Molecular Dynamics Study of Tryptophylglycine:  A Dipeptide Nanotube with Confined Water

Abstract

To investigate the mechanism of structural changes of a peptide nanotube and water confined inside the channel, the helical peptide tryptophylglycine monohydrate (WG‚H 2 O) was studied by molecular dynamics (MD) simulations using the three-dimension parallel MD program ddgmq (software package) and a consistent force field. Simulations were performed on both the water-containing system and a model system without water molecules. The details of the structural behavior with temperature are investigated for the entire simulated temperature range. Phase transitions were obtained at 115, 245, 270, 310, and 385 K, due to the contributions of both the peptide and the confined water subsystems. The crystalline, amorphous, liquidlike, liquid, and superheated phases of water were observed in the temperature ranges 40-115, 115-245, 245-310, 310-385, and >385 K, respectively. At 300 K, the diffusion constant of the confined water is 0.46 × 10 -5 cm 2 s -1 , a value comparable to that of other peptide nanotubes. The empty peptide system melts at 440 K. Mechanisms of the negative thermal expansion (NTE) along the tube axis were investigated for different temperature ranges. The contraction of the crystalline water (or amorphous water) draws also the tube walls in and leads to NTE below 245 K. The other NTEs appear to be connected to the collapse of the ice network or the solid peptide network between 245 K and room temperature or from 310 to 440 K, respectively.

Dipeptides Embedded in a Lipid Bilayer Membrane as Synthetic Water Channels

“…At 300 K, the diffusion coefficient of confined water was estimated to be 4.6 × 10 −6 cm 2 s −1 , comparable with those in other synthetic water channels. 19 Proton transport was found to be facilitated by porous dendritic dipeptides through a Grotthuss mechanism, while impeding Li + , Na + , and Cl − transport. 20 Due to the special arrangement of side chains resulting in 1D hydrophobic and hydrophilic channels, dipeptides might be superior for water transport and act as synthetic channels.…”

Comparison of the interfacial dynamics of water sandwiched between static and free-standing fully flexible graphene sheets

“…In the past few decades there has been ever increasing interest in probing the nature of water in the vicinity of hydrophobic surfaces, 1,2 conned channels 3 and pores [4][5][6] with a broader goal towards possible insights into the role of water in various biological processes, microuidics technology, presence of moisture, and effects of condensation of water on various graphitic based sensors and actuators. Given the ubiquitous role of water in the entire gamut of scientic and technological applications, the phase diagram, 7 static structure and dynamics of conned water [8][9][10][11] have been keenly investigated by experimentalists and theoreticians.…”

Molecular dynamics investigations of modulated phases in organic materials

“…A NPT simulation is then carried out to adjust the system to the required state by applying the compensating pressure tensor. The MD simulations can thus well reproduce the experimental structures at starting temperatures (Pan et al, 2002(Pan et al, , 2003Pan, Birkedal et al, 2004;Pan, Brown et al, 2004a). This gives also the possibility to reproduce the observed phase transition occurring not too far from the starting temperature.…”