Fig 1.
(A) Superposition of the E. coli (red), E. cloacae (blue), C. freundii (green), and P. aeruginosa structures. (B) Neighbor-joining tree of the four considered enzymes.
Fig 2.
Physical descriptions of the original four AmpC structures.
Thermodynamic descriptions of the unfolding transition are characterized by (A) heat capacity and (B) the free energy landscapes. The vertical dashed line indicates the experimental Tm value of the E. coli enzyme. The experimental ΔHunf value is 182 kcal/mol, whereas the calculated value is 212 kcal/mol. (C) Rigid cluster susceptibility curves describe the mechanical transition for a structure predominantly composed of one large rigid cluster to many disjoint and floppy tiny clusters.
Fig 3.
Multiple sequence alignment of the four AmpC enzymes color-coded by flexibility index.
Red indicates positive values, corresponding to flexible regions, whereas blue indicates negative values, corresponding to rigid regions. Green indicates the flexibility index equals zero, corresponding to isostatically rigid regions. The catalytic Ser-64 is indicated by the arrow, whereas asterisks indicate the other active site residues. Boxes indicate the three flexibly correlated regions.
Fig 4.
QSFR descriptions of the four AmpC enzymes.
(Left) The structures of the four AmpC structures are color-coded in the same way as Fig 3. (Right) Cooperativity correlation plots for each of the four AmpC enzymes are shown, which are calculated as pixel-by-pixel averages across the sets of representative structures. Residue pairs that are co-rigid are colored blue; residues pairs that are flexibly correlated are colored red; and white indicates no mechanical coupling therein. The off-diagonal couplings indicating flexibility correlation is indicated by the black bands in the E. coli cooperativity correlation plot.
Fig 5.
The conserved flexibly correlated active site regions.
The structure of the E. cloacae AmpC enzyme is shown to highlight the consensus cooperativity correlation features. The grey residues shown in spacefill correspond to the large rigid cluster that makes up most of the enzyme; whereas the three active site regions are shown as cartoons (red = α-domain, blue = Ω-loop, and orange = α14 and α15 from the α/β-domain). The catalytic Ser-64 is colored green, whereas other active site residues are colored cyan.
Fig 6.
Relating cooperativity correlation variations to fluctuations within the hydrogen bond network.
(Top) Scatter plot of the differences within the total H-bond network strength of the E. coli representative structures are plotted against cooperativity correlation similarity. In both cases, the original 3GTC structures are compared to each of the other representative structures. Cooperativity correlation similarity is calculated as the root mean square deviation (RMSD) across all pixels. (Bottom) The total H-bond network strength is plotted against the average CC value; large numbers indicate the CC plot is more red-shifted.
Table 1.
QSFR sensitivity to model parameters.