Low Force Unfolding of a Single-Domain Protein by Parallel Pathways

Deviations from linearity in the dependence of the logarithm of protein unfolding rates, log k(u)(f), as a function of mechanical force, f, measurable in single molecule experiments, can arise for many reasons. In particular, upward curvature in log k(u)(f) as a function of f implies that the underlying energy landscape must be multidimensional with the possibility that unfolding ensues by parallel pathways. Here, simulations using the SOP-SC model of a wild type beta-sandwich protein and several mutants, with immunoglobulin folds, show upward curvature in the unfolding kinetics. There are substantial changes in the structures of the transition state ensembles as the force is increased, signaling a switch in the unfolding pathways. Our results, when combined with previous theoretical and experimental studies, show that parallel unfolding of structurally unrelated single domain proteins can be determined from the dependence of log k(u)(f) as a function of force (or log k(u)[C] where [C] is the denaturant concentration).

Automated summary

Deviation from linearity in the dependence of protein unfolding rates on mechanical force may indicate multidimensionality and parallel pathways in the underlying energy landscape. Simulations show significant changes in unfolding kinetics and transition state structures as force increases, suggesting a switch in unfolding pathways. This indicates that the parallel unfolding of structurally unrelated single domain proteins can be determined based on the dependence of unfolding rates on force.