456 research outputs found
A simple theory of protein folding kinetics
We present a simple model of protein folding dynamics that captures key
qualitative elements recently seen in all-atom simulations. The goals of this
theory are to serve as a simple formalism for gaining deeper insight into the
physical properties seen in detailed simulations as well as to serve as a model
to easily compare why these simulations suggest a different kinetic mechanism
than previous simple models. Specifically, we find that non-native contacts
play a key role in determining the mechanism, which can shift dramatically as
the energetic strength of non-native interactions is changed. For protein-like
non-native interactions, our model finds that the native state is a kinetic
hub, connecting the strength of relevant interactions directly to the nature of
folding kinetics
Inferring the Rate-Length Law of Protein Folding
We investigate the rate-length scaling law of protein folding, a key
undetermined scaling law in the analytical theory of protein folding. We
demonstrate that chain length is a dominant factor determining folding times,
and that the unambiguous determination of the way chain length corre- lates
with folding times could provide key mechanistic insight into the folding
process. Four specific proposed laws (power law, exponential, and two stretched
exponentials) are tested against one an- other, and it is found that the power
law best explains the data. At the same time, the fit power law results in
rates that are very fast, nearly unreasonably so in a biological context. We
show that any of the proposed forms are viable, conclude that more data is
necessary to unequivocally infer the rate-length law, and that such data could
be obtained through a small number of protein folding experiments on large
protein domains
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