Figure 1.
The native structure of ubiquitin (PDB ID: 1UBQ).
The secondary structural features are denoted.
Figure 2.
Snapshots of the structure of 1UBQ during unfolding.
500 ps (0.5 ns) snapshots are shown here.
Figure 3.
The plot shows the evolution of the RMSD of the backbone C_ atoms from the energy minimized structure of ubiquitin.
Three critical phases are discernible. The first phase at ≈2.5 ns involves the breaking of the β1–β5 interaction. The second phase occurs at ≈5.5 ns and involves the breaking up of the β3–β4 hairpin along with the associated secondary structure. The third phase occurs at ≈7 ns and involves the breaking up of the β1–β2 interaction.
Figure 4.
Variation of the Radius of Gyration (RoG) and the first factor obtained from PCA of the RQA quantitative descriptors REC, DET and ENT over time.
Top-panel: Variation of RoG with time. Bottom-panel: Variation of Factor-1 with time. In both plots, there are two clearly identified regimes with a marked difference in slope aroud 3 ns indicating a possible location of the TS before this point.
Figure 5.
Identification of Transition State: Projection of the RMSD between all pairs of frames onto a 3D cartesian coordinate.
The frames were 50 ps apart. The line connecting two two conformations implies sequential evolution in time. The distance between the conformations is proportional to the RMSD distances between the conformations.
Figure 6.
REC and DET over Unfolding.
Figure 7.
Module composition over unfolding: The plot shows the similarities (differences) in modular composition across the different frames as compared to the composition in the first frame. Each square on the plot represents 0.5 ns.
The colors go from blue (similar modular composition) to red (highly dissimilar modular composition). It can be observed that the only region of long-time similarity is in the upper left region which corresponds roughly to about 3 ns, after which the modular compositions become very dissimilar. See text for more details on how the plot was obtained.
Figure 8.
P/z over unfolding: The figure shows a plot of the time evolution of the |P/z| values of all the residues.
The residues have been sorted by their values in the first frame such that the HPZ residues are collected together at the left end of the x-axis. A point on the plot indicates |P/z|>0 implying that the corresponding residue has at least one contact outside its own module.
Figure 9.
RMSD of Protein without top 5 HPZ residues compared to the RMSD of the top 5 HPZ residues.
The HPZ residues have much lower RMSD values than the other residues.
Figure 10.
Position of HPZ residues as a function of the average RMSD of the residues.
The top 11 HPZ residues are marked with 7/11 of the top HPZ residues lying near the troughs in the plot, indicating their greater stability with respect to the non-HPZ residues.
Figure 11.
The figure shows the hydrogen bonds in the betasheet of ubiquitin along with the positions of seven of the top 11 HPZ residues (Q2,V5,I13,E25,Q41,Q49,L71).
The seven residues are shown in orange. The hydrogen bonds are shown as black dashes with the partners in each hydrogen bond, identified. See text for more details on the comparison of the different structures.
Figure 12.
Top panel: Plot of APSP versus the unfolding time. The APSP increases from its value at the native structure almost monotonically during unfolding. Bottom panel: Plot of APSP/Length versus protein length for 1320 single-chain proteins. The linear scaling obtained here is similar to the scaling of mean FPT/Length versus the source-target distance suggesting that there exists an optimal range of APSP values for a given protein length.