Paper Citing NAMD - Abstract
Feng, Gang; Lu, Hui
Computer simulation of I27 translocation through ClpY reveals a critical role of protein mechanical strength and local stability
2007 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-16, 1213-1216, 2007
Clp family is one type of AAA+ proteases, which catalyze protein degradation and translocation. Because of the steric restriction of the complex structure, the substrates have to be denaturated before accessing the active sites of the peptidases. This type of translocation-induced protein unfolding has been studied in bulk biochemical experiments, but the detailed dynamic process is still unknown. Two models are proposed: the target protein somehow unfolds before it is pulled through a protease or the target protein is unfolded by pulling force during the translocation. We performed steered molecular dynamics (SMD) simulations to pull a model protein I27 and its variants (V11P, V13P and V15P) through ClpY, which is a member of Clp family with the available crystal structure. Resulting force-position profiles showed that the protein translocation needs a large initial force to break it open, and further unfolding needs relatively weaker forces. Comparison of the unfolding forces among translocation of I27 and its variants showed that the local mechanical stability of the protein determines the unfolding force. We also simulated the I27 translocation starting with different orientations and found that the unfolding dynamics are similar. The simulations presented here, combined with published experimental data, support the model that the target protein is pulled apart during translocation, and the force needed to unfold a protein follows the local stability model. This model does not only give a close insight into the processes of force-driven protein unfolding in translocation, but also is instructive to design protein in protein degradation, which is one of the most important steps in cellular cycles.
