With the advent of instruments like the Atomic-Force Microscope and Laser Optical Tweezers, it has become possible to manipulate individual biopolymers. Such manipulation, in turn, is used to investigate the free-energy landscape of biopolymers and the dynamics of the unfolding (refolding) process. In recent work (Pincus and Thirumalai, J. Phys. Chem. B, 2009 [link]) we simulated the unfolding of a single Ubiquitin monomer (a 76 residue protein) under applied tension. The simulations were performed in both the presence and absence of monodisperse spherical crowding agents. Crowding agents are used in experiments to mimic a crowded cellular environment. Our simulations demonstrated that small crowding agents can increase the stability of a protein subject to mechanical stress as gauged by the protein's average unfolding force. (The unfolding force is the tensile stress immeadiately proceeding a rupture event in which the protein's end to end distance shows a dramatic and sudden increase). The movie shows two simulated unfolding trajectories (one at crowder volume fraction 0 and the other at crowder volume fraction 0.3) and corresponding plots of tensile force versus extension.
MOVIE: AUTHORS: Dr. David L. Pincus (firstname.lastname@example.org) Prof. Devarajan (Dave) Thirumalai (email@example.com)