Simultaneous determination of fast and slow dynamics in molecules using extreme CPMG relaxation dispersion experiments

Reddy, Jithender G.; Pratihar, Supriya; Ban, David; Frischkorn, Sebastian; Becker, Stefan; Griesinger, Christian; Lee, Dong Hoon

doi:10.1007/s10858-017-0155-0

Cited by 27 publications

(33 citation statements)

References 49 publications

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“…In addition the new experiment complements R 1ρ measurements on heteronuclei due to the characteristic of the 1 H to extend accessible timescales towards both faster and slower exchange processes, thereby closing the gap in time scales typically arising between CEST and R 1ρ methods for RNAs . The recently proposed 15 N E‐CPMG experiment closes this gap in isotopically labeled proteins and enables to characterize exchange processes between 500 and 40 000 Hz. Unfortunately, 15 N CPMG experiments are only applicable for labeled nucleic acids and deliver very few, Watson–Crick base paired probes.…”

Section: Figurementioning

confidence: 90%

Efficient Detection of Structure and Dynamics in Unlabeled RNAs: The SELOPE Approach

Schlagnitweit

Steiner

Karlsson

et al. 2018

Chemistry A European J

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The knowledge of structure and dynamics is crucial to explain the function of RNAs. While nuclear magnetic resonance (NMR) is well suited to probe these for complex biomolecules, it requires expensive, isotopically labeled samples, and long measurement times. Here we present SELOPE, a new robust, proton‐only NMR method that allows us to obtain site‐specific overview of structure and dynamics in an entire RNA molecule using an unlabeled sample. SELOPE simplifies assignment and allows for cost‐effective screening of the response of nucleic acids to physiological changes (e.g. ion concentration) or screening of drugs in a high throughput fashion. This single technique allows us to probe an unprecedented range of exchange time scales (the whole μs to ms motion range) with increased sensitivity, surpassing all current experiments to detect chemical exchange. For the first time we could describe an RNA excited state using an unlabeled RNA.

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Section: Figurementioning

confidence: 90%

Efficient Detection of Structure and Dynamics in Unlabeled RNAs: The SELOPE Approach

Schlagnitweit

Steiner

Karlsson

et al. 2018

Chemistry A European J

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“…More precise quantitation of the exchange lifetimes would require extension of the dispersion curve above ω 1 = 6 kHz, a regime often difficult to access due to excessive power deposition in the NMR probe. Recent work with the most advanced current cryoprobes allows the extension of this limit in favorable cases (Ban et al 2017;Reddy et al 2018).…”

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confidence: 99%

Coupling between conformational dynamics and catalytic function at the active site of the lead-dependent ribozyme

White

Sumita

Márquez

et al. 2018

RNA

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In common with other self-cleaving RNAs, the lead-dependent ribozyme (leadzyme) undergoes dynamic fluctuations to a chemically activated conformation. We explored the connection between conformational dynamics and self-cleavage function in the leadzyme using a combination of NMR spin-relaxation analysis of ribose groups and conformational restriction via chemical modification. The functional studies were performed with a -methanocarbacytidine modification that prevents fluctuations to C2'-endo conformations while maintaining an intact 2'-hydroxyl nucleophile. Spin-relaxation data demonstrate that the active-site Cyt-6 undergoes conformational exchange attributed to sampling of a minor C2'-endo state with an exchange lifetime on the order of microseconds to tens of microseconds. A conformationally restricted species in which the fluctuations to the minor species are interrupted shows a drastic decrease in self-cleavage activity. Taken together, these data indicate that dynamic sampling of a minor species at the active site of this ribozyme, and likely of related naturally occurring motifs, is strongly coupled to catalytic function. The combination of NMR dynamics analysis with functional probing via conformational restriction is a general methodology for dissecting dynamics-function relationships in RNA.

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“…The chemical shift of the investigated atoms can then be determined by combining Δω with information obtained from an HMQC spectrum, which in turn can be used to determine the solution structure of the excited state . More recently, modified CPMG sequences have allowed broadening of the time‐scales available to probe conformational exchange in proteins down to ∼25 μs phenomena ( k ex ∼40000 s −1 ), or to gather additional information on the structure of the metastable states, such as residual dipolar couplings (RDC), residual chemical shift anisotropy (CSA), order parameters, and diffusion constants …”

Section: New and Promising Techniques To Investigate Enzyme Dynamicsmentioning

confidence: 99%

Enzyme Dynamics: Looking Beyond a Single Structure

et al. 2020

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Simultaneous determination of fast and slow dynamics in molecules using extreme CPMG relaxation dispersion experiments

Cited by 27 publications

References 49 publications

Efficient Detection of Structure and Dynamics in Unlabeled RNAs: The SELOPE Approach

Efficient Detection of Structure and Dynamics in Unlabeled RNAs: The SELOPE Approach

Coupling between conformational dynamics and catalytic function at the active site of the lead-dependent ribozyme

Enzyme Dynamics: Looking Beyond a Single Structure

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