Fig. 5: Nanomechanics of the RBD:H11-H4 complex studied by GōMartini simulations at different pulling speeds.
From: GōMartini 3: From large conformational changes in proteins to environmental bias corrections
A Force-displacement profiles for RBD:H11-H4 complex at vpull = 5 × 10-4 nm/ps in SMD simulations using the GōMartini model, with and without position restraints of the BB beads of the RBD. The pulling SMD spring constant was set to 600 kJ/(mol·nm2). Data show the mean, and the whiskers are the standard deviation of the mean value obtained from N = 50 for each case, respectively. B Same as in (A), but the dissociation of the complex is carried out at vpull = 10-5 nm/ps, and the pulling SMD spring constant was set to 60 kJ/(mol·nm2). Data show the mean and the whiskers are the standard deviation of the mean value obtained from N = 50. The inset in A and B shows the reference AA SMD data, note that the x-axis shows the distance (D) between the center of mass of groups pulled in AA SMD protocol, whereas in the GōMartini study, the displacement is associated with increase of z-value along the pulling direction. C Structure of the RBD:H11-H4 complex placed in a box of CG Martini water represented as blue beads in the initial bound state with F = 0 pN. The fixed LYS-528 residue in the RBD and the LYS-128 residue in H11-H4 used for pulling are highlighted by red beads. D Structure of the complex at Fmax ~ 434 pN. E Magnified view of the last protein segments in contact before the full dissociation of the protein complex at d ~ 6 nm. The structures in (C–E) are taken from a replica simulated with vpull = 10-5 nm/ps. Source data are provided as a Source Data file.
