the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 10 Apr 2025
Can label or protein deuteration extend the phase relaxation time of Gd(III) spin labels?
Abstract. Pulse-dipolar electron paramagnetic resonance (PD-EPR) has emerged as an effective tool in structural biology, enabling distance measurements between spin labels attached to biomolecules. The sensitivity and the accessible distance range of these measurements are governed by the phase memory time (Tm) of the spin labels. Understanding the decoherence mechanisms affecting Tm is crucial for optimizing sample preparation and spin-label design. This study investigates the phase relaxation behavior of two Gd(III) spin-label complexes, Gd-PyMTA and Gd-TPMTA, with various degrees of deuteration. These two complexes have significantly different zero-field splitting (ZFS) parameters. Hahn echo decay and dynamical decoupling (DD) measurements were performed at W-band (95 GHz) in deuterated solvents (D2O/glycerol-d8), both for the free complexes and when conjugated to proteins. The impact of temperature, concentration, and field position within the EPR spectrum on Tm was examined. Results indicate that protons within 5 Å of the Gd(III) ion do not contribute to nuclear spin diffusion (NSD), and protein deuteration offers minimal enhancement in Tm. The dominant phase relaxation mechanisms identified at low concentrations were direct spin-lattice relaxation (T1) and transient ZFS fluctuations (tZFS). Dynamical decoupling (DD) measurements, using the Carr-Purcel sequence with ~140 refocusing pulses, resolved the presence of two populations: one with a long phase relaxation time, Tm,s, and the other with a short one, Tm,f. The dominating mechanism for the slowly relaxing population is direct-T1. Tm,s showed no concentration dependence and was longer by a factor of about 2 from Tm for both complexes. We tentatively assign the increase in Tm,s to full suppression of the residual indirect T1-induced NSD mechanism. For the fast relaxing population, Tm,f is shorter for Gd-TPMTA; therefore, we assign it to populations for which the tZFS mechanism dominates. Because of the relatively short T1 and the contribution of tZFS mechanism, protein deuteration does not significantly affect Tm.
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: final response (author comments only)
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RC1: 'Comment on mr-2025-6', Gunnar Jeschke, 29 Apr 2025
While understanding of decoherence of electron spins in nitroxide spin labels improved substantially during the past few years, data for Gd(III) spin labels were relatively scarce, in particular at high frequencies (95 GHz) where these label;s perform particularly well. The current manuscript addresses this gap in a systematic way and presents very interesting results. Experiments and data analysis are state-of-the-art, data quality is high, and the presentation is clear. I have little to criticize. The following points should be addressed in minor revision.
1. The manuscript would profit from a Table that provides an overview of Tm (or relaxation rate 1/Tm) for the various samples.
2. In the Conclusion (point 3), the authors discuss residual nuclear spin diffusion as a contribution to 1/Tm for C -> 0 and focus this discussion on only the label protons. A potential contribution from residual protons in the deuterated matrix should be mentioned.
3. In principle, simulation tools exist for predicting the contribution of the label protons to 1/Tm (at least for the Hahn echo/CP1 case). While such predictions may be beyond the scope of the current manucsript, I encourage the authors to address this issue in the future, also relating this to point 2 (residual matrix protons).
4. Given the importance of Gd(III) longitudinal relaxation as a contrubtion to 1/Tm, it would be helpful to include a paragraph with a few references to previous work on T1 of Gd(III).
5. Reference (Pannier et al., 2011) points to a 10th anniversary reprint of the original paper [ (Pannier et al., 2000, https://doi.org/10.1006/jmre.1999.1944)]. It might be more appropriate to cite the original paper.
Citation: https://doi.org/10.5194/mr-2025-6-RC1 -
RC2: 'Comment on mr-2025-6', Giuseppe Sicoli, 06 May 2025
The manuscript represents an interesting example of understanding to design and design for understanding related to the impact of the deuteration within the context of the relaxation processes. The message of the manuscript is clear and exhaustively delivered; however, for fulfilling the main ‘take-home’ message of the manuscript, some minor points can be revised:
- For the comparison of the values of 1/Tm,f and bf for different samples and temperatures (figure 7 C, F; please notice into the text at page 20 such figure has been referred as ‘5’), the authors refer to Figure 10 (page 22) for describing the contribution of the fast component. Besides the fairly constant behaviour for the PyMTA, it would be interesting to provide further elements to the discussion on the behaviour of TPMTA, exhibiting a completely different behaviour.
- The general approach proposed does not mention the effect of the pH, which may have an impact into the affinity of the two main ligands described; such an effect on the relaxation is probably beyond the scope of the manuscript, but it can be worth to mention also that tuneable parameter (i.e., pH).
- The assignment of dominating mechanism assigned for the two populations (slow and fast), as summarized on page 23 (lines 8-11) can eventually be reinforced by citing known structures where the T1 and tZFS are distinctively contributing to the relaxation paths. It may support the effect of the deuteration for ‘small’ molecules and validate the less pronounced effect on labelled proteins.
- Please notice that the authors refer to Figure 2D (page 10) but the capital letter on the figure 2 (page 11) is missing. A-B-C-D on the four panel must be revised.
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RC3: 'Comment on mr-2025-6', Alberto Collauto, 08 May 2025
Thanks to a detailed comparative analysis of the relaxation data of two Gd(III) complexes with different zero-field splitting parameters, the authors rationalise their finding that deuterating the protein only results in a very limited enhancement of the phase memory time, a crucial parameter in pulse dipolar spectroscopy measurements.
The manuscript is clearly written. The adopted systematic multi-technique approach to isolate the various contribution to electron spin decoherence, the provided data and the data analysis fully support the conclusions.The specific and technical comments are contained in the attached .pdf file.
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