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THE 3 N-TERMINAL AND 9 C-TERMINAL AMINO ACIDS ARE HIGHLY DISORDERED. DGII STRUCTURES WERE GENERATED WITH NOE, OMEGA-TORSION AND PHI-TORSION CONSTRAINTS AND A MINIMIZATION/DYNAMICS PROTOCOL WAS USED TO FURTHER REFINE THE DISTANCE GEOMETRY STRUCTURES. THE PROTOCOL CONSISTED OF 100 STEPS OF STEEPEST DESCENTS FOLLOWED BY 500 STEPS OF CONJUGATE GRADIENT MINIMIZATION WITHOUT CONSTRAINTS. ALL CONSTRAINTS WERE APPLIED AND EACH STRUCTURE SUBJECTED TO 500 STEPS OF CONJUGATE GRADIENT MINIMIZATION, 5 PS OF 300K MOLECULAR DYNAMICS, 500 STEPS OF CONJUGATE GRADIENT AND 100 STEEPEST DESCENTS MINIMIZATION. SOME MODELS WILL CONTAIN RESIDUES THAT HAVE UNFAVORABLE CONFORMATIONS, TYPICALLY IN THE DISORDERED REGIONS. |
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