Molecular Dynamics Simulations of the SPRED2Leu100Pro EVH-1 Domain Complexed with the GAP-Related Domain of Neurofibromin

The homozygous Leu100Pro amino acid substitution in SPRED2, a protein negatively controlling RAS function, has recently been identified to be causally linked to a recessive form of Noonan syndrome. The amino acid substitution was documented to affect protein stability and cause a decreased and/or less stable interaction with neurofibromin, a RAS-specific GTPase activating protein negatively regulating RAS function. To further investigate the structural and functional impact of Leu100Pro, we structurally characterized the consequences of this change on the interaction of SPRED2 with neurofibromin, by 1 µn-long molecular dynamics (MD) simulations. Our analyses failed in identifying local perturbations predicted to disrupt or dramatically affect SPRED2 binding to neurofibromin, though a rearrangement of their interaction was observed. On the other hand, MD simulations also identified long-range structural rearrangements of the SPRED2 EVH-1 domain, which might be relevant for an aberrant folding of the mutant driving the previously documented accelerated degradation. Overall, the performed MD simulations suggest the occurrence of multiple intramolecular and intermolecular structural perturbations driven by the Leu100Pro change that likely contribute to its LoF behavior.