Fig 1.
A) Strucuture of SufI. N-, M-, and C-domains are depicted in blue, green, and red. Linkers that connet two domains are depicted in yellow. B) The codon-based elongation rate by Spencer et al’s algorithm. A threshold is introduced. The region where the elongation rate is slower than the threshold is drawn in red. C) The elongation schedule used in the CTFcodon simulations. Regions marked in red in B take long elongation time. D) Three CTF schems. The CTFfast (dashed), the CTFslow (dotted), and the CTFcodon (solid) lines. E) A schematic view of the system including the wall-and-tunnel potential.
Fig 2.
Representative time courses of folding simulations.
A) A time course of a refolding trajectory. B) that of the CTFcodon. Some snapshots were drawn with the same color code as Fig 1A.
Table 1.
Number of successful folding casesa out of 100 trajectories.
Table 2.
Pairwise Kolmogorov-Smirnov tests to check the difference of the histograms of Qtotal-scores of the final structures.
Table 3.
Pairwise Mann-Whitney U tests to check the difference of the histograms of Qtotal-scores of the final structures.
Fig 3.
A) Fractions of misfolded domains at the end of simulations in four different schemes; the refolding (black), the CTFfast (red), the CTFslow (green), and the CTFcodon (blue). B) Representative final structures of misfolding. i) structure that is misfolded in N-domain. ii) Misfolded in M-domain. iii) (right) Misfolded in C-domain. (left) Native structure for comparison. See text for the explanation of the block arrows.
Table 4.
Pairwise Kolmogorov-Smirnov tests to check the difference of the histograms of N-domain’s Q-scores of the final structures.
Table 5.
Pairwise Kolmogorov-Smirnov tests to check the difference of the histograms of M-domain’s Q-scores of the final structures.
Table 6.
Pairwise Kolmogorov-Smirnov tests to check the difference of the histograms of C-domain’s Q-scores of the final structures.
Table 7.
Pairwise Mann-Whitney U tests tests to check the difference of the histograms of N-domain’s Q-scores of the final structures.
Table 8.
Pairwise Mann-Whitney U tests to check the difference of the histograms of M-domain’s Q-scores of the final structures.
Table 9.
Pairwise Mann-Whitney U tests to check the difference of the histograms of C-domain’s Q-scores of the final structures.
Fig 4.
SufI folding networks for refolding (A) and for the codon-based CTF (B).
The refolding network possesses 3284 nodes, while the codon-based CTF has only 820 nodes. The size of nodes represent their probabilities. The darkness of the node represents native-ness. The darker one is closer to the native. Diamonds, triangle, and stars indicate that N-, M-, and C-domains are pre-dominantly unfolded, respectively. When pre-dominantly unfolded domains are no uniquely decided, circles are used.
Fig 5.
The correlation between the inverse of elongation rate and the degree of folding in SufI.
A) The degree of folding acquisition ΔQi after averaging over the window size 5. B) One over the translation rate computed from the Spencer et al.’s algorithm [43]. Experimentally-detected translational attenuation regions, 33-40kDa (281-326th residues) and 25-28kDa (214-240th residues), are shaded in grey [16]. C) The scattered plot of the translation time and the degree of folding. Here, residues 200–350 are used. The correlation coefficient was 0.51.