Paper Citing NAMD - Abstract
Li, Rui; Fan, Jianfen; Li, Hui; Yan, Xiliang; Yu, Yi
Exploring the Dynamic Behaviors and Transport Properties of Gas Molecules in a Transmembrane Cyclic Peptide Nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14916-14927, DEC 5 2013
The dynamic behaviors and transport properties of O-2, CO2, and NH3 molecules through a transmembrane cyclic peptide nanotube (CPNT) of 8Xcyclo-(W (L) under bar)(4)/POPE have been investigated by steered molecular dynamics (SMD) simulations and adaptive biasing force (ABF) samplings. Different external forces are needed for three gas molecules to enter the channel. The periodic change of the pulling force curve for a gas traveling through the channel mainly arises from the regular and periodic arrangement of the composed CP subunits of the CPNT. Radial distribution functions (RDFs) between gas and water disclose the density decrease of channel water, which strongly aggravates the discontinuity of H-bond formation between a gas molecule and the neighboring water. Compared to hardly any H-bond formation between CO2 (or O-2) and the framework of the CPNT, NH3 can form abundant H-bonds with the carbonyl/amide groups of the CPNT, leading to a fierce competition to NH3-water H-bonded interactions. In addition to direct H-bonded interactions, all three gases can form water bridges with the tube. The potential profile of mean force coincides with the occurring probability of a gas molecule along the tube axis. The energy barriers at two mouths of the CPNT elucidate the phenomenon that CO2 and O-2 are thoroughly confined in the narrow lumen while NH3 can easily go outside the tube. Intermolecular interactions of each gas with channel water and the CPNT framework and the formation of H-bonds and water bridges illuminate the different gas translocation behaviors. The results uncover interesting and comprehensive mechanisms underlying the permeation characteristics of three gas molecules traveling through a transmembrane CPNT.
