Single molecule mechanical methods provide a unique opportunity for directly probing the free energy landscape of complex biomolecules such as proteins due in part to their ability to monitor partially unfolded conformations. Unfortunately, even if they provide information on the chain extension of the molecule, they still cannot supply full details of the structures of intermediate states. Therefore, employing molecular modeling approaches in conjunction with experimental results is the route to understanding the details of folding and refolding of complex systems. I will present force-ramp and force-quench simulations of a self-organized polymer (SOP) model that predicts the mechanical unfolding and refolding pathways and the associated kinetic barriers of the Green Fluorescent Protein (GFP) (1). This protein is fundamental for a range of biotechnology procedures such as in studies of localization of proteins in living cells and for Ca²⁺ sensors. We find that in all cases the transition to the stretched state occurs through a sequence of intermediates the number of which depends on the native fold and the loading rate in complete agreement with experiments (2). In addition to the two intermediates determined by Rief and collaborators (2), corresponding to the unraveling of the short alpha-helix from the N-term end of the chain followed by the disruption of the N terminus beta-strand, we predict the existence of a third intermediate that involves the disruption of three other strands. Refolding, upon force-quench, is hierarchic and occurs by a rapid formation of a metastable compact intermediate in accord with results of ensemble experiments (3). The rate determining step is the closure of the barrel.

References and Footnotes

1. C. Hyeon, R. I. Dima, and D. Thirumalai. Structure 14, 1-13 (2006).
2. H. Dietz and M. Rief. Proceedings of the National Academy of Sciences USA 101, 16192-16197 (2004).
3. H. Fukuda, M. Arai, and K. Kuwajima. Biochemistry 43, 14238-14248 (2000).