Folding trajectory

Figure C2.5.9. Examples of folding trajectories iT=T derived from the condition = 0.21. (a) Fast folding trajectory as monitored by y/t). It can be seen that sequence reaches the native state very rapidly in a two-state manner without being trapped in intennediates. The first passage time for this trajectory is 277 912 MCS. (b) Slow folding trajectory for the same sequence. The sequence becomes trapped in several intennediate states with large y en route to the native state. The first passage time is 11 442 793 MCS. Notice that the time scales in both panels are dramatically different.

Fig. 9 Comparison of folding trajectories. On the top portion of each trajectory the nine mPE dihedral angles (nine minus the two terminal dihedral angles) between phenyl rings are shown versus time (white as trans, cis as black). The bottom portion represents the longest stretch of folded structure versus time. We see that there is a great deal of variety in the folding pathways. In the upper right frame, we see folding to and unfolding from a trapped state...

The first two stages observed in the folding trajectories corresponded to a fast entropic recoil of the extended polymer, followed by a cooperative collapse that reduces the length of the protein back to its folded length [10]. To further... 

This approximate law holds for both native structure [22] and folding dynamics [2], In this regard, this wrapping motif may be regarded as a structural element that captures the basic component of energy transduction from hydrophobic association to structure formation. Furthermore, it implies that a fundamental constraint in protein architecture applicable to native structures applies also throughout the folding trajectory. 

Fig. 3.8 Dehydronic field averaged over all backbone hydrogen bonds formed at time t for the protein G variant along the ab initio folding trajectory described in Figs. 3.3, 3.2,3.3,3.4, 3.5,3.6, and 3.7...

FIGURE 2.3 Radius of gyration as a function of native contacts. This probability density is the result of 26 folding trajectories for ICSP. It shows a collapse of the protein followed by formation of native contacts. 

FIGURE 13.4 A schematic view of a funnel and a tube. The funnel is drawn with the assumption that the underlining initial structure is made unstable by an abrupt change in the initial condition and the energy surface, e.g., pH. The upper part is the unfolded state and the bottom corresponds to a folded configuration. Also shown a folding trajectory (dotted line) that passes through the tube. Note that the width of the tube does not necessarily correspond to the funnel width. 

Fernandez JM, Li H (2004) Force-clamp spectroscopy monitors the folding trajectory of a single protein. Science 303 1674—1678... 

Although rigorous in nature, Thirumalai s method is numerically costly even for the simplest Go model, because it requires a significant number of folding trajectories to be generated. Because of this limitation, the method has not been used extensively. Systems studied to date include an off-lattice... 

Having a given sequence of amino acids, one can in principle compute the force acting on each of its nuclei at any moment, and therefore in principle one can follow its folding trajectory under its own forces. This is a very complex problem. One needs to write the potential function for at least some 3M coordinates, where M is the number of residues, and compute the forces at any given configuration. Clearly, different sequences will have different trajectories. 

An interesting application of SDEL involved the folding mechanism of cytochrome The folding kinetics of cytochrome c has been studied extensively by a variety of experimental techniques. " The SDEL folding trajectories agree with several experimental observations including (1) the collapse of the protein without formation of secondary structures followed by formation of the terminal helices before the middle helix (see upper side of Figure 12),... 

---