  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.
