Kinetic Mechanism of RNA Helix-Terminal Basepairing—A Kinetic Minima Network Analysis

Kinetic Analysis of Molybdenite Oxidation

Understanding the kinetic mechanism of RNA single base pair formation.

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/s...

Kinetic Analysis of Molybdenite Oxidation

Kinetic mechanism of conformational switch between bistable RNA hairpins.

Transitions between the different conformational states play a critical role in many RNA catalytic and regulatory functions. In this study, we use the Kinetic Monte Carlo method to investigate the kinetic mechanism for the conformational switches between bistable RNA hairpins. We find three types of conformational switch pathways for RNA hairpins: refolding after complete unfolding, folding thr...

Kinetic Steps for a-Helix Formation

The kinetics of a-helix formation in polyalanine and polyglycine eicosamers (20-mers) were examined using torsional-coordinate molecular dynamics (MD). Of one hundred fifty-five MD experiments on extended (Ala)20 carried out for 0.5 ns each, 129 (83%) formed a persistent a-helix. In contrast, the extended state of (Gly)20 only formed a righthanded a-helix in two of the 20 MD experiments (10%), ...