Ubiquitin-like Protein Domains Show High Resistance to Mechanical Unfolding Similar to That of the I27 Domain in Titin:  Evidence from Simulations

The I27 domain in the muscle protein titin can sustain large mechanical forces without unfolding. Recently it has been suggested [Eom, K.; Li, P.-C.; Makarov, D. E.; Rodin, G. J. J. Phys. Chem. B 2003, 107, 8730] that the “clamp” formed by the parallel strands in this domain represents an optimal topology maximizing the mechanical strength of cross-linked polymer chains. Here we use simulations to demonstrate that protein G IgG-binding domain III and ubiquitin, both exhibiting a parallel strand arrangement similar to that in I27 but otherwise having a distinctly different fold and not involved in an obvious load-bearing function, exhibit high resistance to mechanical unfolding. Using molecular dynamics simulations, we compute the potential of mean force as a function of the distance between the domains' C- and N-termini and use transition state theory to calculate the force-dependent rates of unfolding. We further predict the outcome of a hypothetical single-molecule AFM pulling experiment, in which one of the I27 domains in titin is replaced by one of the above two proteins. For typical AFM pulling rates, the predicted unfolding force is in the range 190−220 pN for ubiquitin and 100−150 pN for the IgG-binding domain.