TEDOR with adiabatic inversion pulses: Resonance assignments of 13C/15N labelled RNAs

Riedel, Kerstin; Leppert, Jörg; Ohlenschläger, Oliver; Görlach, Matthias; Ramachandran, Ramadurai

doi:10.1007/s10858-004-6066-x

Cited by 33 publications

(25 citation statements)

References 38 publications

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“…Chemical shift assignments were achieved via 3D 15 N- 13 C- 13 C spectra 25,26 using one bond 15 N- 13 C ZF-TEDOR mixing followed by 13 C- 13 C RFDR mixing, similar to previously described 2D experiments 27 and the commonly used N-C cross-polarization (DCP) based experiments. 28–31 The sequence is depicted in Figure 3 and allows both the NCOCX and NCACX connectivity experiments to be efficiently acquired in a single spectrum (Figure 4).…”

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confidence: 99%

Magic-Angle-Spinning NMR of the Drug Resistant S31N M2 Proton Transporter from Influenza A

et al. 2012

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We report chemical shift assignments of the drug-resistant S31N mutant of M218-60 determined with magic angle spinning (MAS) 3D spectra acquired with a 15N-13C ZF-TEDOR transfer followed by 13C-13C mixing by RFDR. The MAS spectra reveal two sets of resonances, indicating that the tetramer assembles as a dimer of dimers, similar to the wild type channel. The two sets of chemical shifts are shown to be in close proximity at residue H37, and assignments reveal a difference in the helix torsion angles, as predicted by TALOS+, for the key resistance residue N31. In contrast to wild type M218-60, chemical shift changes are minimal with addition of the inhibitor rimantadine, suggesting that the drug does not bind to S31N.

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confidence: 99%

Magic-Angle-Spinning NMR of the Drug Resistant S31N M2 Proton Transporter from Influenza A

et al. 2012

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“…However, TEDOR has not been widely applied for one-bond transfers in 3D NCC experiments. Although a 2D version of the NCC transfer experiment has been used for assignment of RNAs (Riedel et al 2005), and the 3D version has recently been implemented for a membrane protein (Andreas et al 2012), neither of these studies addressed the merits of the TEDOR transfer step relative to other N-C transfer mechanisms.…”

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Efficient resonance assignment of proteins in MAS NMR by simultaneous intra- and inter-residue 3D correlation spectroscopy

et al. 2013

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Resonance assignment is the first step in NMR structure determination. For magic angle spinning NMR, this is typically achieved with a set of heteronuclear correlation experiments (NCaCX, NCOCX, CONCa) that utilize SPECIFIC-CP 15N-13C transfers. However, the SPECIFIC-CP transfer efficiency is often compromised by molecular dynamics and probe performance. Here we show that one-bond ZF-TEDOR 15N-13C transfers provide simultaneous NCO and NCa transfers with at least as much sensitivity as SPECIFIC-CP for some non-crystalline samples. Furthermore, a 3D TEDOR-CC experiment provides heteronuclear sidechains correlations and robustness with respect to proton decoupling and radiofrequency power instabilities. We demonstrate transfer efficiencies and connectivities by application of 3D ZF-TEDOR-DARR to a model microcrystalline protein, GB1, and a less ideal system, GvpA in intact gas vesicles.

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“…The resonance assignments indicated are based on our recent studies. [5,14] The expected crosspeaks arising from direct or relayed magnetization transfers originating from sugar proton-sugar proton dipolar interactions and corresponding to intranucleotide proton-proton distances of < 3.0 are seen. By contrast, crosspeaks between the aromatic and sugar C1' and C4' carbon atoms, which would reflect the spatial proximity of the corresponding attached protons, are essentially absent.…”

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Constraints on the Structure of (CUG)₉₇ RNA from Magic‐Angle‐Spinning Solid‐State NMR Spectroscopy

et al. 2006

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Expansions of short nucleotide sequence repeats are associated with a number of neuromuscular diseases. [1][2][3] CTG triplet repeat expansions in the 3' noncoding region of the myotonic dystrophy protein kinase (DMPK) gene give rise to transcripts harboring CUG triplet repeat expansions on the RNA level. Repeats containing > 50 CUG triplets cause in trans-dominant fashion the most frequent form of adult-onset muscular dystrophy (DM1). The current model for DM1 pathogenesis strongly suggests that such repeats fold into large stable double-stranded RNA hairpins, which bind and sequester muscleblind (MBNL) proteins that are involved in the alternative splicing of a number of pre-mRNAs. As a consequence, the MBNL proteins are unavailable to the splicing machinery, and a number of important muscular premRNAs, for example, for the chloride channel ClC-1 and the insulin receptor, are aberrantly spliced; this process ultimately leads to the clinical manifestations of DM1.To decipher the structural basis of DM1, which could potentially permit the development of suitable drugs that would interfere with the sequestration of MBNL proteins by CUG repeats, we have recently initiated, as a first step, a magic-angle-spinning (MAS) solid-state NMR study of a % 100-kDa RNA composed of 97 CUG repeats ((CUG) 97 ). 15 N-15 N chemical-shift correlation experiments have enabled us to show the presence of canonical GC base pairs in this RNA. [4] In addition, analysis of the observed 13 C chemical shifts for the sugar carbon atoms suggested that (CUG) 97 adopts an A-form helix conformation with a C3'-endo sugar pucker and an anti conformation of the glycosidic torsion angle c.[5] Herein, we have explored the possibility of obtaining structural information directly by exploiting the dependence of inter-and intranucleotide 1 H-1 H distances on RNA conformation. Since the extraction of 1 H-1 H distances by direct 1 H observation techniques is still difficult in the solid state, we have utilized in this study the potential of protonproton dipolar-coupling-mediated chemical-shift correlation spectroscopy of low-gamma nuclei [6][7][8][9][10][11][12][13] for mapping the spatial proximity of the sugar and aromatic protons in (CUG) 97 .The radio frequency (RF) pulse sequence [13] and a schematic representation of the double-stranded (CUG) 97 employed are shown in Figure 1. Longitudinal 1 H magnetization exchange mediated by proton-proton dipolar coupling is allowed to take place during the spin diffusion period t mix . The experiment is carried out with a very short CP contact time ( % 100 ms) and a proton spin diffusion mixing time, t mix , of 100-200 ms. This time regime minimizes relayed magnetization transfers during the CP and t mix periods and, hence, crosspeaks with appreciable intensities are expected only between proton-attached 13 C sites that are connected by 1 H-1 H distances of less than % 3 . [8][9][10][11][12][13] 13 C homonuclear isotropic chemical-shift correlation spectra of a uniformly { 15 N, 13 C}-labeled sample of (CUG)...

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TEDOR with adiabatic inversion pulses: Resonance assignments of 13C/15N labelled RNAs

Cited by 33 publications

References 38 publications

Magic-Angle-Spinning NMR of the Drug Resistant S31N M2 Proton Transporter from Influenza A

Magic-Angle-Spinning NMR of the Drug Resistant S31N M2 Proton Transporter from Influenza A

Efficient resonance assignment of proteins in MAS NMR by simultaneous intra- and inter-residue 3D correlation spectroscopy

Constraints on the Structure of (CUG)₉₇ RNA from Magic‐Angle‐Spinning Solid‐State NMR Spectroscopy

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TEDOR with adiabatic inversion pulses: Resonance assignments of 13C/15N labelled RNAs

Cited by 33 publications

References 38 publications

Magic-Angle-Spinning NMR of the Drug Resistant S31N M2 Proton Transporter from Influenza A

Magic-Angle-Spinning NMR of the Drug Resistant S31N M2 Proton Transporter from Influenza A

Efficient resonance assignment of proteins in MAS NMR by simultaneous intra- and inter-residue 3D correlation spectroscopy

Constraints on the Structure of (CUG)97 RNA from Magic‐Angle‐Spinning Solid‐State NMR Spectroscopy

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Constraints on the Structure of (CUG)₉₇ RNA from Magic‐Angle‐Spinning Solid‐State NMR Spectroscopy