Journal of Physical Chemistry B, Vol.117, No.43, 13435-13443, 2013
Engineering Folding Dynamics from Two-State to Downhill: Application to lambda-Repressor
One strategy for reaching the downhill folding regime, primarily exploited for the lambda(6-85) protein fragment, consists of cumulatively introducing mutations that speed up folding. This is an experimentally demanding process where chemical intuition usually serves as a guide for the choice of amino acid residues to mutate. Such an approach can be aided by computational methods that screen for protein engineering hot spots. Here we present one such method that involves sampling the energy landscape of the pseudo-wild-type protein and investigating the effect of point mutations on this landscape. Using a novel metric for the cooperativity, we identify those residues leading to the least cooperative folding. The folding dynamics of the selected mutants are then directly characterized and the differences in the kinetics are analyzed within a Markov-state model framework. Although the method is general, here we present results for a coarse-grained topology-based simulation model of lambda-repressor, whose barrier is reduced from an initial value of similar to 4k(B)T at the midpoint to similar to 1k(B)T, thereby reaching the downhill folding regime.