Amjj. Bonvin et At. Brunger, CONFORMATIONAL VARIABILITY OF SOLUTION NUCLEAR-MAGNETIC-RESONANCE STRUCTURES, Journal of Molecular Biology, 250(1), 1995, pp. 80-93
In structure determination by X-ray crystallography and solution NMR s
pectroscopy experimental data are collected as time and ensemble-avera
ges. Thus, in principle, appropriate time and ensemble-averaged models
should be used. Refinement of: an ensemble of conformers rather than
one single structure against the experimental NMR data could, however,
result in overfitting the data because of the significantly increased
number of parameters. To avoid overfitting, complete cross-validation
, which provides an unbiased measure of the fit, has been applied to n
uclear Overhauser effect derived distance refinement. Using two synthe
tic test cases, a correlation was demonstrated between the cross-valid
ated measure to the fit (defined in terms of root-mean-square deviatio
ns from the distance restraints and number of violations) and the numb
er of models that best reproduce the conformational variability in sol
ution. A new method, based on a probability map, has been used to gene
rate good representations of the resulting ensembles of structures. Th
e method has also been applied to observed NMR data for two proteins,
interleukin 4 and interleukin 8. For interleukin 4, cross-validation i
ndicates that a single-conformer model gives the most accurate represe
ntation of the structure, whereas conventional measures of fit between
the experimental data and those calculated from the model decrease wh
en increasing the number of conformers, indicating overfitting. For in
terleukin 8, complete cross-validation predicts a twin-conformer model
to be the most faithful representation of the experimental data. Two
distinct conformations for the loop formed by residues 16 to 22 emerge
from the family of twin-conformer structures. The putative alternate
conformation of the loop is not observed in the crystal structure of i
nterleukin 8. However, because of crystal packing contacts in this reg
ion this does not necessarily exclude the presence of the alternate co
nformation in solution. The twin-conformer model is supported by obser
ved chemical exchange line broadening for the amide of His18 obtained
by N-15 relaxation studies. This region has also been implied to be in
volved in receptor binding.