Table 2.
Binding properties for eight candidate peptides calculated from all-atom MD simulations
| Peptide | Stable binding duration (ns) | Binding free energy (kcal/mol) | SEM | Protein-peptide interaction energy (kcal/mol) | Desolvation energy (kcal/mol) | Sequence | No. of stable peptide-protein hydrogen bonds | |
|---|---|---|---|---|---|---|---|---|
| Y36_cls3_M2_M4_R8 | 278 | −25.9 | 0.06 | −85.6 | 59.7 | ACE-AMAMGYPRASY-NH2 | 0 | |
| Y36_cls3_R2_M4∗ | 394 | −46.2 | 0.06 | −140.4 | 94.2 | ACE-ARAMGYPGASY-NH2 | 2 | Peptide 1 |
| Y36_cls5_M2_R4_W8_Y9 | 184 | −22.3 | 0.08 | −64.1 | 41.8 | ACE-AMARGYPWYSY-NH2 | 0 | |
| Y36_cls5_R2_F4_I8_Y9∗ | 500 | −42.3 | 0.06 | −124.5 | 82.2 | ACE-ARAFGYPIYSY-NH2 | 1 | Peptide 2 |
| Y45_cls1_M3_R4_M8_I10 | 172 | −16.2 | 0.06 | −66.2 | 50 | ACE-SYMRAYPMQIP-NH2 | 0 | |
| Y45_cls1_M3_R4_M8_M10 | 91 | −35.5 | 0.2 | −87.8 | 52.3 | ACE-SYMRAYPMQMP-NH2 | 0 | |
| Y45_cls70_Y1_M8_R9_F10_R11 | 500 | −34.4 | 0.5 | −136.6 | 102.2 | ACE-YYPGAYPMRFR-NH2 | 0 | |
| Y45_cls70_Y1_R8_R9_Y10_R11∗ | 500 | −29.5 | 0.04 | −169.3 | 139.8 | ACE-YYPGAYPRRYR-NH2 | 2 | Peptide 3 |
∗These peptides are the best binders according to their duration of binding to the CTD, number of protein-peptide hydrogen bonds, and binding free energy. These peptides were selected for experimental testing and were designated as peptides 1, 2, and 3 in the experimental assays. The last row shows peptide 3, which was found to be a positive hit in the agglutination assay.