Table 1.
Torsion angles (in degrees) of β-turn residues as obtained from the DFT-calculated structures.
Fig 1.
Extent of sampling and statistical significance.
Results from the application of Good-Turing statistics to the three trajectories for both the full-length peptides and their four-residue central part. See text for details.
Fig 2.
Dihedral angle principal component analysis.
Diagrams illustrating the free energy landscape of each heptapeptide along the top two principal components, as obtained by the dihedral angle Principal Component Analysis (blue peaks correspond to high density regions). Shown with numbers are the different clusters derived by the dPCA analysis.
Fig 3.
dPCA-derived β-turn representative structures.
Clusters’ backbone plus Cβ representative structures that correspond to β-turn motifs. The structural analysis was performed using the PROMOTIF program and structures were generated using the PyMOL program. The color coding used here is representative of the atoms’ type (blue color corresponds to N atoms, red color corresponds to O atoms and light grey color corresponds to C atoms). Shown are only representative β-turn structures that correspond to clusters of population > 1%.
Table 2.
Populations (%) of the various β-turn types sampled in the MD trajectoriesa.
Fig 4.
Distribution of deviations (in degrees) between MD trajectory-derived and DFT-calculated φ,ψ angles.
Histograms showing the distribution of deviations (in degrees) between a reference DFT-obtained φ,ψ value and the corresponding φ,ψ values obtained from the MD simulations for selected residues. While there are torsion angles of specific residues that fluctuate around the DFT values (d = 0°) during the simulation [Gaussian distributions in the middle of panels (A)-(B)], some torsions present a significant divergence from the proposed values (C-H).
Fig 5.
DFT-derived structures colored according to the magnitude of deviation from MD simulations.
Shown are the DFT-obtained structures illustrating the torsion angle discrepancies in relation with the MD-derived angles. The color coding is indicative of the mean deviation of the MD φ,ψ values from the corresponding DFT-obtained ones, varying from blue (small deviations) to green (moderate deviations) and red (large deviations). Shown with a label, are the torsion angles presenting the greatest deviation throughout the simulations.
Table 3.
MD torsion angles exceeding the ±30° deviation limit from the DFT-calculated angles, along with their corresponding deviationsa in terms of absolute value.
Table 4.
Absolute differences between the calculated Gaussian mean values (μ)a and the ideal β-turn φ,ψ torsion angles, for Asn/Gly residues of each turn type.