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