Exploring Metastable States along UUCG Unfolding Pathway Using Drude Force Field

Hairpin loops in RNA play a vital role in critical biological processes such as RNA folding, interaction with ribozymes, and mRNA degradation prevention and can serve as a substrate for RNA binding proteins and enzymatic reactions. Of all of the available hairpins, UUCG hairpins are one of the most common, and their unfolding pathway is important for understanding the more significant problem involving RNA tertiary folding. In this work, a hybrid approach was used to study the metastable states along the UUCG unfolding pathway, which first involved partitioning of 100 μs long trajectory derived using a nonpolarizable CHARMM36 force field into kinetic states using the Markov State Model. Based on the kinetic data, the hairpin unfolding followed the parallel pathway model with unfolding time scales in the order of microseconds. The resulting four metastable states were studied using the polarizable Drude force field, which better described their structural properties. The four states sampled distinct regions of conformational space which depended on the underlying force field and were differentiable regarding the number of base-base hydrogen bonds, stacking contacts, main chain torsions, sugar pucker torsions, and pseudotorsion angles. The impact of explicit polarization during the simulation was felt through the enhanced presence of noncanonical hydrogen bonds, BI, syn, and non-C3'-endo conformations. The study concluded that the CHARMM36 force field provided an incomplete picture regarding the conformations sampled in different metastable states, whose better description obtained using the Drude force field may help explain the role of non-native UUCG states in different biological processes.