Energy landscape of ubiquitin modulated by periodic forces: Asymmetric protein stability and shifts in unfolding pathways

TL;DR

This study investigates how periodic mechanical forces influence ubiquitin's stability and unfolding pathways, revealing frequency- and amplitude-dependent effects on protein mechanics through simulations and energy landscape modeling.

Contribution

It introduces a novel simulation approach to analyze the effects of repetitive forces on protein stability and unfolding pathways, advancing understanding of dynamic protein biomechanics.

Findings

Periodic forces weaken ubiquitin and alter unfolding pathways.

Protein response is complex, involving transient refolding and local interactions.

Energy landscape model explains the frequency- and amplitude-dependent effects.

Abstract

Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is known about how proteins process repetitive mechanical stresses. To obtain first insights into dynamic protein mechanics, we probed the mechanical stability of single and multimeric ubiquitins perturbed by periodic forces. Using coarse-grained molecular dynamics simulations, we were able to model repetitive forces with periods about two orders of magnitude longer than the relaxation time of folded ubiquitins. We found that even a small periodic force weakened the protein and shifted its unfolding pathways in a frequency- and amplitude-dependent manner. Our results also showed that the dynamic response of even a small protein can be complex with transient refolding of secondary structures and an increasing importance of local interactions in asymmetric protein stability. These observations were qualitatively and quantitatively explained using an energy landscape model and discussed in the light of dynamic single-molecule measurements and physiological forces. We believe that our approach and results provide first steps towards a framework to better understand dynamic protein biomechanics and biological force generation.