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

TL;DR

This study uses force-clamp experiments to analyze protein collapse, revealing the free energy landscape and diffusion properties, highlighting internal friction's role over viscous effects in protein dynamics.

Contribution

It introduces a method to reconstruct free energy profiles from nonequilibrium force-clamp data and characterizes the diffusion coefficient during protein collapse.

Findings

Reconstructed downhill free energy profile at 5pN

Identified an energy plateau at 10pN

Diffusion coefficient around 100nm^2/s

Abstract

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.