Title: Investigation of the functional mechanism of small G protein Ran

 

Supervisor: Erika Balog PhD, Dr. habil.

 

Summary: Molecular dynamics (MD) simulations offer an effective approach to study the conformational dynamics of small GTPases. We investigated the nucleotide-dependent conformational dynamics of Ran, with a particular focus on the C-terminal region and the molecular mechanism underlying switch I opening by MD and aMDeNM simulations. Our results reveal pronounced nucleotide-dependent differences in Ran dynamics. In the GTP-bound state, the C-terminus exhibits substantially higher flexibility than in the GDP-bound form. These features suggest that Ran requires enhanced conformational plasticity in its active state, consistent with its role in nucleocytoplasmic transport.

Across all simulations, a conserved anchoring interaction between the N-terminal segment of the C-terminus and the α5-β2 interface of the G-domain was identified, providing a structural explanation for the frequent disorder of distal C-terminal residues in RanGTP crystal structures.

In addition, our study elucidates the molecular basis of switch I opening in RanGTP. Disruption of Mg²⁺ coordination alone induces only a partially open switch I conformation corresponding to the state 1 conformation described for Ras proteins, an open, effector-nonbinding state. A full transition to the RanGDP-like, fully open switch I conformation requires coordinated disruption of both Mg²⁺ coordination and the Phe35-GTP-Lys152 stabilizing triad. Triad destabilization is initiated by reorientation of Lys152 toward Glu186, leading to formation of a Lys152-Glu186 salt bridge. Together, these findings define a two-step mechanism for switch I opening and provide a framework for understanding Ran’s unique conformational regulation.