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Molecular Dynamics Simulation of Water Transportation Properties of Transmembrane Cyclic Peptide Nanotubes Modeling Biological Water Channels

Author: TangMin
Tutor: FanJianFen
School: Suzhou University
Course: Physical and chemical
Keywords: Cyclic peptide nanotubes Molecular Dynamics Water channel
CLC: TB383.1
Type: Master's thesis
Year: 2010
Downloads: 61
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Abstract


In this paper, molecular dynamics (MD) method of three diameters respectively 6,8 and 10? Transmembrane cyclic peptide nanotubes 8 × cyclo (WL) n = 3,4,5 - PNT / POPE, equilibrium and nonequilibrium molecular dynamics simulations to study the structure of water molecules in such transmembrane nanochannel characteristics and transmission characteristics (including water chain structure, dipole orientation, density distribution and penetration and diffusion characteristics) The key findings are as follows: 1. conformational search method using simulated annealing and MD simulations of three different diameters cyclic peptide nanotubes 8 × cyclo (WL) n = 3, 4, 5 -PNT lowest energy conformations. The effects of cyclic peptide nanotubes simulation process stability of the skeleton structure. Fully hydrated POPE lipid membranes obtained after pre-equilibrium of each area and the effective thickness of the lipid molecules remained constant POPE lipid membranes equilibrium configuration. Insert the water balance of the equilibrium configuration of the cyclic peptide nanotubes - lipid membranes, after pre-equilibration of the corresponding equilibrium configuration. Of the transmembrane Central octapeptide nano tube 8 × cyclo (WL) 4-PNT/POPE system for 50 ns MD simulation, detailed study of the structure and formation mechanism of nanotube water chain. Water molecules in the nano-tube Ordering memory water chain of the wavy pattern, the \The wavelength is exactly the distance between two adjacent cyclic peptide 4.8 A. (1) the cylindrical water molecules in the tube distribution function curve and PMF (Potential of Mean Force) instructions the transmembrane ring octapeptide nanotubes formation \The space of the tube limiting effect. The radial distribution function of water molecules in the tube (OO and HH) octapeptide nanotubes ring is a reasonable interpretation of the \Chance of a strong hydrogen bond is formed between the water molecules and the skeleton of the tube within the area of ??each of the mid-plane of less than 0.1, indicating that hydrogen bonding interactions between the ring octapeptide nanotubes with water molecules than affecting tube \The major factor in the formation of chain structure. Ring octapeptide nanotube water molecules to form hydrogen bond network modes are: a water molecule with an adjacent region of the mid-plane in the region of α-plane two water molecules form hydrogen bonds, the mid-plane area of ??each water molecule form hydrogen bonds with the water molecules and the adjacent region of the α-plane nanotubes skeleton C = O. (2) within the nanotube dipole orientation of the water molecules and water molecules along the tube axis potential energy curves show that the dipole of the water molecule flip occurs between the third and fourth ring, the nanotubes from the cyclic peptide, lipid membrane and bulk water molecules together on the tube near the nozzle of the water molecules (| z | GT; 10?) has a strong orientation effect; outside influence is not enough in the middle of the tube part of the water molecule (| Z | LT; 10?) strong enough to overcome the thermal motion. 3 balance MD and non-equilibrium MD simulation, analysis of the water molecules in the three transmembrane cyclic peptide nanotubes 8 × cyclo (WL) n = 3,4,5 -PNT/POPE transport properties, and the features and characteristics of the transmission parameters of the water molecules in the three nanotubes diffusion permeability (pd) and Osmotic permeability (PF). (1) transmembrane cyclic hexapeptide nanotubes, the water molecules are single-chain arrangement, most of the water molecules occupy the position of the region of the mid-plane; the transmembrane ring octapeptide nanotube, the water molecules to \-2 \(2) The water molecules in the three transmembrane cyclic peptide nanotubes the 8 × Cyclo (WL) n = 3,4,5 -PNT/POPE moving is a movement of one-dimensional diffusion along the nano tube The axial direction movement, satisfy the Fick movement. (3) using the balance MD simulation obtained for the first time the water molecules in the diffusion characteristics of the ring of three transmembrane peptide nanotubes 8 × Cyclo (WL) n = 3,4,5 -PNT/POPE The Parameters diffusion permeability (pd), respectively 0.488,21.17 and 94.08? 3/ns,. The balanced and unbalanced MD simulation of the first two methods to obtain the osmotic permeability (pf) with the penetration of water molecules in the above three nanochannel characteristic parameters were 3.97,66.15 and 496.86? The 3/ns (balanced MD), 2.30 71.85 and 473.31? 3/ns (of non-equilibrium MD). Certain comparability the pf values ??obtained by simulation of this article AQP1 pf the measured value. Comparison of three cyclic peptide nanotubes pf / pd value lt; N gt; 1 (lt; N gt; relationship between the average number of water molecules in the tube), found only ring hexapeptide nano tube pf / pd value approximately equal to lt; N gt; 1, the cooperative motion of water molecules in the tube, no exchange and cross the line with the characteristics of the single-chain transmission. With the nanotube diameter becomes large, the chain of water is no longer present in single-chain form, (N 1) / (pf / pd) value as the diameter becomes large. Mechanized, the article selected cyclic peptide nanotubes 8 × 8 Cyclo (WL) n = 3,4,5 -PNT embedded into the fully hydrated POPE lipid membrane composition having a suitable hydrophobic side chain system as a simplified model of the biological water channel, the water chain structure and formation analysis of the mechanism and the diffusion of water molecules in the three transmembrane channel and penetration characteristics analysis will help reveal the nano-scale water at the atomic level the essential characteristic of the channel.

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