Table 3.
MD Simulations of Class II AARSs.
| AARS | Ligands | Starting Structure(s) | Time | Reference |
|---|---|---|---|---|
| AspRS | +Asp:ATP (modeled), + Asn:ATP (modeled) | 1IL2, 1COA and models | 500 ps | Thompson et al., Chem. Bio. Chem., 2006 [127] |
| AspRS | +Asp:ATP (modeled), +Asn:ATP (modeled) | 1IL2, 1COA and models | 0.5–3 ns | Thompson et al., JBC, 2006 [128] |
| AspRS | - | 1ASZ and models | 5 ns | Ul-Haq et al., J. Mol. Graph. Model., 2010 [129] |
| AspRS | +Asp, +Asn (modeled) | 1C0Z | 300 ps | Archontis et al., JMB, 2001 [130] |
| AsnRS | +Asn-AMP, +Asp-AMP (modeled) | T. thermophilus AsnRS | 4 ns | Polydorides et al., Proteins, 2011 [131] |
| HisRS | +His-AMP, +His (modeled), +HisOH (modeled) | 1KMM, 1KMN and modeled variants | 600 ps | Arnez et al., Proteins, 1998 [132] |
| LysRS (LysU) | +Lys:AMPPCP | 1E22, dimer modeled | 1 ns | Hughes et al., BMC Struct. Biol., 2003 [133] |
| LysRS (LysU) | +Lys:AMPPCP | 1E22, dimer modeled | 520 ps | Hughes et al., Proteins, 2006 [134] |
| ProRS | +Pro-AMP (modeled) | 2J3M | 30 ns | Strom et al., J. Mol. Model., 2014 [115] |
| ProRS | - | 2J3M and modeled variants | 12 ns | Sanford et al., Biochemistry, 2012 [135] |
| SerRS | +tRNASer | 3W3S and modeled dimer | 2 ns | Dutta et al., J. Phys. Chem. B, 2015 [136] |
| ThrRS | +tRNAThr:Thr-AMP (modeled) | 1QF6 | 15 ns | Bushnell et al., J. Phys. Chem. B, 2012 [137] |