Figure 1.
Location of Active and Inactive Pro Mutants of CcdB in the Context of the Overall 3D Structure of the Protein
(A) In this stereo view, one of the protomers is shown in grey and the other in color.
(B) Secondary structure representation of CcdB. Locations where Pro mutations could not be generated are shown in green, while red and blue represent locations of active and inactive mutants, respectively. Every 20th residue is labeled.
Table 1.
Fraction of Active and Soluble Mutants as a Function of Total Side Chain Accessibility (ACC) in the Absence and Presence of the Inducer Arabinose
Figure 2.
Correlation of Pro Mutant Activity with Various Structural Parameters of WT and Mutant Models of CcdB
Solid circles represent active mutants and empty circles represent inactive mutants. (A) WT residue ACC, (B) WT residue depth, (C) |φ(WT) − (−65)| (D) solubility of mutant (0 denotes insoluble and 1 denotes soluble), (E) number of H-bonds formed by WT residue in native structure and acceptor in mutant models (−1 denotes WT amide not involved in H-bond, 0 denotes WT amide involved in H-bond but acceptor of this amide group not satisfied in any of the mutant models and 1 denotes acceptor forms new H-bond in at least one mutant model). Correlations with p-values less than 0.05 are considered statistically significant.
Table 2.
Secondary Structure and Main Chain H-Bond Prediction from Pro Scanning Mutagenesis
Figure 3.
The flowchart of scheme for prediction of effects of Pro mutations on protein stability derived from structural analysis of WT crystal structure and mutant models. A and I refer to active and inactive predictions, respectively. Letters in lowercase (a–f) refer to each node of the scheme as described in the text. Numbers at each branch indicate the number of active and inactive mutants satisfying the “Yes” or “No” criteria of the respective branch. The numbers at each A and I prediction bubble correspond to the number of CcdB Pro mutants ending at that bubble. The numbers of misclassified mutants are shown in italics. Active mutants correspond to nonperturbing Pro substitutions and inactive ones to perturbing Pro substitutions in case of CcdB.
Figure 4.
The flowchart of scheme for prediction of effects of Pro mutations on protein stability derived from structural analysis of WT-CcdB crystal structure alone. A and I refer to active and inactive predictions, respectively. The numbers at each branch indicate the number of active and inactive mutants satisfying the “Yes” or “No” criteria of the respective branch. The numbers at each A and I prediction bubble correspond to the number of CcdB Pro mutants ending at that bubble. The numbers of misclassified mutants are shown in italics.
Table 3.
Overall Prediction Results in Terms of Accuracy, Precision, and Recall