Chemistry Reference
In-Depth Information
Figure 13
Snapshots of SOD trajectory. The arrow indicates the direction of folding.
The top structure is the initial unfolded conformation. The second structure is an
intermediate structure in the trajectory with partial secondary structure formation. The
bottom structure is the folded dimer. The monomer size and separation are not shown to
scale to enhance clarity. The center-of-mass distances in the first two snapshots
121
are
280 and 50
˚
greater than the equilibrium dimer distance, respectively. The disulfide
bridge between Cys57 and Cys146 was conserved during the simulations.
large molecular systems at long time scales. This is the only algorithm from the
methods discussed in this chapter that can be used to compute trajectories for
complex processes that take milliseconds or longer, such as the folding of cyto-
chrome c or the SOD dimer. Although the trajectories are approximate, they
can provide structural data to explain experimental observations; if a more
detailed and accurate description is required, snapshots taken from these
SDEL trajectories can be used to extract thermodynamic information using
MD, umbrella sampling, or replica exchange methodologies.
The major limitation of the SDEL algorithm is the inaccessibility of abso-
lute times and computation of rates. A promising algorithm called milestoning
