Abstract :
From extensive biophysical studies of protein folding, two competing mechanisms emerged: hydrophobic collapse and the framework model. Our protein of choice is Barstar—a barnase inhibitor. The approximation algorithm we used to study Barstar folding trajectories is called SDEL—stochastic difference equation in length. Using the native structure as the final boundary value and a collection of unfolded structures as the varying initial boundary value, SDEL calculates an ensemble of least action pathways between these boundaries. The results are atomically detailed folding pathways, with as many intermediate structures as you request in the input. We generated 12 pathways, starting from a structurally wide selection of unfolded conformations. Using the proteinʹs radius of gyration as our primary reaction coordinate, we tracked H-bonds, dihedral angles, native and non-native contacts, and energy along the folding pathways. This paper will follow our findings, with special emphasis on pinpointing hydrophobic collapse as a more appropriate mechanism for Barstar. Comparison with pathway predictions for Barstar using experimental techniques will also be discussed.
