Fig. 2: Different MD force fields agree on the conformational preferences of the reduced form of the two cysteines of TRAP1311–567. | Cell Death & Disease

Fig. 2: Different MD force fields agree on the conformational preferences of the reduced form of the two cysteines of TRAP1311–567.

From: TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins

Fig. 2

The panels show the mono-dimensional free energy profiles associated with the collective variables (A) χ1(SNO), (B) χ1(proxy) and (C) Sγ-Sγ distance for the metadynamics simulations. We performed metadynamics using CHARMM22* (light blue), CHARMM27 (dark blue), CHARMM36 (light green), ff99SBnmr1 (dark green), ff99SB*-ILDN (light orange), GROMOS54a7 (dark orange) force fields. Overall, the MD force fields agree that the SNO site and the proximal cysteine could populate three possible rotameric states for their χ1 dihedrals, with the plus state as the least favorable one. Furthermore, they agree in describing the distances between the two cysteines with minima in the free energy landscape at a distance of 4–6.5 Å. We observed that GROMOS54a7 is the only exception showing a less stable behavior, with χ1(proxy) equally populating all the dihedral states and the Sγ-Sγ distance sampling minima at distances higher than 7 Å.

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