Fig 1.
Flowcharts of the AmphiScan calculations: (A) zα-scan flowchart, (B) zαβ-scan flowchart, (C) visual representation of the rotation and tilt operations used to place the helices with respect to the membrane surface. Note that the plane of the membrane corresponds to the xy-plane and the membrane normal corresponds to the z-axis.
Table 1.
Sequences of the LK peptides used for the AmphiScan calculations.
Fig 2.
Heatmaps for the Rosetta scans at the best-scoring tilt angle for six LK peptides calculated with the RosettaMembrane (A), franklin2019 (B), and ref2015_memb score functions (C). The x-axis represents the rotation along screw axis of the helices and the y-axis stands for the depth of the membrane. Color coding was done separately for each helix where blue color represents the low-scoring regions and the red color represents the high-scoring regions. The black bars represent the boundary of the hydrophobic thickness of the implicit membrane model.
Fig 3.
Example alignment poses for the native (green) and best pose structures (blue) from the OPM zαβ calculations. The structures in the top row had RMSD values smaller than 2Å, the middle row had RMSD values between 2 and 4Å, and the bottom row had RMSD values larger than 4Å.
Table 2.
The RMSD values calculated for the best Rosetta zα-scan and zαβ-scan poses with the RosettaMembrane score function where the depth and helix rotation around the screw axis were allowed, and the source of the starting structure used for the calculations.
The standard deviations were calculated as the standard deviation among the RMSD values of the same helix with the starting structures from three different sources. All units are in Ångstroms (Å).
Table 3.
The RMSD and membrane-embedded residue accuracies calculated with the RosettaMembrane score function in reference to the MD simulations.