Exploring the dynamic information content of a protein NMR structure: Comparison of a molecular dynamics simulation with the NMR and X-ray structuresof Escherichia coli ribonuclease HI
M. Philippopoulos et C. Lim, Exploring the dynamic information content of a protein NMR structure: Comparison of a molecular dynamics simulation with the NMR and X-ray structuresof Escherichia coli ribonuclease HI, PROTEINS, 36(1), 1999, pp. 87-110
The multiconformer nature of solution nuclear magnetic resonance (NMR) stru
ctures of proteins results from the effects of intramolecular dynamics, spi
n diffusion and an uneven distribution of structural restraints throughout
the molecule. A delineation of the former from the latter two contributions
is attempted in this work for an ensemble of 15 NMR structures of the prot
ein Escherichia coli ribonuclease HI (RNase HI). Exploration of the dynamic
information content of the NMR ensemble is carried out through correlation
with data from two crystal structures and a 1.7-ns molecular dynamics (RID
) trajectory of RNase HI in explicit solvent, Assessment of the consistency
of the crystal and mean MD structures with nuclear Overhauser effect (NOE)
data showed that the NMR ensemble is overall more compatible with the high
-resolution (1.48 Angstrom) crystal structure than with either the lower-re
solution (2.05 Angstrom) crystal structure or the MD simulation, Furthermor
e, the NMR ensemble is found to span more conformational space than the MD
simulation for both the backbone and the sidechains of RNase HI. Nonetheles
s, the backbone conformational variability of both the NMR ensemble and the
simulation is especially consistent with NMR relaxation measurements of tw
o loop regions that are putative sites of substrate recognition. Plausible
side-chain dynamic information is extracted from the NMR ensemble on the ba
sis of (i) rotamericity and syn-pentane character of variable torsion angle
s, (ii) comparison of the magnitude of atomic mean-square fluctuations (msf
) with those deduced from crystallographic thermal factors, and (iii) compa
rison of torsion angle conformational behavior in the NMR ensemble and the
simulation, Several heterogeneous torsion angles, while adopting non-rotame
ric/syn-pentane conformations in the NMR ensemble, exist in a unique confor
mation in the simulation and display low X-ray thermal factors, These torsi
ons are identified as sites whose variability is likely to be an artifact o
f the NMR structure determination procedure. A number of other torsions sho
w a close correspondence between the conformations sampled in the NMR and M
D ensembles, as well as significant correlations among crystallographic the
rmal factors and atomic msf calculated from the NMR ensemble and the simula
tion. These results indicate that a significant amount of dynamic informati
on is contained in the NMR ensemble. The relevance of the present findings
for the biological function of RNase HI, protein recognition studies, and p
revious investigations of the motional content of protein NMR structures ar
e discussed. Proteins 1999;36:87-110, (C) 1999 Wiley-Liss, Inc.