Table 1.
Binding free energies (kcal/mol) between PBP2x protein and cefuroxime (CES) in the two complexes.
Figure 1.
Sequence alignment between PBP2x-R61 (R61), PBP2x-A7 (A7), and the template protein (PDB code 1QMF).
Figure 2.
Ramachandran plot of modeled PBP2x-R61 and PBP2x-A7.
The most favored regions are red. Additionally allowed, generously allowed, and disallowed regions are indicated as yellow, light yellow, and white, respectively.
Figure 3.
Comparison of PBP2x-R61 and PBP2x-A7.
(A) The superimposition of initial structures of the complex between PBP2x-R61 (white color) and PBP2x-A7 (cyan color) with the drug (green color). (B) The structure of the cefuroxime drug.
Figure 4.
RMSD values for PBP2x-R61-CES and PBP2x-A7-CES relative to the starting structure during MD simulation.
(A) The whole backbone atoms. (B) The drug molecule.
Figure 5.
Relative decomposed energies of the corresponding residues between PBP2x-R61-CES and PBP2x-A7-CES.
The ovals characterize the two active site areas and the blocks mark the three essential mutated residues.
Table 2.
The list of the residues with absolute energy larger than 1.0 kcal/mol or the residues with the difference between the two complexes larger than 0.5 kcal/mol.
Figure 6.
The distance variation of the five hydrogen bonds during MD simulation.
(A) for PBP2x-R61-CES. (B) for PBP2x-A7-CES. Bond 1: Ser396 O - CES O7; Bond 2: Gly350 N - CES O3; Bond 3: Thr351 OG1 - CES N2; Bond 4:Thr351 OG1 - CES O5; and Bond 5: Thr351 N - CES O5.
Figure 7.
LIGPLOT representation of cefuroxime (CES) binding to PBP2x-R61 and PBP2x-A7.
Ligand, protein, and hydrogen bonds are in thick blue, thick brown, and broken green lines, respectively. Residues involved in hydrophobic contact are associated with a curved comb. (A) Open form of cefuroxime (CES) bound to PBP2x-R61. (B) Open form of cefuroxime (CES) bound to PBP2x-A7.
Table 3.
The property of the mutated residues in the binding site of the two complexes PBP2x-R61-CES and PBP2x-A7-CES.