2L56
NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations
SOLUTION NMR
NMR Refinement | ||
---|---|---|
Method | Details | Software |
molecular dynamics | molecular 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 Criteria | conformational cluster analysis |
Conformers Calculated Total Number | 20000 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (occurrence frequencies) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | refinement | GROMOS | 53A6 FORCE FIELD | van Gunsteren and Berendsen |