Multiscale Modeling of PCNA - Ubiquitin Interactions

Abstract

Covalent attachment of ubiquitin (Ub) to proliferating cell nuclear antigen (PCNA) plays a crucial role in translesion synthesis (TLS). However, structural knowledge of the complex between Ub and PCNA is currently lacking. The problem is important from a biological perspective since ubiquitinated PCNA is involved in the recruitment of specialized lesion bypass polymerases. A loss of regulation of TLS and other damage-avoidance pathways can lead to a variety of cell fates including apoptosis and uncontrolled cell growth. We have modeled the Ub-PCNA complex using a combination of tethered Brownian dynamics (TBD), protein-protein docking with RosettaDock, flexible loop modeling with ModLoop, and molecular dynamics(MD). The TBD simulations were used to generate a large ensemble of electrostatically and geometrically favorable configurations, subsequently used as a starting point for local docking searches. The final models were refined with all-atom explicit solvent MD simulations. Ubiquitin was found to bind in a groove on the PCNA surface directly above the PCNA subunit interface. A mutation originally identified in genetics screens (pol30-113) and known to interfere with TLS, is positioned directly beneath the bound ubiquitin in our models. Thus, the results provide unexpected insight into previously unexplained biological observations.View Large Image | View Hi-Res Image | Download PowerPoint Slide