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

Abstract

SummaryResidual 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 tRNA Val that many of the commonly used liquid crystalline alignment media result in very similar alignment tensors, which does not eliminate the 4-fold degeneracy for orienting the two helical domains in tRNA. The intrinsic magnetic susceptibility anisotropy (MSA) of the nucleobases in tRNA Val 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 tRNA Val . 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 two helical domains in tRNA Val .

Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings

“…Compared to values reported for proteins, these scalar products suggest fairly correlated datasets but for comparison, aligning tRNA in phospholipid bicelles, negatively charged bicelles, fd bacteriophage or C 8 E 5 /octanol mixtures leads to at best, a scalar product of 0.87 as compared to Pf1 phage 58 .…”

Structural Analysis of Multi-Helical RNAs by NMR–SAXS/WAXS: Application to the U4/U6 di-snRNA

“…A potential solution to this problem is to measure RDCs in two or more different alignment media that result in different alignment tensors [24]. However, in practice this has not been achieved because alignment media tend to sterically and electrostatically align nucleic acids with their longest helical axis along the z- component of the alignment tensor [25]. Although very few RNAs have been analyzed in this way, Pardi and coworkers showed that the 6 most commonly used alignment media resulted in very similar alignment tensors for tRNA Val [25], and thus do not solve the RDC degeneracy problem.…”

Information content of long-range NMR data for the characterization of conformational heterogeneity

“…They arise in the presence of partial molecular orientation, which can be achieved by interactions with alignment media surrounding the molecule (Tolman et al, 1995; Tjandra and Bax, 1997; Hansen et al, 1998; Losonczi and Prestegard, 1998; Ramirez and Bax, 1998; Wang et al, 1998; Al-Hashimi et al, 2000; Prestegard et al, 2000; Zweckstetter and Bax, 2001; Lakomek et al, 2008) and/or by the preferential orientation of the molecule itself in a magnetic field due to its magnetic susceptibility anisotropy (Lohman and Maclean, 1978; Tolman et al, 1995; Zhang et al, 2003; Latham et al, 2008; Ravera et al, 2014; Musiani et al, 2014). RDCs obtained by alignment induced by an external orienting medium, herein referred to as diamagnetic RDCs (dRDC), depend on the nature of the interactions of the biomolecule with the medium.…”