Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments

TL;DR

This study uses molecular dynamics simulations with grand-canonical reweighting to investigate how cooperative effects influence RNA reactivity in chemical probing experiments like SHAPE, revealing concentration-dependent binding behaviors.

Contribution

It introduces a novel simulation technique to calculate molecule affinity as a function of concentration, demonstrating its application to RNA reagent binding and reactivity.

Findings

Cooperative binding affects RNA reactivity in SHAPE experiments.

Reactivity depends on reagent concentration at typical experimental levels.

Simulation results align qualitatively with experimental data.

Abstract

Chemical probing experiments such as SHAPE are routinely used to probe RNA molecules. In this work, we use atomistic molecular dynamics simulations to test the hypothesis that binding of RNA with SHAPE reagents is affected by cooperative effects leading to an observed reactivity that is dependent on the reagent concentration. We develop a general technique that enables the calculation of the affinity for arbitrary molecules as a function of their concentration in the grand-canonical ensemble. Our simulations of an RNA structural motif suggest that, at the concentration typically used in SHAPE experiments, cooperative binding would lead to a measurable concentration-dependent reactivity. We also provide a qualitative validation of this statement by analyzing a new set of experiments collected at different reagent concentrations.