Studying ribosome dynamics with simplified models

Abstract

With the broad accessibility of high-performance computing resources, the significance of a molecular dynamics simulation is now rarely limited by hardware and/or software availability. Rather, the scientific value of each calculation is determined by the principles that underlie the theoretical model. The current review addresses this topic in the context of simplified models applied to large-scale (∼20-100 Å) dynamics in the ribosome. Specifically, we focus on applications of the "SMOG" class of structure-based models, which can be used to simulate spontaneous (i.e. non-targeted) conformational rearrangements in complex molecular assemblies. Here, we aim to provide an entry-level assessment of the methods, which can help bridge conceptual and communication gaps between the experimental and computational communities. In addition, inspecting the strategies that have been deployed previously can provide guidelines for future computational investigations into the relationship between structure, energetics and dynamics in other assemblies.

Keywords: Structure based models; tRNA.