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Steered molecular dynamics investigations of Na+ transport through cyclic peptide nanotube

Jie Cheng

In order to explore Na+ constrained in cyclic octa-peptide nanotube, {cyclo[(-D-Ala-L-Ala)4-]}10was selected as the model to investigate the mechanisms of cyclic peptide nanotube-mediated transmembrane transport of Na+ using steered molecular dynamics (SMD). Results show that Na+ adopt an leaping transport mode, and the leap distance is just the distance between neighboring rings. The transport speed of Na+ during the entire process is 0.00637 Å /ps. The instantaneous speed is nearly zero at ring plane and it is 3.3-3.5 Å/ps at inter ring. Na+ tends to stayed at the center axis of nanotube at the ring planes, and approaches to the side of the wall at the ring plane under the electrostatic interactions come from the nanotube.