NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations
Exploring the trigger sequence of the GCN4 coiled-coil: Biased molecular dynamics resolves apparent inconsistencies in NMR measurements
Molecular basis of coiled-coil formation
NMR structure of the GCN4 trigger peptide. THIS ENTRY 2L56 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (2OVN.MR) DETERMINED BY AUTHORS OF THE PDB ENTRY 2OVN
THIS ENTRY 2L56 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (2OVN.MR) DETERMINED BY AUTHORS OF THE PDB ENTRY 2OVN: M.O.STEINMETZ,I.JELESAROV,W.M.MATOUSEK,S.HONNAPPA,W.JAHNKE,J.H.MISSIMER,S.FRANK,A.T.ALEXANDRESCU,R.A.KAMMERER. HYDROGEN BOND DISTANCE RESTRAINTS IN 2OVN.MR WERE NOT USED IN THE NEW REFINEMENT PROCEDURE BECAUSE THEY ARE NOT BASED ON THE EXPERIMENTAL NMR DATA.
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.
GCN4, COILED-COIL, TRIGGER PEPTIDE, TRANSCRIPTION, MOLECULAR DYNAMICS SIMULATIONS