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Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints

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Abstract

Determination of the accurate three-dimensional structure of large proteins by NMR remains challenging due to a loss in the density of experimental restraints resulting from the often prerequisite perdeuteration. Solution small-angle scattering, which carries long-range translational information, presents an opportunity to enhance the structural accuracy of derived models when used in combination with global orientational NMR restraints such as residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs). We have quantified the improvements in accuracy that can be obtained using this strategy for the 82 kDa enzyme Malate Synthase G (MSG), currently the largest single chain protein solved by solution NMR. Joint refinement against NMR and scattering data leads to an improvement in structural accuracy as evidenced by a decrease from ∼4.5 to ∼3.3 Å of the backbone rmsd between the derived model and the high-resolution X-ray structure, PDB code 1D8C. This improvement results primarily from medium-angle scattering data, which encode the overall molecular shape, rather than the lowest angle data that principally determine the radius of gyration and the maximum particle dimension. The effect of the higher angle data, which are dominated by internal density fluctuations, while beneficial, is also found to be relatively small. Our results demonstrate that joint NMR/SAXS refinement can yield significantly improved accuracy in solution structure determination and will be especially well suited for the study of systems with limited NMR restraints such as large proteins, oligonucleotides, or their complexes.

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Abbreviations

MSG:

Malate synthase G

SAXS:

Small-angle solution X-ray scattering

RDC:

Residual dipolar coupling

RCSA:

Residual chemical shift anisotropy

NOE:

Nuclear Overhauser enhancement

SVD:

Singular value decomposition

R G :

Gyration radius

d max :

Maximum particle dimension

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Acknowledgements

This work was supported by the Intramural Research Program of the NIDDK, NIH, and the Intramural Antiviral Target Program of the Office of the Director, NIH (A. G. and A. B.) an ARC Federation Fellowship and a grant from the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FG02-05ER64026, NAAR #843 (J. T.). This work utilized facilities supported in part by the National Science Foundation under Agreement No. DMR-0454672. Portions of this research were carried out at the Stanford Synchrotron Radiation Laboratory, a national user facility operated by Stanford University on behalf of the U.S. Department of Energy, Office of Basic Energy Sciences. The SSRL Structural Molecular Biology Program is supported by the Department of Energy, Office of Biological and Environmental Research, and by the National Institutes of Health, National Center for Research Resources, Biomedical Technology Program. We thank Dr. Hiro Tsuruta (SSRL) for assistance with beamline instrumentation.

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Authors and Affiliations

  1. Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Building 5, Bethesda, MD, 20892-0520, USA

    Alexander Grishaev & Ad Bax

  2. Departments of Medical Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, ON, Canada, M5S 1A8

    Vitali Tugarinov & Lewis E. Kay

  3. School of Molecular and Microbial Bioscience, University of Sydney, Sydney, NSW, 2006, Australia

    Jill Trewhella

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  1. Alexander Grishaev
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Correspondence to Alexander Grishaev.

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Grishaev, A., Tugarinov, V., Kay, L.E. et al. Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints. J Biomol NMR 40, 95–106 (2008). https://doi.org/10.1007/s10858-007-9211-5

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