2L56

NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations


SOLUTION NMR
NMR Refinement
MethodDetailsSoftware
molecular dynamicsmolecular dynamics simulation with time-averaged NOE distance restraining and local elevation biased 3J-value restraining using 179 NOE distances and 15 3J-coupling constants; the 10 deposited structures were selected from a set of 20000 trajectory configurations by conformational cluster analysis; the occurrence frequencies of the clusters that correspond to the deposited model structures are the following: cluster 1 32% cluster 2 14% cluster 3 6% cluster 4 6% cluster 5 6% cluster 6 3% cluster 7 3% cluster 8 2% cluster 9 2% cluster 10 2%. Authors state that The deviations of the deposited trajectory structures from the so-called "ideal" values for geometrical and stereochemical quantities are partially due to the biasing force derived from the NOE distance bounds and 3J-coupling constants, and partially due to the finite temperature (278K) of the simulations. The ideal geometric and stereochemical values of the GROMOS force field are close to those of Engh and Huber.GROMOS
NMR Ensemble Information
Conformer Selection Criteriaconformational cluster analysis
Conformers Calculated Total Number20000
Conformers Submitted Total Number10
Representative Model1 (occurrence frequencies)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementGROMOS53A6 FORCE FIELDvan Gunsteren and Berendsen