RNA polymerase dynamics and function

RNA polymerase synthesizes RNA during transcription, which is a highly complex process with many open questions on its mechanism remain to be answered. We are particularly interested in dynamics of RNA polymerase at the active site as well as at the larger scale at the elongation complex RNA polymerase forms with basal elongation factors. Molecular dynamics simulations, Markov state modeling, machine learning techniques are the methods we use to study RNA polymerase systems for obtaining mechanistic insight of transcription.

Publications:

Protein–Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations

Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability

Molecular Basis for Impacts of DSIF on the Dynamics of RNA Polymerase II Elongation Complex

Spatial organizations during transcription

Inside cells, biomolecules form condensates that result in higher density regions that are necessary for their functions. RNA polymerase is also known to be compartmentalized during the transcription process. We are following a multi-scale computational approach to study RNA polymerase compartmentalization and specifically to understand the components and the nature of interactions of RNA polymerase enriched condensates.

Publications:

Complex Conformational Space of the RNA Polymerase II C-Terminal Domain upon Phosphorylation

Clustering of RNA Polymerase II C-Terminal Domain Models upon Phosphorylation