Week 4: G. Lois, J. Blawzdziewicz, and C. S. O'Hern, "Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks", Phys. Rev. E 81 (2010) 051907
Levinthal's paradox is the thought experiment coducted by Levinatal in 1969 that points out that it would take an nfinite amount of time for a system to sample all of the possible protien conformations. However, protiens reach a stable coformation in a matter of miliseconds. From a thermodynamic perspective, one may ask "How does a protien reach a stable state quickly when a large number of metastable states exhist?". The timescales of protein folding and proability of misfolding is largely dependent on eh nature o the energy landscape. For instance, rough energy landscapes in which the local variation in energy is small compared to the total energy barier. Rough energy landscapes, in which the local variation is onthe same magnitude as teh total eerg barieier, exibit much different first passage properties. An example is shown belowin Figure 1.
While funneled energy lanscapes may describe quick a reliable protien foling, roughenergy lanscaps may describe a mechanism for misfolding, and the conformational dysnamics of proteins in a metastable state. In this paper, the author's present a computational study on the dynamics of protien folding in two dimensions of a model protein with a rugged energy landscape.