Description
We apply novel atomistic simulations based on potential energy surface exploration to investigate the constant force-induced unfolding of ubiquitin. We first report new unfolding mechanisms at the experimentally applied force of 100 pN and demonstrate that these events occur at lower clamping forces where thermal energy has a larger effect. We further report, in contrast to earlier single molecule constant force experiments, that when the clamping force becomes smaller than ~300 pN, the number of intermediate configurations increases dramatically, where almost all unfolding events at 100 pN involve an intermediate configuration. By directly calculating the life times of the intermediate configurations from the height of the barriers that were crossed on the potential energy surface, we demonstrate that these intermediate states were likely not observed experimentally due to their lifetimes being about one order of magnitude smaller than the available experimental temporal resolution.
Recommended Citation
Park, H. (2014). Potential energy surface-based atomistic model for the unfolding of protein at experimental timescales. In A. Bajaj, P. Zavattieri, M. Koslowski, & T. Siegmund (Eds.). Proceedings of the Society of Engineering Science 51st Annual Technical Meeting, October 1-3, 2014 , West Lafayette: Purdue University Libraries Scholarly Publishing Services, 2014. https://docs.lib.purdue.edu/ses2014/bio/nanomeso/1
Potential energy surface-based atomistic model for the unfolding of protein at experimental timescales
We apply novel atomistic simulations based on potential energy surface exploration to investigate the constant force-induced unfolding of ubiquitin. We first report new unfolding mechanisms at the experimentally applied force of 100 pN and demonstrate that these events occur at lower clamping forces where thermal energy has a larger effect. We further report, in contrast to earlier single molecule constant force experiments, that when the clamping force becomes smaller than ~300 pN, the number of intermediate configurations increases dramatically, where almost all unfolding events at 100 pN involve an intermediate configuration. By directly calculating the life times of the intermediate configurations from the height of the barriers that were crossed on the potential energy surface, we demonstrate that these intermediate states were likely not observed experimentally due to their lifetimes being about one order of magnitude smaller than the available experimental temporal resolution.