Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts.

ABSTRACT: Messenger RNA regulatory elements, such as riboswitches, can display a high degree of flexibility. By characterizing their energy landscapes, and corresponding distributions of 3D configurations, structure-function relationships can be elucidated. Molecular dynamics simulation with enhanced sampling is an important strategy used to computationally access free energy landscapes characterizing the accessible 3D conformations of RNAs. While tertiary contacts are thought to play important roles in RNA dynamics, it is difficult, in explicit solvent, to sample the formation and breakage of tertiary contacts, such as helix-helix interactions, pseudoknot interactions, and junction interactions, while maintaining intact secondary structure elements. To this end, we extend previously developed colle

SUBMITTER: Prajapati JD 

PROVIDER: S-EPMC10042644 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature