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RAS superfamily and the interactions with their effectors: functional specificity (Ras:effectors)
Start date: 01 Sep 2007, End date: 31 Aug 2009 PROJECT  FINISHED 

Ras genes code for small GTPases that act as GDP/GTP-regulated molecular switches. This exchange induces a conformational change that allows them to interact with their downstream effectors, and thus participate as central control elements in signal transduction. Mutated forms of the Ras oncoprotein are found in more than 30% of all human cancers, justifying the extensive research on them. Ras effectors have convergently developed a common subdomain in their unrelated overall structure for their interaction with Ras. Although detailed knowledge about the thermodynamics and dynamics of the interaction with Ras has accumulated, the molecular mechanism at atomic detail of effector activation and thus specificity is still elusive. Crystallographic, NMR, and other spectroscopic studies show that the flexibility of their so-called “switch regions” majorly contributes to the adaptability of the Ras proteins to their various partners, including disorder-to-order transitions upon binding to their partners, and “structural polymorphism” in their different complexes and in the unbound forms. This incorporates another degree of difficulty on the understanding of the Ras:effector association. Although some studies have been previously carried out in order to rationalize the specificity of the Ras proteins towards their different effectors, they have been based only in the availability of Ras:effector crystal structures and taking a rather static point of view. In this work we intend to extend this to a large-scale bioinformatics and computational study, including driven-docking of Ras proteins and their effectors for which no complex structure is available but biological data supports complex formation. In a further step, Molecular Dynamics simulations both on the unbound partners and on their complexes will yield information accounting both for the binding affinity and for the intrinsic plasticity crucial in the recognition and regulation of Ras pathways
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