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Understanding the kinetic mechanism of RNA single base pair formation
- Publication Year :
- 2015
- Publisher :
- National Academy of Sciences, 2015.
-
Abstract
- RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model.
- Subjects :
- 0301 basic medicine
Quantitative Biology::Biomolecules
RNA Folding
Multidisciplinary
Chemistry
Base pair
Stacking
RNA
Biological Sciences
Molecular Dynamics Simulation
03 medical and health sciences
Molecular dynamics
Crystallography
Kinetics
030104 developmental biology
Ion binding
Master equation
Native state
Kinetic Monte Carlo
Base Pairing
Monte Carlo Method
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Accession number :
- edsair.doi.dedup.....e7e61d2aa6223c109e3ea03936a68fd0