LIGAND-INDUCED CONFORMATIONAL-CHANGES IN RAS P21 - A NORMAL-MODE AND ENERGY MINIMIZATION ANALYSIS

A normal mode and energy minimization of ras p21 is used to determine the flexibility of the protein and the origin of the conformational di fferences between GTP and GDP-bound forms. To preserve the integrity o f the structures, a hydration shell of water molecules was included as part of the system. Certain low-frequency modes were found to have hi gh involvement coefficients with the conformational transition between the Gm and GDP-bound structures; the involvement coefficients of some of the modes increase when the gamma-phosphate group is removed. Two unstable modes that appear in the GTP-bound structure upon deletion of the gamma-phosphate group were determined and shown to have dominant contributions in the regions of switch I and switch II; there was also a significant displacement of loop 1. The initial motion in these reg ions is predicted by the modes to be approximately perpendicular to th e direction of the transition from the GTP-bound state to the GDP-boun d state. The overall conformational change in the switch I and II regi ons involves rearrangements of the protein backbone within these regio ns, rather than rigid body motion. Differences in the low-frequency mo des of the Gm and GDP-bound forms appear to play a role in ligand bind ing. A coupling between the helix alpha 3 position and the deletion of the gamma-phosphate group may be involved in the interaction with GAP . The mutation G12D leads to a global increase in the rigidity of the protein. Thus, the mutant is Likely to have a higher barrier for the c onformational change to the inactive form; this would slow the transit ion and could be related to its oncogenic properties. (C) 1997 Academi c Press Limited.