Table 1.
Presumptive residues of P. aeruginosa LasB (elastase) that were predicted by computer simulation to form the contact interface with residues and domains of the effective human single-chain antibodies, HuscFv-N42 and HuscFv-N45.
| LasB Protein | HuscFv-N42 | Interactive Bond (s) | |
|---|---|---|---|
| Residue | Residue | Domain (s) | |
| S45 | S140 | Linker | Hydrogen |
| T46 | S140 | Linker | Hydrogen |
| D47 | S140 | Linker | Hydrogen |
| D48 | S168 | VL-CDR1 | Hydrogen |
| R108 | D62 | VH-CDR2 | Salt bridge |
| E111 | Y59 | VH-CDR2 | Hydrogen |
| Y114 | N232 | VL-CDR3 | Hydrogen |
| T127 | T57/R106 | VH-CDR2/CDR3 | Hydrogen |
| Y155 (substrate binding) | K190 | VL-CDR2 | Hydrogen |
| R208 | Q102 | VH-CDR3 | Hydrogen |
| D221 (substrate binding) | K190 | VL-CDR2 | Salt bridge |
| H223 (substrate binding) | W103 | VH-CDR3 | Hydrophobic (π-π stacking) |
| LasB Protein | HuscFv-N45 | Interactive Bond(s) | |
| Residue | Residue | Domain(s) | |
| T97 | K13 | VH-FR1 | Hydrogen |
| W115 | S7/R19/S21 | VH-FR1 | Hydrogen |
| E141 (located at the center of the catalytic site) | K76/Y80 | VH-FR1/FR3 | Salt bridge |
| Q149 | K13 | VH-FR1 | Hydrogen |
| R156 | K58/Y60 | VH-CDR2 | Hydrogen |
| E164 (ligand of zinc co-factor) | R19 | VH-FR1 | Salt Bridge |
| I220 | K58 | VH-CDR2 | Hydrogen |
| D221 (substrate binding) | K58/R72 | VH-CDR2/FR3 | Ionic |
| H223 (substrate binding) | K76 | VH-FR3 | Hydrogen |