A solvated Ace-Gly-Pro-Nme structure. The dynamics of the proline peptidyl-prolyl (ω) angle (yellow) and the hydrogen bonding of C=O with solvents are the focused properties of this study. Hydrogen bonding network involving the backbone carbonyl group is colored by blue, while surrounding solvent hydrogen bonds are in green.
(a) Pressure dependent changes in the system's density. (b) The free energy profiles of the ω torsional angle of the peptide VP at 300 K, obtained from an accelerated molecular dynamics simulation using boost parameters, E = 70.0 kcal/mol and α = 15.0 kcal/mol.
(a) Effect of some parameters (NPT, NVT, collision frequency, and pressure relaxation time) on the calculated autocorrelation function of ω torsion angle. Autocorrelation function of ω for (b) VP (1 bar/200 K), and (c) VP (10 000 bar/200 K) showing a glassy effect.
Autocorrelation function of ω at various pressures and at temperatures of (a) 300 K and (b) 500 K for GP system. The sample standard deviations are shown in black (10 000 bar) and blue (1 bar) symbols. They give a sense of the level of fluctuations around the mean.
Autocorrelation function of ω at various temperatures and at pressure of (a) 1000 bar and (b) 10 000 bar for Ace-Gly(or Val)-Pro-Nme systems. C(t) = C n (t) 〈ω2〉. Inset shows pressure-independent short-time decay feature of the autocorrelation function. (c) Autocorrelation function of ω at combined P (1000 bar and 10 000 bar) and T (300 K and 500 K) effect for GP system.
The effect of pressure at different temperatures (a-d), and the effect of temperature (e) on the survival probability of the hydrogen bonded (“on”) state and non-hydrogen bonded (“off”) state for GP.
Normalized dynamic factor (D/D o ) as a function of pressure obtained from Figs. 4(b) and 6(d) (on).
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