Simulations of the villin headpiece
The
villin headpiece is a small, 36-residue alpha helical protein. It has
been heavily studied experimentally and by simulation since is perhaps
one of the smallest, fastest folding proteins. It has a hydrophobic core
made of 3 phenylalanines, but also has two groups (a tryptophan and another
phenylalanine) which are hydrophobic, but are solvent exposed (for functional
reasons). Duan and Kollman simulated 1 microsecond of MD time, in a ground
breaking simulation. However, since the folding time is on the order of
10 microseconds, it is not surprising that they did not see it fold. Our
simulations contain hundred of microseconds of MD time, and we have seen
35 simulations which have folded. Below, we detail the trajectory of one
of these simulations.
MPEG movies
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More detailed view from individual frames
Frames from a villin folding trajectory. You can click on a picture about to get a zoomed view.