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A comparison of 15 N NMR relaxation measurements with a molecular dynamics simulation: Backbone dynamics of the glucocorticoid receptor DNA‐binding domain
Author(s) -
Eriksson Mats A. L.,
Berglund Helena,
Härd Torleif,
Nilsson Lennart
Publication year - 1993
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340170406
Subject(s) - heteronuclear molecule , molecular dynamics , chemistry , nuclear overhauser effect , relaxation (psychology) , crystallography , side chain , peptide bond , two dimensional nuclear magnetic resonance spectroscopy , chemical physics , nuclear magnetic resonance , nuclear magnetic resonance spectroscopy , computational chemistry , stereochemistry , physics , peptide , psychology , social psychology , biochemistry , organic chemistry , polymer
The rapid motions of the backbone of the DNA‐binding domain of the glucocorticoid receptor (GR DBD) have been investigated using proton‐detected heteronuclear NMR experiments on 15 N‐labeled protein at pH 6.0 and with a 200 psec molecular dynamics simulation of hydrated GR DBD. The experimental data were interpreted in terms of a generalized order parameter ( S 2 ) and an effective correlation time (τ e ) for the internal motion of each amide bond. A back calculation, using the same model, yielded the { 1 H}‐ 15 N nuclear Overhauser effects (NOEs) and the 15 N spin‐lattice relaxation times ( T 1 ) from the simulated data. The rapid motions of the backbone turned out to be rather limited and uniform throughout the protein, with a somewhat reduced mobility in the two major α‐helical regions and a slightly enhanced flexibility for some residues in the first zinc coordinating region. The agreement between the experimental and simulated S 2 ‐values was as good as quantitative for most of the residues, except for some residues that were subject to a more large‐scale, and in the simulation thus poorly sampled, motion. Examples of such motions that were found in the simulation include jumps of the amide bond of Ile‐487 between the charged oxygens of the side chain of Asp‐485 and less distinct large scale motions for some of the residues in the extended regions, that were shown to give rise to noisy and/or fast decaying internal reorientational correlation functions. For these residues large differences in the simulated and experimental τ e ‐values were found, indicating that motions on different time scales were dominating in the experimental and simulated values. The lower (<0.7) experimental NOEs for these residues could not be reproduced in the simulation and were shown to be a consequence of the lower τ e ‐values estimated in the simulation. By combining information from the simulation and the experiment a more complete picture of the motions for these residues can be obtained as is illustrated with an estimation of the jump angle and jump frequency for the amide bond of Ile‐487. © 1993 Wiley‐Liss, Inc.