of ionic transport properties on the channel radius. A huge energy barrier keeps Ca2+ out of the octa-CPNT, while Na+ and K+ can be trapped in two CPNTs. The dominant electrostatic interaction of a cation with water molecules leads to a high distribution of channel water around the cation and D-defects in the first and last gaps, and significantly reduces the axial diffusion of channel water. Water-bridged interactions were Mostly found between the artificially introduced Ca2+ and the framework of the octa-CPNT, and direct coordinations with the tube wall mostly occur for K+ in the octa-CPNT. A cation may drift rapidly or behave lazily in a CPNT. K+ behaves most actively and can visit the whole deca-CPNT quickly. The first solvation shells of Ca2+ and Na+ are basically saturated in two CPNTs, while the hydration of K+ is incomplete in the octa-CPNT. The solvation structure of Ca2+ in the octa-CPNT is most stable, while that of K+ in the deca,CPNT is most labile. Increasing the channel radius induces numerous interchange attempts between the first-shell water molecules of a cation and the ones in the outer region, especially for the K+ system.
