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

• Published in: Journal of the American Chemical Society Vol. 127; no. 47; pp. 16621 - 16628
• Main Authors: Grishaev, Alexander, Wu, Justin, Trewhella, Jill, Bax, Ad
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 30.11.2005
• Subjects: Analytical, structural and metabolic biochemistry; Biological and medical sciences; Computational Biology; Fundamental and applied biological sciences. Psychology; General aspects, investigation methods; Magnetic Resonance Spectroscopy; Models, Molecular; Protein Conformation; Proteins; Proteins - chemistry; Scattering, Radiation; X-Rays; Biochemical analysis; Three dimensional structure; Molecular structure; Solution structure; NMR spectrometry; Small angle X ray scattering; Structural analysis
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja054342m

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, γS 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 γB 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.