Table 4.
Secondary structure of the RBD of the S-protein in its initial conformation, of the adsorbed S-protein, and of the freely relaxed S-protein.
| RBD | S-protein initial structure | Adsorbed S-protein | Free S-protein |
|---|---|---|---|
| α-Helixa | Phe338-Gly339-Glu340-Val341-Phe342-Asn343 | Phe338-Gly339-Glu340-Val341-Phe342-Asn343 | |
| Tyr365-Ser366-Val367-Leu368-Tyr369-Asn370 | Tyr365-Ser366-Val367-Leu368-Tyr369 | Ser366-Val367-Leu368-Tyr369-Asn370 | |
| Pro384-Thr385-Lys386 | Pro384-Thr385-Lys386-Leu387-Asn388-Asp389 | ||
| Glu406-Val407-Arg408-Gln409 | Gly404-Asp405-Glu406-Val407-Arg408 | ||
| Ile418-Ala419-Asp420-Tyr421-Asn422 | Ile418-Ala419-Asp420-Tyr421-Asn422 | ||
| 5-Stranded β-sheet | Asn354-Arg355-Lys356-Arg357-Ile358, Thr376-Phe377-Lys378-Cys379-Tyr380, Asn394-Val395-Tyr396-Ala397-Asp398-Ser399-Phe400-Val401-Ile402, Gly431-Cys432-Val433-Ile434-Ala435-Trp436, Tyr508-Arg509-Val510-Val511-Val512-Leu513-Ser514-Phe515-Glu516 |
Asn354-Arg355-Lys356-Arg357-Ile358, Thr376-Phe377-Lys378-Cys379-Tyr380, Asn394-Val395-Tyr396-Ala397-Asp398-Ser399-Phe400-Val401-Ile402, Gly431-Cys432-Val433-Ile434-Ala435-Trp436-Asn437, Tyr508-Arg509-Val510-Val511-Val512-Leu513-Ser514-Phe515-Glu516 |
Lys356-Arg357-Ile358, Thr376-Phe377-Lys378-Cys379-Tyr380, Asn394-Val395-Tyr396-Ala397-Asp398-Ser399-Phe400-Val401-Ile402, Gly431-Cys432-Val433-Ile434-Ala435-Trp436-Asn437, Tyr508-Arg509-Val510-Val511-Val512-Leu513-Ser514-Phe515-Glu516 |
| 2-Stranded β-sheet | Thr323-Glu324-Ser325-Ile326, Val539-Asn540-Phe541-Asn542 |
Glu324-Ser325-Ile326, Cys538-Val539-Asn540-Phe541- Asn542-Phe543 |
Glu324-Ser325-Ile326, Val539-Asn540-Phe541-Asn542-Phe543 |
MD, molecular dynamics; RBD, receptor-binding domain.
a
During the MD simulations, some short α-helices transiently transformed into 310-helices.