Abstract
Data integration in structural biology has become a paradigm for the characterization of biomolecular systems, and it is now accepted that combining different techniques can fill the gaps in each other’s blind spots. In this frame, one of the combinations, which we have implemented in REFMAC-NMR, is residual dipolar couplings from NMR together with experimental data from X-ray diffraction. The first are exquisitely sensitive to the local details but does not give any information about overall shape, whereas the latter encodes more the information about the overall shape but at the same time tends to miss the local details even at the highest resolutions. Once crystals are obtained, it is often rather easy to obtain a complete X-ray dataset, however it is time-consuming to obtain an exhaustive NMR dataset. Here, we discuss the effect of including a-priori knowledge on the properties of the system to reduce the number of experimental data needed to obtain a more complete picture. We thus introduce a set of new features of REFMAC-NMR that allow for improved handling of RDC data for multidomain proteins and multisubunit biomolecular complexes, and encompasses the use of pseudo-contact shifts as an additional source of NMR-based information. The new feature may either help in improving the refinement, or assist in spotting differences between the crystal and the solution data. We show three different examples where NMR and X-ray data can be reconciled to a unique structural model without invoking mobility.
Highlights
Integrated Structural Biology tries to merge the results from different experimental techniques, making the most of the information encoded in each (Ward et al 2013; van den Electronic supplementary material The online version of this article contains supplementary material, which is available to authorized users.Bedem and Fraser 2015; Carlon et al 2016b; Schlundt et al 2017)
The two most common experimental techniques for biomolecular structure determination are X-ray diffraction and solution NMR spectroscopy, and single particle cryo electron microscopy is progressing rapidly
X-ray crystallographic diffraction data give information that progress from the overall shape of the molecule up to individual atom positions as the resolution increases; on the contrary, NMR data mostly progress from short-range inter-atom distances and bond orientations to the overall shape of the molecule with increasing number and quality of restraints
Summary
X-ray crystallographic diffraction (and cryo-EM) data give information that progress from the overall shape of the molecule up to individual atom positions as the resolution increases; on the contrary, NMR data mostly progress from short-range inter-atom distances and bond orientations to the overall shape of the molecule with increasing number and quality of restraints. The combination of these techniques yields valuable information throughout the whole range of distances, even in the presence of suboptimal X-ray and/or NMR data.
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