Atomistic and Coarse-Grained MD Simulations of the Intrinsically Disordered Bacillus Subtilis Ribonuclease P Protein

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The Bacillus subtilis Ribonuclease-P (RNase P) holoenzyme is a protein-RNA complex; however, the protein becomes disordered in the absence of its RNA binding partner. To identify the main determinants of why the RNase P protein becomes disordered, we performed (i) a statistical analysis of its interactions to identify the critical minimally frustrated residues that are important for structural stabilization, (ii) atomistic MD simulations in the presence and absence of the osmolyte Trimethylamine N-Oxide (TMAO), which has been shown experimentally to stabilize its native structure even without its RNA binding partner, and (iii) coarse-grained Go-type MD simulations to determine the folding/unfolding mechanism. We observed an intermediate in our coarse-grained MD simulations that we propose is the partially disordered state in the absence of its RNA binding partner and the intermediate seen experimentally in TMAO-induced folding experiments. We also identified critical residues for stabilization that can be tested experimentally using standard mutagenesis folding kinetic experiments.