Accelerated Simulations Reveal Physicochemical Factors Governing Stability and Composition of RNA Clusters.

ABSTRACT: Under certain conditions, RNA repeat sequences phase separate, yielding protein-free biomolecular condensates. Importantly, RNA repeat sequences have also been implicated in neurological disorders, such as Huntington's disease. Thus, mapping repeat sequences to their phase behavior, functions, and dysfunctions is an active area of research. However, despite several advances, it remains challenging to characterize the RNA phase behavior at a submolecular resolution. Here, we have implemented a residue-resolution coarse-grained model in LAMMPS─that incorporates both the RNA sequence and structure─to study the clustering propensities of protein-free RNA systems. Importantly, we achieve a multifold speedup in the simulation time compared to previous work. Leveraging this efficiency, we study t

SUBMITTER: Aierken D 

PROVIDER: S-EPMC11603615 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature