2014/02/25 by Changbong Hyeon, Hyeon, Changbong, Natalia A. Denesyuk +3
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Bacteriophages and microbial interactions #Biomolecules (q-bio.BM) #DNA and Nucleic Acid Chemistry #FOS: Biological sciences #FOS: Physical sciences #RNA and protein synthesis mechanisms #Soft Condensed Matter (cond-mat.soft)
paper · pdf · doi:10.48550/arxiv.1402.6030
openalex publication_date 2014/02/25 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
In contrast to proteins much less attention has been focused on development of computational models for describing RNA molecules, which are being recognized as playing key roles in many cellular functions. Current atomically detailed force fields are not accurate enough to capture the properties of even simple nucleic acid constructs. In this article, we review our efforts to develop coarse-grained (CG) models that capture the underlying physics for the particular length scale of interest. Two models are discussed. One of them is the Three Interaction Site (TIS) model in which each nucleotide is represented by three beads corresponding to sugar, phosphate, and base. The other is the Self-Organized Polymer (SOP) model in which each nucleotide is represented as a single interaction center. Applications of the TIS model to study the complexity of hairpin formation and the effects of crowding in shifting equilibrium between two conformations in human telomerase pseudoknot are described. The work on crowding illustrates a direct link to the activity of telomerase. We use the SOP model to describe the response of \it Tetrahymena ribozyme to force. The simulated unfolding pathways agree well with single molecule pulling experiments. We also review predictions for the unfolding pathways for \it Azoarcus ribozyme. The success of the CG applications to describe dynamics in RNA gives hope that more complex processes involving RNA-protein interactions can be tackled using variants of the proposed models.