| simulated annealing |
NOE cross-peak intensities were converted into distance restraints as follows: strong, 1.8-2.7 ; medium, 1.8-3.4 ; weak, 1.8-4.5 , and very weak 1.8-6.0. An additional 1.0 was added to upper limits involving methyl protons, 0.5 for methylene protons and 2.3 for degenerate Hd and He protons of tyrosines and phenylalanines. Also, a 0.2 was added to the upper limits of NOEs involving amide protons. Backbone F angles were restrained to -120 50 for 3JHNHa = 8-9 Hz, and -120 40 for JHNHa > 9Hz. A restraint of 100 80 was also applied to F angle for residues that show stronger NHi-Hai-1 NOE than the intraresidue NH-Ha NOE. A total of 329 NOE restraints and 18 F restraints were used in structure determination.
Random structures were generated by subjecting the peptide to an initial 10000-step minimization at 298K. The temperature was then raised gradually to 1000K during a 1000 step dynamics simulation. The peptide was subjected to minimization and a 10ps dynamics at 1000K. The NMR-derived restraints were then imposed on the peptide and the peptide was slowly annealed to 298K in a 100ps trajectory. Finally, the structures were subjected to further minimization at 298K. The force constant for the distance restraints was 100 kcal/mol 2 and the dielectric constant was 4. |
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