Volume 14, Issue 9, Pages 1401-1410 (September 2006) Correlation between Protein Stability Cores and Protein Folding Kinetics: A Case Study on Pseudomonas aeruginosa Apo-Azurin  Mingzhi Chen, Corey J. Wilson, Yinghao Wu, Pernilla Wittung-Stafshede, Jianpeng Ma  Structure  Volume 14, Issue 9, Pages 1401-1410 (September 2006) DOI: 10.1016/j.str.2006.07.007 Copyright © 2006 Elsevier Ltd Terms and Conditions

Figure 1 Structure of Azurin (Left) Three-dimensional illustration showing the structure of P. aeruginosa azurin (PDB code: 1azu). Trp48, with a unique fluorescence that reports on an intact core, is shown in green; the copper is shown in blue space filling, and its ligands are shown in stick representation. (Right) Two-dimensional view of azurin's secondary structure elements. The β strands are represented by arrows, and the helix is represented by an elongated box. The two sheets forming the sandwich are indicated. The numbering of the strands is the same as in Tables 1 and 2 and the text. Structure 2006 14, 1401-1410DOI: (10.1016/j.str.2006.07.007) Copyright © 2006 Elsevier Ltd Terms and Conditions

Figure 2 Three-Dimensional Illustration of P. aeruginosa Azurin with Residues for which ϕ Values Have Been Derived in Stick Representations The probed side chains are color coded as follows: ϕ = 0–0.29, yellow; ϕ = 0.3–0.79, red; ϕ = 0.8–1.0, purple. The four strands constituting the highest-ranking substructure in our computation (i.e., strands 3, 4, 6, and 7; Table 2) are highlighted in blue. Structure 2006 14, 1401-1410DOI: (10.1016/j.str.2006.07.007) Copyright © 2006 Elsevier Ltd Terms and Conditions

Figure 3 Structure of TNfnIII Three-dimensional illustration showing the three-dimensional structure of TNfnIII (PDB code: 1ten); the 4 residues for which high ϕ values have been reported (Hamill et al., 2000) are shown in red stick representations. The four strands constituting the highest-ranking substructure in our computation (i.e., strands 2, 3, 5, and 6; Table 3) are highlighted in blue. Structure 2006 14, 1401-1410DOI: (10.1016/j.str.2006.07.007) Copyright © 2006 Elsevier Ltd Terms and Conditions

Figure 4 Distributions of Computational Scores (A and B) Plots of total score distributions in the computations for (A) azurin and (B) TNfnIII. The x axis corresponds to the sorted indices of all combinations of four secondary structure elements; the y axis indicates the total score of each combination. Additional energetic details for the ten lowest-scoring combinations are listed in Tables 2 and 3. Structure 2006 14, 1401-1410DOI: (10.1016/j.str.2006.07.007) Copyright © 2006 Elsevier Ltd Terms and Conditions

Figure 5 Schematic Description of Hydrogen Bonding Interactions Used in Constructing the Statistical Energy Function Structure 2006 14, 1401-1410DOI: (10.1016/j.str.2006.07.007) Copyright © 2006 Elsevier Ltd Terms and Conditions

Figure 6 Schematic Description of the Procedure Used for Computing the Solvent-Accessible Surface In this figure, atom j casts some burial area on atom i (the shaded region), while atom j′ does not. Structure 2006 14, 1401-1410DOI: (10.1016/j.str.2006.07.007) Copyright © 2006 Elsevier Ltd Terms and Conditions

Figure 7 Energy of Residue Solvation Two examples (i.e., Leu and Lys) of the energy terms associated with the solvent-accessible area. The minimum of Leu appears at a smaller ratio of solvent-accessible surface, which indicates that this hydrophobic residue has a higher probability of being buried than the hydrophilic residue Lys. Structure 2006 14, 1401-1410DOI: (10.1016/j.str.2006.07.007) Copyright © 2006 Elsevier Ltd Terms and Conditions