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Refinement of Multidomain Protein Structures by Combination of Solution Small-Angle X-ray Scattering and NMR Data

Alexander Grishaev,* Justin Wu, Jill Trewhella, and Ad Bax*

Contribution from the Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850

J. Am. Chem. Soc.; 2005; 127(47) pp 16621 - 16628;

Abstract:

Determination of the 3D structures of multidomain proteins by solution NMR methods presents a number of unique challenges related to their larger molecular size and the usual scarcity of constraints at the interdomain interface, often resulting in a decrease in structural accuracy. In this respect, experimental information from small-angle scattering of X-ray radiation in solution (SAXS) presents a suitable complement to the NMR data, as it provides an independent constraint on the overall molecular shape. A computational procedure is described that allows incorporation of such SAXS data into the mainstream high-resolution macromolecular structure refinement. The method is illustrated for a two-domain 177-amino-acid protein, S crystallin, using an experimental SAXS data set fitted at resolutions from ~200 Å to ~30 Å. Inclusion of these data during structure refinement decreases the backbone coordinate root-mean-square difference between the derived model and the high-resolution crystal structure of a 54% homologous B crystallin from 1.96 ± 0.07 Å to 1.31 ± 0.04 Å. Combining SAXS data with NMR restraints can be accomplished at a moderate computational expense and is expected to become useful for multidomain proteins, multimeric assemblies, and tight macromolecular complexes.