Fig. 8: Improving transmembrane peptide insertion and beta-sheet aggregation.
From: GōMartini 3: From large conformational changes in proteins to environmental bias corrections
Tilt angle distributions from simulations of WALP peptides inserted in DMPC membranes using the GōMartini model with either (A) no additional LJ interaction, or (B) an additional LJ interaction between the virtual Gō sites and water beads of ε = − 1.0 kJ/mol; tilt angle states close to 0° correspond to TM configurations, whereas those close to 90° correspond to peripherally membrane-adsorbed ones. C Representative WALP16 configurations, both fully inserted in its preferred transmembrane configuration and in its peripherally membrane-adsorbed state. WALP16 backbone shown in blue, with side chains in white. Membrane phosphate beads are represented in orange. D Normalized average contacts between two RAD16-I peptide beta strands. Solid lines show the running averages of 500 frames, while the shaded area shows the running standard deviation. Simulations were run with a GōMartini model applied between the two chains (red), with an additional LJ interaction between the virtual Gō sites and water beads with ε = − 0.5 kJ/mol (green), and without any structural or interaction bias (blue). E Representative RAD16-I strand configurations, both aggregated and dissociated. Each backbone chain is colored either brown or green, with the side chains colored in a lighter shade of the same color. Source data are provided as a Source Data file.
