Figure 1.
The 30S Subunit In Vitro Experimental Assembly Map for E. coli
The primary, secondary and tertiary binding proteins are shown in black, orange, and blue, respectively. Arrows indicate facilitating effect of binding of one protein on another. Adapted from the review of Culver [6] based on the work of the Nomura Laboratory [4,5].
Table 1.
Comparing Computed versus Experimental B-Factors with a Ranking Measure (Spearman's rs)
Figure 2.
The Influence Network of the Presence of Single Proteins on the Binding Stability of the Other Proteins
The three clusters and the four unaffected proteins are visible. The colors of the arrows indicate Δr (the larger the number, the stronger the influence). The arrows point from the removed protein to the affected protein, e.g., removal of S4 alters the binding strength of S5 with the “influence strength” of 3. The gray arrows indicate the interaction that is due to very small relative energy change and involves the “suspicious” protein S12 (see text for details).
Figure 3.
Color-Coded Contribution to Destabilization, Determined by Eigenvector Analysis of the Two-Protein Removal Experiment
Red diamonds indicate contributions from the smallest and blue diamonds from the largest eigenvalue, respectively. The symbol × indicates influences that were already found in the one protein removal experiment of the previous section. The green × were discussed in the previous section. The respective energy differences of those two interdependencies are rather small and enter into the magnitude of entries of the eigenvectors only slightly. Entries for were marked if the value deviated more than 10% from their most likely value, while for
this threshold was set to 1%, reflecting the respective order of magnitude of λ1/20.
Figure 4.
The Additional Destabilization from the Two-Protein Removal Case Mapped onto the E. coli Map (Blue Diamonds in Figure 3)
The green proteins are not in contact with any other protein. The peptide THX was placed close to the proteins that influence its binding stability. All interactions are non-local, as the respective proteins are not in proximity.
Table 2.
The Contact Interaction Strengths Applied in Our Model
Table 3.
The Covalent Bond Strengths Applied in Our Model
Figure 5.
The Angle αs between the Respective Eigenvectors for an Interaction Strength κ of Protein S12 and for the Full Parameter Set
The broken vertical lines indicate the average values used in the first two validation experiments in the section Sensitivity to Parameters. The full parameter set refers to the one in the Results section under Influence Map, Second-order stabilization revealed by two-protein removal.
Inset: Illustration of the deviation in the eigenvector contributions for the two different average interaction values (shown for the worst case of S7).