the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Inter-residue through-space scalar 19F–19F couplings between CH2F groups in a protein
Abstract. Using cell-free protein synthesis, the protein G B1-domain (GB1) was prepared with uniform high-level substitution of leucine by (2S,4S)-5-fluoroleucine, (2S,4R)-5-fluoroleucine, or 5,5’-difluoroleucine. 19F nuclear magnetic resonance (NMR) spectra showed chemical shift ranges spanning more than 9 ppm. Through-space scalar 19F-19F couplings between CH2F groups arising from transient fluorine-fluorine contacts are readily manifested in [19F,19F]-TOCSY spectra. The 19F chemical shifts correlate with the three-bond 1H–19F couplings (3JHF), confirming the γ-gauche effect as the predominant determinant of the 19F chemical shifts of the CH2F groups. Different 3JHF couplings of different CH2F groups indicate that the rotation of the CH2F groups can be sufficiently restricted in different protein environments to result in the preferential population of a single rotamer. The 3JHF couplings also show that CH2F groups populate the different rotameric states differently in the 5,5’-difluoroleucine residues than in the monofluoroleucine analogues, showing that two CH2F groups in close proximity influence each other’s conformation. Nonetheless, the 19F resonances of the Cδ1H2F and Cδ2H2F groups of difluoroleucine residues can be assigned stereospecifically with good confidence by comparison with the 19F chemical shifts of the enantiomerically pure fluoroleucines. 1H-19F NOEs observed with water indicate hydration with subnanosecond residence times.
Competing interests: At least one of the (co-)authors is a member of the editorial board of Magnetic Resonance.
Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims made in the text, published maps, institutional affiliations, or any other geographical representation in this preprint. The responsibility to include appropriate place names lies with the authors.- Preprint
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Status: open (until 16 Apr 2025)
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EC1: 'Comment on mr-2025-4', Michael Summers, 19 Mar 2025
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This is an interesting study that is likely to prompt others to use this approach to study protein structure and macromolecular interactions. One quick question: Were the authors able to detect 19F-19F scalar couplings in their constructs containing 19F- and 2H-labeled leucines? I ask because others (long ago) detected scalar couplings between methyl protons and 113Cd, mediated by Methyl-to-Sulfur(Cys) "hydrogen bonding" (or better, orbital overlap). It seems chemically more plausible that the F-F J couplings are mediated by 3-bond CH--F orbital overlap compared to direct F--F orbital overlap. Perhaps their calculations address this possibility?
Citation: https://doi.org/10.5194/mr-2025-4-EC1 -
AC1: 'Reply on EC1', Gottfried Otting, 21 Mar 2025
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Thank you for the thought-provoking comments! The supplement of this author response explains why we think that the through-space scalar 19F-19F couplings observed in our work come about by direct contacts rather than some indirect mechanism.
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EC2: 'Reply on AC1', Michael Summers, 23 Mar 2025
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Thanks for providing data for the 2H,19F-labeled sample and describing your inability to detect 19F scalar couplings to other nuclei. I agree that these findings make it very unlikely that the observed 19F-19F couplings are mediated by H-bond-like couplings. Nice work!
Citation: https://doi.org/10.5194/mr-2025-4-EC2
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EC2: 'Reply on AC1', Michael Summers, 23 Mar 2025
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AC1: 'Reply on EC1', Gottfried Otting, 21 Mar 2025
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RC1: 'Comment on mr-2025-4', Ad Bax, 21 Mar 2025
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The manuscript describes a highly novel and innovative 19F-based study of a small model protein, GB1, aiming to form a basis for future applications to important biological problems. 19F NMR is known to be a sensitive probe for both structure and dynamics, and results in the present study amplify that message. The authors show clear-cut through-space 19F-19F J couplings between methyl signals, TOCSY spectra, weak 19F-19F NOEs that have a very different distance dependence compared to 19F-19F J couplings, heteronuclear intramolecular NOEs between 1H and 19F, as well as 19F to water NOEs reporting on hydration.
This work presents a true smorgasbord of what can be achieved and learned by advanced 19F NMR of specifically labeled proteins, and significantly expands on their recent PpiB paper.
I enthusiastically recommend publication of this interesting work after the authors address a few minor, mostly trivial issues.
- I’m a bit confused about the gamma gauche effect when talking about two monofluorinated methyl groups in Leu. Both 19F nuclei can simultaneously be trans relative to Cgamma, so it’s not clear that this helps with stereo assignment, even though the correlation between JHF and 19F shift clearly shows it to be correct. Is it conceivable that Calpha_Cdelta gamma gauche effects contribute to the 19F chemical shift (as they do for 13Cdelta)?
- For the HOESY measurements, I suspect the NOE effect to be very sensitive to internal motion due to the closeness of wH and wF. Heteronuclear 1H-19F NOE can be negative or positive, depending on applicable spectral densities and some comments may be helpful.
- 19F line widths are reported to be 7-15 Hz, which corresponds to R2 values of 20-40/s, but this seems fast considering the 60-ms TOCSY mixing times used. Could incomplete decoupling or isotope effects contribute to these line widths? Perhaps a R1rho number would be helpful.
- Line 146-147: “faster rotation of the CH2F group about the Cgamma-Cdelta bond results in slower transverse relaxation”. This may well be true, but the magnitude of this effect seems larger than expected considering the modest chemical shift difference of ~10ppm. Could crank-shaft sidechain motions, previously suggested to be responsible for different Cdelta 13C relaxation rates, play a role?
- Line 199: “different” from what? Perhaps use “multiple”?
- Line 201: “greater conformational freedom than suggested by 3GB1”. This is a bit of a philosophical issue, but the width of an “NMR bundle” does not reflect motional freedom but the certainty at which the structure that agrees best with NMR restraints can be determined. If not, measuring fewer restraints would make the protein more dynamic.
- Line 322: “the third example of the gamma-gauche effect”. Probably correct, but perhaps useful to remind the reader of how commonly this is used in 13C analysis, including proteins (e.g. https://link.springer.com/article/10.1007/BF00202043 )
- There is a considerable amount of older literature on TS-JFF couplings, with an empirically determined very steep distance dependence. See e.g. Bakhmutov and references therein. Perhaps including some reference to this historic work would be helpful, e.g. https://doi.org/10.1002/mrc.1260231117
- Lines 358-362, c=chi; d=delta
- Please include the RF field strength and mixing scheme (DIPSI?) used for the TOCSY spectrum.
- Can the authors provide approximate TS-JHH values based on the cross/diagonal peak ratios?
- Trivialities: Spell out CFPS upon first use; Juszewski is really Kuszewski (3 times).
Citation: https://doi.org/10.5194/mr-2025-4-RC1
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