Redesigning the hydrophobic core of a model beta-sheet protein: destabilizing traps through a threading approach

An off-lattice 46-bead model of a small all-beta protein has been recently criticized for possessing too many traps and long-lived intermediates compared with the folding energy landscape predicted for real proteins and models using the principle of minimal frustration. Using a novel sequence design approach based on threading for finding beneficial mutations for destabilizing traps, we proposed three new sequences for folding in the beta-sheet model. Simulated annealing on these sequences found the global minimum more reliably, indicative of a smoother energy landscape, and simulated thermodynamic variables found evidence for a more cooperative collapse transition, lowering of the collapse temperature, and higher folding temperatures. Folding and unfolding kinetics were acquired by calculating first-passage times, and the new sequences were found to fold significantly faster than the original sequence, with a concomitant lowering of the glass temperature, although none of the sequences have highly stable native structures. The new sequences found here are more representative of real proteins and are good folders in the T(f) > T(g) sense, and they should prove useful in future studies of the details of transition states and the nature of folding intermediates in the context of simplified folding models. These results show that our sequence design approach using threading can improve models possessing glasslike folding dynamics.