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

Force-clamp experiments reveal the free energy profile and diffusion coefficient of the collapse of proteins