Research Article
AtTRB1–3 Mediates Structural Changes in AtPOT1b to Hold ssDNA
Table 6
Evaluation of molecular dynamics studies for the chosen proteins.
| Protein | POT1B | TRB1 | TRB2 | TRB3 |
| RMSD profile (from 3 ns MD trajectory) | Equilibration period (ps) | 250 | 2000 | 1200 | 2200 | RMSD (nm) | 0.41 | 0.35 | 0.45 | 0.48 | Potential energy (kJ/mol) | | | | | Minimum | −2233890 (2696 frame) | −796525.75 (1522 frame) | −988556.44 (2500 frame) | −912086.94 (1844 frame) | Maximum | −2219754.8 (222 frame) | −788678.81 (8 frame) | −980101.88 (8 frame) | −903493.06 (14 frame) |
| Ramachandran plot assessment | Residues in favored region (%) | 80.5 | 80.1 | 83.8 | 84 | Residues in additionally allowed region (%) | 17 | 14.7 | 14.7 | 14.4 | Residues in generously allowed region (%) | 1.9 | 3.8 | 0.8 | 0.4 | Residues in disallowed region (%) | 0.5 | 1.5 | 0.8 | 1.2 | Verify_3D score | 82.64 | 80.17 | 77.33 | 82.84 | ERRAT score | 78.93 | 89.66 | 89.55 | 77.47 |
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