Abstract
Abstract Molecular dynamics (MD) simulations were used to investigate the dissociation of the Ras/Raf complex. Three models of Ras/Raf complexes were used in this study: two active GTP-bound forms with either GTP or GDP and one inactive GDP-bound form. The dissociation process in these short time scale (10 ns) MD simulations was accelerated by adding random velocities to phosphate groups in the GTP or GDP molecule. Only the complex with the inactive GDP-bound form heated with the random velocities showed dissociation. The Raf in it was unable to recover its initial position during the MD simulations. In simulations with and without added random velocities the Raf in the other complexes moved back to its initial position. The Raf in complexes with the active GTP-bound form recovered its initial position even when the ligands in the complexes were heated. The details of these mechanisms are discussed here.
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