Molecular dynamics simulation studies on <i>Bacillus subtilis</i> RbgA: insights into the RbgA-ribosome association and GTPase activity

RbgA (ribosome biogenesis GTPase A) is involved in the maturation of later stages of the 50S ribosomal subunit by associating with the 45S ribosomal subunit. However, this binding relies on the specific nucleotide-bound state of RbgA-GTP-bound state is more favorable compared GDP-bound state, attributed to the conformational variations between those states. Therefore, to explore the conformational changes of RbgA, all-atom MD simulations of <i>Bs</i>RbgA were carried out under various nucleotide bound states (GDP, GTP, GTP-Mg²⁺ and GMPPNP-Mg²⁺). The analysis of overall conformational changes using RMSD and Rg revealed sharp equilibration for GTP-Mg²⁺ and GMPPNP-Mg²⁺ nucleotide bound systems. Investigating internal variations through RMSF and cluster analyses helps us to identify the functionally important regions and nucleotide driven conformational variations that may stabilize/destabilize the RbgA-ribosome association. In addition, the construction and analyses of the dynamical protein contact network from the simulated trajectory reveal the nucleotide dependent allosteric connections between the nucleotide binding site and the rRNA interacting residues. Furthermore, the visualization followed by the dynamical distance calculations exhibited the possible role of Mg²⁺ in assisting GTP hydrolysis, such as (i) positioning the Asp150 of the switch-I (Sw-I) loop residue in a catalytically feasible configuration and (ii) stabilizing the solvated water molecules at the active-site through Mg²⁺ coordination. The results of our study can be used to design better chemical agents to regulate ribosome biogenesis through modulation of the function of the RbgA.