Apr 9, 2020

Molecular Simulations of Mg2+-induced Folding of the Central Domain of the 16S Ribosomal RNA

BioRxiv : the Preprint Server for Biology
N. HoriD Thirumalai

Abstract

The central domain of the 16S ribosomal RNA folds independently driven either by Mg2+ ions or by interaction with a ribosomal protein. In order to provide a quantitative description of ion-induced folding of the ~350 nucleotide RNA, we carried out extensive simulations using the coarse-grained Three Interaction Site (TIS) model with explicit Mg2+ ions at a fixed K+ ion concentration typically used in the Tris buffer. The Mg2+ dependence of the radius of gyration shows that globally the RNA folds cooperatively. However, various structural elements order at different Mg2+ concentrations, indicative of the hierarchical assembly even within a single domain of the rRNA. Binding of Mg2+ ions is highly specific with successive ion condensation resulting in increasing tertiary structure formation. We also predict the Mg2+-dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg2+-induced folding. As a byproduct of the simulations, we provide a molecular basis of the structural rearrangements in the three-way junction in the intact central domain whose folding in isolation has been studied experimentally. In accord with experiments, we find that the three coplanar hel...Continue Reading

  • References
  • Citations

References

  • We're still populating references for this paper, please check back later.
  • References
  • Citations

Citations

  • This paper may not have been cited yet.

Mentioned in this Paper

Genome-Wide Association Study
Study
Biochemical Pathway
Genome
Schizophrenia
Dysequilibrium Syndrome
Virus Replication
Genetic Pleiotropy
Candidate Gene Identification
Entire Putamen

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Basal Ganglia

Basal Ganglia are a group of subcortical nuclei in the brain associated with control of voluntary motor movements, procedural and habit learning, emotion, and cognition. Here is the latest research.