BPS2026 – Visualizing Ser2 and Ser5 phosphorylation in RNA polymerase II CTD through clustering and contact map analysis

The RNA polymerase II C-terminal domain (CTD) is an intrinsically disordered region that regulates the transcription of RNA. Residues within CTD are phosphorylated and unphosphorylated during transcription, but the mechanism by which phosphorylation affects the conformation is not fully understood. Our project aims to understand how phosphorylation affects the conformation of the CTD and how the ability of RNA polymerase II CTD to regulate transcription is altered. To do this, we have run Gaussian-accelerated molecular dynamics (GaMD) simulations on three sequences of the CTD structure composed of three repeating heptads (YSPTSPS): one with phosphorylated Ser2, one with phosphorylated Ser5, and the last as an unphosphorylated sequence. 40 simulations were previously run on the phosphorylated and unphosphorylated Ser5 sequences, for which we reweighted the data and ran K-means clustering on the contact map data. Through grouping frames with this algorithm, we were able to create an averaged contact map for each unique cluster, and also identify a centroid or representative frame of the simulated CTD structure for each cluster. By taking a large ensemble of conformations of the CTD and clustering to group similar sets of data, we are able to better visualize the most common conformations that occur in our simulations on the CTD. We intend to apply the same methods to data retrieved from our GaMD simulations on phosphorylated Ser2, which will give us more insight into the changes in the CTD’s global conformation for different sites of phosphorylation.