Coarse-grain Modeling of Nucleic Acid-Protein Interaction

The transcription termination factor Rho is a ring-like protein that requires the binding of a long single-stranded RNA to its surface in order to activate the ATPase activity of its motor domain. The binding event is associated with a large conformational change that converts the ring from an open lock-washer to a planar ring which is competent to terminate transcription. We combine a coarse-grain model of RNA and a Monte Carlo approach to simulate the distribution of single-stranded RNA under the electrostatic potential field of Rho for several conformations of the protein.