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Journal of Biomolecular NMR

, Volume 40, Issue 2, pp 83–94 | Cite as

Comparison of alignment tensors generated for native tRNAVal using magnetic fields and liquid crystalline media

  • Michael P. Latham
  • Paul Hanson
  • Darin J. Brown
  • Arthur PardiEmail author
Article

Abstract

Residual dipolar couplings (RDCs) complement standard NOE distance and J-coupling torsion angle data to improve the local and global structure of biomolecules in solution. One powerful application of RDCs is for domain orientation studies, which are especially valuable for structural studies of nucleic acids, where the local structure of a double helix is readily modeled and the orientations of the helical domains can then be determined from RDC data. However, RDCs obtained from only one alignment media generally result in degenerate solutions for the orientation of multiple domains. In protein systems, different alignment media are typically used to eliminate this orientational degeneracy, where the combination of RDCs from two (or more) independent alignment tensors can be used to overcome this degeneracy. It is demonstrated here for native E. coli tRNAVal that many of the commonly used liquid crystalline alignment media result in very similar alignment tensors, which do not eliminate the 4-fold degeneracy for orienting the two helical domains in tRNA. The intrinsic magnetic susceptibility anisotropy (MSA) of the nucleobases in tRNAVal was also used to obtain RDCs for magnetic alignment at 800 and 900 MHz. While these RDCs yield a different alignment tensor, the specific orientation of this tensor combined with the high rhombicity for the tensors in the liquid crystalline media only eliminates two of the four degenerate orientations for tRNAVal. Simulations are used to show that, in optimal cases, the combination of RDCs obtained from liquid crystalline medium and MSA-induced alignment can be used to obtain a unique orientation for the two helical domains in tRNAVal.

Keywords

Alignment tensor Liquid crystalline medium Magnetic susceptibility anisotropy RDC RNA Domain orientation 

Notes

Acknowledgments

We thank Gabe Gittings for purification of the fd and fd mutant bacteriophage, Dr. Jinfa Ying for advice in acquiring the NMR spectra for magnetic alignment, Dr. Alexander Grishaev for the FORTRAN program for calculating the MSA-induced alignment tensor and Dr. Ad Bax for critical advice in collection of the MSA-induced RDCs and for valuable discussions. This work is supported in part by NIH grant AI33098, and MPL was supported in part by a NIH training grant T32 GM65103. The NMR instrumentation was purchased with partial support from NIH grants RR11969, RR16649 and GM068928, NSF grants 9602941 and 0230966, and the W. M. Keck Foundation.

Supplementary material

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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Michael P. Latham
    • 1
  • Paul Hanson
    • 1
  • Darin J. Brown
    • 1
    • 2
  • Arthur Pardi
    • 1
    Email author
  1. 1.Department of Chemistry and Biochemistry, 215 UCBUniversity of Colorado, BoulderBoulderUSA
  2. 2.Department of BiochemistryUniversity of Colorado at Denver, Health Science CenterAuroraUSA

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