Molecular dynamics simulation studies and dynamic network analysis of Bacillus subtilis YsxC in GDP and GTP-Mg 2+ bound states

Abstract

Ribosomes are essential cellular organelles made up of rRNA and rproteins found in both prokaryotic and eukaryotic cells, and play an important role in protein synthesis. The functional ribosomes are synthesized through the process called ribosome biogenesis, which proceeds with the help of certain factors such as chaperones, ribosomal proteins, and GTPases. GTPases bind to the premature ribosomal subunit and function as a checkpoint, ensuring the proper assembly of other proteins. To aid this process, GTPase undergoes conformational changes, alternating between an active GTP-bound state and an inactive GDP bound state. YsxC is a GTPase that functions this way, to help in the maturation of 50S subunit. Although YsxC plays an important role in ribosome biogenesis, a detailed knowledge of how the GDP and GTPMg2+ states of YsxC assist in the switching process is yet to be realized. Therefore, a study on the GDP and GTP-Mg2+ bound states is done for YsxC GTPase of Bacillus subtilis by all-atom molecular dynamics simulation for a period of 500 ns. The simulations aided the analysis of the RMSD from which it was noticed that both the GDP and GTP-Mg2+ states of YsxC attained equilibration after 200ns. The analysis of the Rg for the systems showed that the GTP-Mg2+ system showed higher values, in comparison to the GDP system, indicating conformational changes in the two systems. Thus, a residue-wise calculation for the difference in the SASA (solvent accessible surface area) of the GTP-Mg2+ and GDP system is done, and it is noticed that the GTP-Mg2+ system, especially in the regions recognized as Switch I and Switch II had a higher difference in SASA value. In which Switch I’s Lys55 (positive residue) and Switch II’s Arg89 (positive residue) showed a distinct difference, indicating that Switch I has more accessibility to solvent. Giving rise to a supposition that the residue Lys55 attracts the negative rRNA and aids in the binding of YsxC with the premature 50S subunit in the GTP-Mg2+ bound state by associating with the rRNA. To fathom the role of the GTP-Mg2+ bound state in increasing the SASA value of Switch I region, a community network is constructed to extract the shortest path. More number of paths are observed between the selected residue in the GTP-Mg2+ bound state inferring that the increased SASA in the Lys55 is due to the stronger connection with the nucleotide. Overall this study suggest that enhanced surface exposure of YsxC’s Sw-I in the GTP-Mg2+ bound state facilitate the GTP-Mg2+ bound system to involve in ribosome biogenesis by interacting with ribosomal constituents (rRNA and rproteins).