Joint X-ray/NMR structure refinement of multidomain/multisubunit systems

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...

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Bibliographic Details
Published in:Journal of biomolecular NMR 2019-07, Vol.73 (6-7), p.265-278
Main Authors: Carlon, Azzurra, Ravera, Enrico, Parigi, Giacomo, Murshudov, Garib N., Luchinat, Claudio
Format: Article
Language:English
Subjects:
Algorithms
Biochemistry
Biological and Medical Physics
Biophysics
Couplings
Crystallography, X-Ray
Crystals
Data integration
Experimental data
Models, Molecular
Models, Theoretical
NMR
Nuclear magnetic resonance
Nuclear Magnetic Resonance, Biomolecular
Physics
Physics and Astronomy
Proteins
Spectroscopy/Spectrometry
X-ray diffraction
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Summary: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.
ISSN:0925-2738
1573-5001
DOI:10.1007/s10858-018-0212-3