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High-pressure effect on the dynamics of solvated peptides
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View: Figures


Image of FIG. 1.
FIG. 1.

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.

Image of FIG. 2.
FIG. 2.

(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.

Image of FIG. 3.
FIG. 3.

(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.

Image of FIG. 4.
FIG. 4.

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.

Image of FIG. 5.
FIG. 5.

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.

Image of FIG. 6.
FIG. 6.

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.

Image of FIG. 7.
FIG. 7.

Normalized dynamic factor (D/D o ) as a function of pressure obtained from Figs. 4(b) and 6(d) (on).


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: High-pressure effect on the dynamics of solvated peptides