Upendra, N. and Krishnaveni, S. (2022) Conformational exploration of RbgA using molecular dynamics: Possible implications in ribosome maturation and GTPase activity in different nucleotide bound states. Journal of Molecular Graphics & Modelling, 111. ISSN 1873-4243
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Ribosome biogenesis GTPase A (RbgA) is involved in the late steps of the 50S ribosomal subunit maturation by binding into the 45S pre-ribosomal subunit. The association of RbgA to the 45S intermediate subunit depends on its bound nucleotide (GTP/GDP), probably because of the conformational shifts that occur between the GTP and GDP bound states. However, the available crystal structures of Staphylococcus aureus RbgA (SaRbgA) do not show any significant variations between different nucleotide bound states. Therefore, conformational exploration of SaRbgA in different nucleotide bound states was carried out using all-atom molecular dynamics (MD) simulations. Exploration of conformational distribution using cluster analysis and principal component analysis (PCA) revealed that GDP and pppGpp bound systems exhibit a larger distribution. This is majorly due to the fluctuations of the C-terminal tail (C-tail) as a result of the unwinding of alpha-helical secondary conformations into loop conformations which are observed from RMSF and DSSP analyses. Further investigation of the network of interactions revealed that the GTP and GMPPNP bound systems hold the C-tail in an alpha-helical form through stronger interactions between the active-site and C-tail. We also find that the presence of Mg2+ positions Sw-I loop away from the bound nucleotide and stabilizes the active-site water molecules. This seems to assist SaRbgA GTPase activity. In addition, mutations at the C-terminal and Sw-II conserved residues exhibit a larger conformational distribution majorly due to the C-tail fluctuations suggesting that the C-tail of SaRbgA probably interacts with the rRNA or rprotein in the process of ribosome biogenesis.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | Molecular dynamics; Conformational changes; RbgA; GTPase; Ribosome; Staphylococcus aureus |
| Subjects: | D Physical Science > Physics |
| Divisions: | Department of > Physics |
| Depositing User: | C Swapna Library Assistant |
| Date Deposited: | 13 Jul 2023 07:23 |
| Last Modified: | 13 Jul 2023 07:23 |
| URI: | http://eprints.uni-mysore.ac.in/id/eprint/17617 |
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