Computer simulations of the bacterial ribosome using coarse-grained models

Josef Cikhart, Aneta Leskourová, Michal H. Kolář

Department of Physical Chemistry, University of Chemistry and Technology Prague

Molecular dynamics simulations serve as valuable tools for investigating biomolecules and biomolecular complexes such as the ribosome. However, the sheer scale of the ribosome presents significant computational challenges for all-atom simulations. Coarse-grained (CG) models offer a solution by replacing groups of atoms with a single bead. This reduces the number of degrees of freedom of the system and, in turn, allows longer simulation times, enabling the study of slower biochemical processes. In this study, we delve into refining the parameters for a coarse-grained representation of the bacterial ribosome. Through a series of CG computer simulations, we scrutinize the so-called elastic networks, pivotal for maintaining tertiary structure of proteins and RNA in CG systems. Our findings demonstrate that coarse-grained simulations yield reasonable structure of the ribsosome across various elastic network parameter values as compared with experimental structural models and all-atom simulations. Moreover, we refine parameter values to better capture the fine dynamics of the ribosome. These results establish a robust framework for our future ribosome studies and also shed light on specific inquiries regarding the nuances of the dynamics that can be studied further by variation of CG simulation parameters.

 This work was supported by the Czech Science Foundation (project 23-05764S).