  An increasing number of proteins are being discovered with a remarkable and
somewhat surprising feature, a knot in their native structures. How the
polypeptide chain is able to knot itself during the folding process to form
these highly intricate protein topologies is not known. Here, we perform a
computational study on the 160-amino acid homodimeric protein YibK which, like
other proteins in the SpoU family of MTases, contains a deep trefoil knot in
its C-terminal region. In this study, we use a coarse-grained C-alpha-chain
representation and Langevin dynamics to study folding kinetics. We find that
specific, attractive nonnative interactions are critical for knot formation. In
the absence of these interactions, i.e. in an energetics driven entirely by
native interactions, knot formation is exceedingly unlikely. Further, we find,
in concert with recent experimental data on YibK, two parallel folding pathways
which we attribute to an early and a late formation of the trefoil knot,
respectively. For both pathways, knot formation occurs before dimerization. A
bioinformatics analysis of the SpoU family of proteins reveals further that the
critical nonnative interactions may originate from evolutionary conserved
hydrophobic segments around the knotted region.
