Table 5.
Interactions at the interface between scFv 10FG2 and different toxins through molecular dynamics (MD) simulations.
| Residues of scFv 10FG2 | Residues of Cll1 Toxin | Residues of Cn2 Toxin | Residues of Css2 Toxin | Residues of Cll2 Toxin | Residues of Ct1a Toxin | Residues of Cell9 Toxin |
|---|---|---|---|---|---|---|
| Y59 | L8 | |||||
| L105 | I5 | L5 | L5 | |||
| L105 | V6 | V6 | V6 | V6 | V6 | V6 |
| L105 | L8 | |||||
| L105 | Y33 | Y33 | Y33 | Y33 | Y33 | Y33 |
| L105 | A55 | |||||
| L105 | V56 | I56 | V56 | V56 | V56 | V56 |
| W231 | V56 | I56 | V56 | V56 | V56 | |
| L236 | L8 | |||||
| L236 | V56 | I56 | V56 | V56 | V56 | |
| L236 | L60 | L60 | L60 | L60 | ||
| Hydrogen Bonds | ||||||
| S31(O) | K35(NZ) | K35(NZ) | K35(NZ) | K35(NZ) | K35(NZ) | K35(NZ) |
| S31(OH) | K35(NZ) | K35(NZ) | K35(NZ) | K35(NZ) | ||
| S52(OH) | Q31(O) | Q31(O) | Q31(O) | |||
| S52(OH) | Q31(OE1) | Q31(OE1) | Q31(OE1) | Q31(OE1) | Q31(OE1) | Q31(OE1) |
| G54(N) | Q31(OE1) | Q31(OE1) | Q31(OE1) | Q31(OE1) | Q31(OE1) | Q31(OE1) |
| G55(N) | Q31(OE1) | |||||
| G56(N) | Q31(OE1) | Q31(OE1) | Q31(OE1) | Q31(OE1) | Q31(OE1) | Q31(OE1) |
| Y53(OH) | K30(O) | K30(O) | K30(O) | R30(O) | R30(O) | |
| S57(OH) | Q32(OE1) | Q32(OE1) | K32(NZ) | Q32(OE1) | ||
| S57(OH) | Q31(O) | Q31(O) | ||||
| Y59(OH) | Q32(OE1) | Q32(OE1) | Q32(OE1) | Q32(OE1) | Q32(OE1) | |
| Y59(OH) | Q32(NE2) | Q32(NE2) | K32(NZ) | Q32(NE2) | ||
| Y59(OH) | D7(O) | |||||
| Y59(OH) | N7(OD1) | N7(OD1) | ||||
| Y59(OH) | N7(ND2) | |||||
| Y59(OH) | L8(N) | K8(N) | K8(N) | H8(N) | H8(N) | H8(N) |
| Y60(O) | K8(NZ) | K8(NZ) | ||||
| D62(OD1) | K8(NZ) | |||||
| D62(OD1) | K63(NZ) | |||||
| K65(NZ) | S9(O) | N9(OD1) | S9(O) | S9(O) | ||
| K65(NZ) | S9(OH) | |||||
| R101(NH2) | Q54(OE1) | Q54(OE1) | Q54(OE1) | Q54(OE1) | Q54(OE1) | Q54(OE1) |
| R101(NH1) | Q54(NE2) | Q54(NE2) | Q54(OE1) | Q54(OE1) | ||
| D102(OD1) | Y52(OH) | Y52(OH) | Y52(OH) | Y52(OH) | Y52(OH) | Y52(OH) |
| D102(OD2) | K35(NZ) | K35(NZ) | K35(NZ) | K35(NZ) | K35(NZ) | K35(NZ) |
| D102(OD2) | K35(N) | K35(N) | K35(N) | K35(N) | K35(N) | K35(N) |
| L104(N) | Q32(O) | Q32(O) | Q32(O) | Q32(O) | K32(O) | Q32(O) |
| L105(N) | Q32(O) | Q32(O) | Q32(O) | Q32(O) | K32(O) | Q32(O) |
| L105(O) | V56(N) | L56(N) | V56(N) | V56(N) | V56(N) | V56(N) |
| S107(N) | Q54(O) | Q54(O) | Q54(O) | Q54(O) | Q54(O) | Q54(O) |
| S107(OH) | Q54(O) | Q54(O) | Q54(O) | Q54(O) | Q54(O) | |
| S107(OH) | Q54(NE2) | Q54(NE2) | Q54(NE2) | Q54(NE2) | ||
| D108(OD2) | Q54(NE2) | Q54(NE2) | Q54(NE2) | Q54(NE2) | Q54(NE2) | |
| D108(OD1) | Q54(NE2) | |||||
| S165(O) | K62(NZ) | |||||
| N171(OD1) | Q54(NE2) | |||||
| T172(OH) | Q54(OE1) | |||||
| T172(N) | Q54(OE1) | |||||
| AS190(OH) | Q54(NE2) | |||||
| D233(O) | K62(NZ) | N62(ND2) | N62(OD1) | K62(NZ) | ||
| D233(OD2) | N62(ND2) | K62(NZ) | ||||
| S234(OH) | K62(NZ) | N62(NZ) | K62(NZ) | K62(NZ) | ||
| T235(O) | K8(NZ) | K8(NZ) | ||||
| T235(OH) | K62(NZ) | N62(ND2) | K62(NZ) | K62(NZ) | ||
| T235(OH) | K63(NZ) | |||||
| L236(O) | K8(NZ) | K8(NZ) | ||||
| G237(O) | K8(NZ) | |||||
| Ionic Interactions within Six Angstroms | ||||||
| D102 | K35 | |||||
| Cation–Pi Interactions within Six Angstroms | ||||||
| Y53 | K35 | |||||
| R101 | Y52 | |||||
| Number contacts α | 42 | 36 | 34 | 27 | 29 | 36 |
| Hydrogen Bonds δ | 10.3 | 10.8 | 10.3 | 10.4 | 9.1 | 10.4 |
Bold types denote main-chain atoms involved in contacts. Underlined types denote toxin residue positions in which there are differences among toxins (see Figure 2A). α Total number of contacts along MD simulations; δ Hydrogens bonds average of MD simulations.