  We present force-clamp data on the collapse of ubiquitin polyproteins in
response to a quench in the force. These nonequilibrium trajectories are
analyzed using a general method based on a diffusive assumption of the
end-to-end length to reconstruct a downhill free energy profile at 5pN and an
energy plateau at 10pN with a slow diffusion coefficient on the order
of~100nm^2/s. The shape of the free energy and its linear scaling with the
protein length give validity to a physical model for the collapse. However, the
length independent diffusion coefficient suggests that internal rather than
viscous friction dominates and thermal noise is needed to capture the
variability in the measured times to collapse.
