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Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data

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Abstract

A procedure is presented for refinement of a homology model of E. coli tRNAVal, originally based on the X-ray structure of yeast tRNAPhe, using experimental residual dipolar coupling (RDC) and small angle X-ray scattering (SAXS) data. A spherical sampling algorithm is described for refinement against SAXS data that does not require a globbic approximation, which is particularly important for nucleic acids where such approximations are less appropriate. Substantially higher speed of the algorithm also makes its application favorable for proteins. In addition to the SAXS data, the structure refinement employed a sparse set of NMR data consisting of 24 imino N–HN RDCs measured with Pf1 phage alignment, and 20 imino N–HN RDCs obtained from magnetic field dependent alignment of tRNAVal. The refinement strategy aims to largely retain the local geometry of the 58% identical tRNAPhe by ensuring that the atomic coordinates for short, overlapping segments of the ribose-phosphate backbone and the conserved base pairs remain close to those of the starting model. Local coordinate restraints are enforced using the non-crystallographic symmetry (NCS) term in the XPLOR-NIH or CNS software package, while still permitting modest movements of adjacent segments. The RDCs mainly drive the relative orientation of the helical arms, whereas the SAXS restraints ensure an overall molecular shape compatible with experimental scattering data. The resulting structure exhibits good cross-validation statistics (jack-knifed Q free = 14% for the Pf1 RDCs, compared to 25% for the starting model) and exhibits a larger angle between the two helical arms than observed in the X-ray structure of tRNAPhe, in agreement with previous NMR-based tRNAVal models.

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Abbreviations

MSA:

Magnetic susceptibility anisotropy

NCS:

Non-crystallographic symmetry

RDC:

Residual dipolar coupling

SAXS:

Small angle X-ray scattering

rms:

Root mean square

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Acknowledgments

This work was supported by the Intramural Research Program of the NIDDK, NIH, and by the Intramural AIDS-Targeted Antiviral Program of the Office of the Director, NIH and NIH grant AI33098 (AP).

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Authors and Affiliations

  1. Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA

    Alexander Grishaev, Jinfa Ying & Ad Bax

  2. Department of Chemistry and Biochemistry, 215 UCB, University of Colorado, Boulder, Boulder, CO, 80309-0215, USA

    Marella D. Canny & Arthur Pardi

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  1. Alexander Grishaev
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  2. Jinfa Ying
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  3. Marella D. Canny
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  4. Arthur Pardi
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  5. Ad Bax
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Correspondence to Alexander Grishaev, Arthur Pardi or Ad Bax.

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Grishaev, A., Ying, J., Canny, M.D. et al. Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data. J Biomol NMR 42, 99–109 (2008). https://doi.org/10.1007/s10858-008-9267-x

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