NDLI: Molecular dynamics study of Na+ transportation in a cyclic peptide nanotube and its influences on water behaviors in the tube

Content Provider	Springer Nature Link
Author	Song, Xuezeng Fan, Jianfen Liu, Dongyan Li, Hui Li, Rui
Copyright Year	2013
Abstract	The dynamics of Na+ transportation in a transmembrane cyclic peptide nanotube of 8 × (WL)4/POPE has been simulated. The curve of PMF (potential of mean force) for Na+ moving through the tube, based on ABF (adaptive biasing force) method, indicates that Na+ possesses lower free energy in an α-plane region than in a mid-plane one. It was found that Na+ would desorb one or two water molecules in the first solvation shell when entering the tube and later maintain in a solvation state. The average numbers of water molecules around Na+ are 4.50, 4.09 in the first solvation shell, and 3.10, 4.08 in the second one for Na+ locating in an α-plane zone and a mid-plane region, respectively. However, water molecules far away from Na+ location still nearly arrange in a form of 1-2-1-2 file. The dipole orientations of water molecules in the regions of gaps 1 and 7 display “D-defects”, resulted from the simultaneous electrostatic potentials generated by Na+ and the bare carbonyls at the tube mouths. Such “D-defects” accommodate the energetically favorable water orientations thereby. Figure The PMF profile of Na+ transportation in an octa-CPNT and D-defects emerging in the tube.
Starting Page	4271
Ending Page	4282
Page Count	12
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	19
Issue Number	10
e-ISSN	09485023
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2013-07-31
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Cyclic peptide nanotube Molecular dynamics Na+ PMF curve Water chain Computer Applications in Chemistry Molecular Medicine Computer Application in Life Sciences Characterization and Evaluation of Materials Theoretical and Computational Chemistry
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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