Relation between native ensembles and experimental structures of proteins

Abstract

Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of ''high-sequence similarity Protein Data Bank'' (HSP) structures and consider the extent to which such ensembles represent the structural heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest that even a modest number of structures of a protein determined under different conditions, or with small variations in sequence, capture a representative subset of the true native-state ensemble.NMR order parameters ͉ protein dynamics ͉ residual dipolar couplings T he rapidly growing Protein Data Bank (PDB) (1) is testament to the revolution in structural biology that has occurred over the last 15 years. These newly available protein structures contain a wealth of information that can be used to rationalize and predict the function of proteins. At the same time, however, it has long been realized that native states are best represented as ensembles of similar structures and that the dynamics of proteins are also important for understanding their function (2-5). NMR spectroscopy (4, 6), which can reveal protein dynamics in atomic detail, is thus being applied to characterize protein stability and the effect of mutations (7), the changes upon ligand binding (5,8,9), the comparison of homologous proteins (10), and the structure of unfolded states (11).A number of recent studies have analyzed the extent to which the dynamical information is represented by existing protein structures, with the aim of predicting experimental data on dynamics from single structures, using relatively simple models based on structural properties. The prediction of properties arising from essentially harmonic dynamics, such as x-ray crystallographic B-factors (12) and NMR order parameters for the protein backbone (13), has been reasonably successful using contact-based models or normal mode analysis. However, side-chain order parameters, which depend in many cases on anharmonic dynamics (14, 15), have proved more challenging, because they exhibit only limited correlations with structural properties, such as contact density and the solventaccessible surface area (16). Improved prediction has been achieved by combining a contact model with the number of rotatable bonds in the side chain (17).Here we investigate the extent to which the diversity present within different structures of the same protein, or proteins with high sequence identity, in t...

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