Activation-pathway transitions in human voltage-gated proton channels revealed by a non-canonical fluorescent amino acid

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1. 

   Version published to 10.7554/elife.85836 on eLife

   Jan 25, 2023
2. 

   Biophysics Colab

   Dec 23, 2022

   Endorsement statement (22 December 2022)

   The preprint by Suarez-Delgado et al. explores the mechanisms by which the Hv1 voltage-activated proton channel is dependent upon transmembrane voltage and pH by incorporating the small fluorescent non-canonical amino acid Anap into the S4 helix and monitoring its fluorescence. Anap spectra suggest the fluorophore resides in an aqueous environment and moves relative to a quenching aromatic residue (F150) in the S2 helix upon depolarization. Two kinetically distinct components of fluorescence change support the presence of at least three conformational states in the activation pathway of Hv1. Measurements using different pH gradients suggest that S4 movement and channel opening are similarly affected by pH gradients. This is the first study to incorporate Anap into Hv1, and provide a rigorous and …

   Endorsement statement (22 December 2022)

   The preprint by Suarez-Delgado et al. explores the mechanisms by which the Hv1 voltage-activated proton channel is dependent upon transmembrane voltage and pH by incorporating the small fluorescent non-canonical amino acid Anap into the S4 helix and monitoring its fluorescence. Anap spectra suggest the fluorophore resides in an aqueous environment and moves relative to a quenching aromatic residue (F150) in the S2 helix upon depolarization. Two kinetically distinct components of fluorescence change support the presence of at least three conformational states in the activation pathway of Hv1. Measurements using different pH gradients suggest that S4 movement and channel opening are similarly affected by pH gradients. This is the first study to incorporate Anap into Hv1, and provide a rigorous and thorough characterization of how the fluorophore can be used to explore mechanisms of gating and regulation, paving the way for future studies. The work will be of interest to physiologists and biophysicists investigating membrane protein mechanisms using non-canonical fluorescent amino acids.

   (This endorsement by Biophysics Colab refers to version 2 of this preprint, which has been revised in response to peer review of version 1.)

   Read the original source
3. 

   Biophysics Colab

   Nov 29, 2022

   Authors' response (28 November 2022)

   GENERAL ASSESSMENT

   This interesting preprint by Suárez-Delgado et al. explores the mechanism by which activation of the Hv1 voltage-activated proton channel is dependent upon both the voltage and pH difference across the membrane. The authors are the first to incorporate the fluorescent unnatural amino acid, Anap, into the extracellular regions of the S4 helix of human Hv1 to monitor transitions of S4 upon changes in voltage or pH. The authors first checked that Anap is pH insensitive for practical use in Hv1, where changes in local pH are known to occur when the voltage sensor activates and the proton pore opens. Anap was incorporated at positions throughout the S3-S4 linker and the extracellular end of S4 (up to the 202nd residue) of hHv1 and some positions showed clear voltage-dependent changes …

   Authors' response (28 November 2022)

   GENERAL ASSESSMENT

   This interesting preprint by Suárez-Delgado et al. explores the mechanism by which activation of the Hv1 voltage-activated proton channel is dependent upon both the voltage and pH difference across the membrane. The authors are the first to incorporate the fluorescent unnatural amino acid, Anap, into the extracellular regions of the S4 helix of human Hv1 to monitor transitions of S4 upon changes in voltage or pH. The authors first checked that Anap is pH insensitive for practical use in Hv1, where changes in local pH are known to occur when the voltage sensor activates and the proton pore opens. Anap was incorporated at positions throughout the S3-S4 linker and the extracellular end of S4 (up to the 202nd residue) of hHv1 and some positions showed clear voltage-dependent changes in fluorescence intensity. The authors also obtained fluorescence spectra at different voltages and observed no spectral shifts, raising the possibility that voltage dependent changes in fluorescence intensity could primarily be due to fluorescence quenching. Upon mutation of F150, the Anap signal at the resting membrane voltage increased, suggesting dequenching upon removal of F150. The authors also discovered that the kinetics of Anap fluorescence upon membrane repolarization have two phases (rapid and slow) under certain pH conditions and that there is a pH-dependent negative shift of the conductance-voltage (G-V) relation compared with the fluorescence-voltage (F-V) relation in some mutants. The biphasic kinetics of the fluorescence decay upon repolarization were explained by modelling a slower transition of return from intermediate resting state to a resting state. The pH-dependent shift of the G-V relation from the F-V relation provides insight into mechanisms of ΔpH-dependent gating of Hv1, a longstanding enigma. Overall, the approaches are rigorous, the figures show important results, and this work paves the way for the use of Anap fluorescence to study Hv1 gating and modulation.

   We thank the reviewers for the careful reading and assessment of our manuscript and for the constructive criticism. We have tried to respond to all the essential revisions, both by rewriting sections and performing some experiments or new analysis. Below we respond one by one to all the points raised. Please also note that we have added an author to the manuscript, who has carried out new experiments included in this revised version of the preprint.

   RECOMMENDATIONS

   Revisions essential for endorsement:

   1. In its current form, the narrative of the preprint has two threads. One on the mechanisms of Anap fluorescence changes (mainly quenching) and another on a previously unappreciated transition of the voltage sensor, as revealed by Anap. Our impression is that the preprint suffers somewhat from this split focus, which could be resolved by explaining why Anap was used to explore voltage sensor activation in Hv1 in the introduction. Perhaps the authors could also explain the advantage of smaller sized fluorophores compared to other maleimide-based fluorophores earlier in the introduction, or the utility of being able to insert Anap into transmembrane segments. The authors should more clearly point out how they exploited the advantages of Anap as a tool in this study. It would furthermore be helpful to discuss previous studies using nongenetic tools for VCF and spell out how they have delineated key aspects of Hv1, which would help to emphasize how several positions studied here (for example, 201 and 202) could not be labelled with cysteine-based fluorophores.

   We think that this is a very useful suggestion and we have expanded the introduction to more pointedly indicate the contributions of previous voltage-clamp fluorometry experiments in Hv1 channels and to clearly explain why we chose to pursue the use of a genetically-encoded small fluorophore such as Anap.

   1. We think the authors should be cautious about understanding the physicochemical nature of Anap using prodan as a model. It would be helpful to discuss the possibility that undetected spectral shifts due to a nonquenching mechanism could be overlooked, even though major signal changes can be explained by fluorescence quenching in their data. Regarding the mechanisms of remaining voltage-dependent fluorescence changes of F150A-A197Anap, it would be helpful for the authors to suggest possible ideas about which residues might account for remaining signals.

   The beautiful spectral data for Anap is impressive. However, the physicochemical basis of the fluorescence change of Anap cannot be understood by simple extension of findings for prodan, which shows structural similarity to Anap. Our understanding is that changes in Anap fluorescence can only reveal a change in the structural relationship between Anap and one of its neighbors because the physicochemical basis of Anap fluorescence is complicated. For example, fluorescence could also be affected by the electrostatic environment, stretch of peptide bond, etc. Previous studies, including those of TRP channels, showed that the kind of environmental changes that Anap faces in ion channels do not necessarily induce large spectral shifts, unlike in cell-free spectral analyses using distinct solvents. Further, only minor shifts in spectra occur upon local structural change, as seen in previous work including Xu et al. Nat. Commun. 2020 11:3790. Such minor shifts could be perhaps overlooked even when Anap is incorporated into S4 and exposed to environmental change. Therefore, it is not easy to decode the physicochemical basis of Anap fluorescence changes. F150A-A197Anap has increased fluorescence and no change in spectral pattern, leading the authors to conclude that F150 quenches Anap fluorescence of A197 position. However, a significant amount of fluorescence change still occurs upon changes in membrane potential after F150 is changed to alanine (Figure 4). It is very likely that quenching is not the only mechanism underlying the observed voltage induced change of Anap fluorescence of Hv1. The authors suggest that remaining voltage-dependent fluorescence change of F150A-A197Anap could be due to interaction with other aromatic residues, but this has not been tested.

   Thank you for pointing out our oversimplified discussion of the mechanisms of Anap fluorescence changes in Hv1 channels. We have taken into account your comments and present a more nuanced and toned-down discussion of the possible mechanisms at play in our experimental system.

   1. The current version of the preprint is missing important control experiments, ideally performed using western blots to measure protein expression or, if that is not possible, proton current and fluorescence measurements, to demonstrate that protein expression or functional channels are not seen for all mutants in the absence of ANAP (but in the presence of the tRNA and Rs construct). A similar control for imaging would be to use ANAP alone without encoding.

   We thank the reviewers for this recommendation. We show that the number of cells showing mCherry fluorescence is greatly diminished in the absence of L-Anap, but in the presence of the tRNA and synthetase. As suggested, we have included results of control experiments in which we attempted to record currents from cells expressing the constructs: F150A-A197tag, Q191tag, A197tag and L201tag co-expressed with the tRNA and synthetase-coding plasmid (pANAP) and in the absence of L-Anap. We struggled to find red fluorescing cells and recorded currents from a relatively small number of these cells, most of which was leak current. We now include these data in Figure 1-Supplement 1B. These control experiments show that there is very little leakage of expression of channels that did not incorporate Anap.

   1. Aromatics in the S4 segment were ruled out as potential quenchers on the assumption that they would move together with Anap during gating. It should be noted, however, that Hv1 is a dimer and therefore a fluorophore attached to S4 in one subunit could be quenched by S4 aromatics in the neighboring subunit if were close to the dimer interface. In Fujiwara et al. J. Gen. Physiol. 2014 143:377-386, for example, W207 does not appear very far from labeled positions in the adjacent S4. This possibility should be mentioned in the discussion.

   We appreciate the reviewers' concern regarding the role of other aromatic residues near Anap incorporation sites, especially the ones close to the subunit interface given that Hv1 is a dimer. We now mention the possibility that other residues could be quenching groups, especially given the fact that some quenching remains in the double mutant F150A-A197Anap (line 272 in results and line 432 in discussion). We have also included a new analysis of the ratio of Anap/mCherry fluorescence (at resting membrane potential) for all insertion sites. This shows a decreased ratio as Anap gets inserted in residues closer to the c-terminus of S4, which is evidence of a quenching group located near the center of the transmembrane domains (Figure 4-Supplement 1).

   1. It is not clear whether the Anap spectra purely represent Hv1 incorporated into the plasma membrane or perhaps include signals from the cytoplasm or channels in internal membranes (whether assembled or incompletely assembled). It would be helpful to provide a more complete presentation of the data obtained and to provide more information in the Methods Section. In the Methods section, it is stated "The spectra of both fluorophores (Anap and mCherry) were recorded by measuring line scans of the spectral image of the cell membrane, and the background fluorescence from a region of the image without cells was subtracted". How are signals from cell membranes specified in this method being discriminated from those associated with the cytoplasm and intracellular membranes? If spectral data include signals from free Anap in the cytoplasm or Hv1 in intracellular membranes, spectral shifts upon membrane potential changes will be difficult to detect, even when Anap is incorporated into Hv1 and senses environmental change by voltage-induced conformational change. In Figure 3E, wavelength spectra were shown as standardized signals for different voltages. Amplitude change would be demonstrated (spectrum at different voltages without standardization should be shown).

   We appreciate the concern related to the origin of the fluorescence signals and we have improved both the presentation and the associated figures. Since this is also a concern for the experiments that determined the pH-dependence of Anap incorporated at position Q191, we have included a figure supplement 1 to Figure 2 in which we explain how the membrane was visualized. We use mCherry fluoresce as an indication of plasma membrane-associated channels, since its red fluorescence is easier to detect in the membrane than Anap fluorescence (even though cytoplasm dialysis in whole-cell should diminish the amount of free Anap, it is difficult to distinguish Anap fluorescence in the membrane by itself). Once the membrane associated mCherry fluorescence is detected, the measurement of the spectrum from a very small membrane area is insured because the spectrograph slit delimits light collection to a very small vertical area and the horizontal line scan further limits light measurement. These procedures are now made explicit in methods section and supplementary figure mentioned before. Moreover, we explain that they were also followed in experiments where the cell was under voltage-clamp. The spectral data in Figure 3E is now presented without normalization to show the voltage-dependent change in amplitude without changes in peak emission wavelength.

   In Figure 4, spectra were compared between A197Anap and F150A-A197Anap, showing increases of fluorescence in F150A-A197Anap. Was this signal measured at resting membrane potential? How does the spectrum change when the membrane potential is changed?

   As in the experiments of figure 1E, the spectra were obtained in non-patched cells. Thus, the signal was measured at the HEK cell resting potential (~ -30 mV) and a ΔpH ≈ 0.2. We have now incorporated that information in the methods section and the figure description. On the other hand, we did not perform experiments measuring the double mutant spectra at different voltage steps, so we cannot respond to the second question.

   Rationales for the confirmation of signals originating from the cell surface for Hv1 Anap might include the observations that: a) some mutants showed slightly different spectral patterns (in particular, Q191Anap showed a small hump at longer wavelengths, which is proposed to represent FRET between mCherry and Anap) and b) signal intensity was voltage dependent (if signals originate from endomembranes, they should not be voltage dependent). Mentioning these two points earlier in the text might help to alleviate concerns about the location of the protein that contributes to the measured signals.

   These are great suggestions and we have incorporated them to the text (lines 156, 190 and 216 Results section), along with a better explanation of procedures followed to measure mostly membrane-associated fluorescence (see new Figure 2-Supplement 1).

   1. In Fig 5, the fluorescence kinetics do not really match the current activation kinetics for panels A, B, and C. Is there an explanation for this mismatch? It would be helpful to have the fitted data in the figure. A more thorough comparison of the kinetics of currents and fluorescence would be helpful throughout the study.

   We believe that the kinetics of fluorescence and current does not match because the current activation rate is overestimated due to a small amount of proton depletion present in recordings from large currents. This is an unavoidable problem in proton current recordings, even with the high concentration of proton buffer used in our experiments and the long time-intervals between each voltage pulse. For this reason, we did not undertake a systematic exploration of kinetics. Nonetheless, the current and fluorescence rates are very close and have the same voltage dependence, indicating a close correlation between voltage-sensor movement and current activation. We now explain this limitation in the manuscript text (line 223 and 327, results section).

   1. Which construct of hHv1 was used to obtain the data in Figure 6? Unless we missed it, this information is not provided in the text or figure legend. Is it for L201Anap? This figure also shows an intriguing finding that the G-V relationship is negatively shifted from the F-V relationship at pHo7-pHi7 but not at pHo5.5-pHi5.5. A shifted G-V relation with the same ΔpH contrasts with what has been reported in other papers. However, the authors did not really discuss this surprising finding in the light of previous references. Could the shift of the G-V relation between two pH conditions with the same ΔpH be due to any position-specific effect of Anap? If Figure 6 represents L201Anap mutant, the presence of Anap at L201 probably makes such shift of G-V curve in Figure 6C? The authors should openly discuss this finding in relation to what has been reported in the literature.

   Yes, construct L201Anap was used in Figure 6. This is stated now in the figure legend and in the corresponding main text. We agree that the leftward shift of the GV with respect to the FV in pHi7-pHo7 is an intriguing finding, suggesting that coupling between S4 movement and proton permeation can be regulated by the absolute value of the pH. We discuss this in the results section. The DeCoursey group has shown evidence in W207 mutants of hHv1 that the absolute value of pH can modulate the voltage dependence of the conductance. Although we had mentioned these results, we now mention them more prominently and also discuss the possibility that this might be a unique feature of introducing Anap at L201.

   1. The authors suggest that the small hump near 600 nm in Figure 1E represents FRET between Anap and mCherry. It is surprising that FRET can take place across the membrane. Can the authors point to another case of FRET taking place across a cell membrane? One possibility might be that misfolded proteins place mCherry and Anap close to each other. It is also curious that only A191Anap did not show such a FRET-like signal. Also, if there is FRET, why wouldn't this also contribute to the voltage-dependent changes in fluorescence?

   We thank the reviewers for bringing up this point. Based on published data, we assumed that mCherry could not be excited by 405 nm radiation, thus our conclusion that the observed emission near 604 nm is FRET between Anap and mCherry. We have now measured the excitation of the Hv1-mCherry construct and observe that the 405 nm laser is capable of exciting mCherry and produced ~2 % emission (as compared to 514 nm excitation), which is almost the same as that observed for the Hv1Anap-mCherry channels. We now conclude that the second hump in the emission spectrum near 600 nm is due to direct excitation of mCherry.

   On the other hand, FRET across the membrane has been demonstrated for the membrane-bound hydrophobic anion dipicrylamine and membrane-anchored GFP (Chanda, et al. A hybrid approach to measuring electrical activity in genetically specified neurons. Nature neuroscience, 2005, vol. 8, no 11, p. 1619-1626.) and dipicrylamine and GFP in the c-terminus of CNG channels (Taraska & Zagotta, Structural dynamics in the gating ring of cyclic nucleotide–gated ion channels. Nature structural & molecular biology, 2007, vol. 14, no 9, p. 854). Finally, single-molecule FRET between dyes placed extracellularly and intracellularly in Hv1 channels has been demonstrated (Han et al. eLife 2022;11:e73093. DOI: https:// doi. org/ 10. 7554/ eLife. 73093).

   A191Anap shows the hump at ~600 nm, but we think it's less evident because Anap at 191 is less quenched (see Figure 4-Supplement 1 and answer to point 4 above).

   1. F150A-A197Anap shows a leftward shift of the F-V relation compared with the G-V relation only when ΔpH=1. Another unusual finding with F150A-A197Anap is the very small shift of the G-V relation between ΔpH=0 and ΔpH=1, when other reports in the literature suggest it should be 40 mV or more. Are these peculiar properties simply due to the absence of Phe at position 150, which might play a critical role in gating as one of the hydrophobic plugs of Hv1? To address this possibility, it would be ideal to compare different ΔpH values with and without F150 when Anap is incorporated at a different position (such as L201Anap). Regardless, it would be helpful to discuss this point.

   We now discuss these changes in the discussion (lines 440-446).

   1. In Figure 1E, I202Anap exhibits a blue shift in its spectrum suggesting the environment of Anap on I202 is more hydrophobic than the other sites. We presume these spectra were obtained at a negative membrane voltage, but the text or legend should clearly state how these were obtained. The authors should also explain whether the whole cell or edge was imaged. If these are at negative membrane voltages, might the Anap spectrum shift to higher wavelengths (i.e. more hydrophilic) when the membrane is depolarized? Did the authors find any spectral shift for I202Anap when doing a similar test as depicted in Figure 3E?

   Yes, the spectrum of I202Anap was obtained at the resting potential (~ -30 mV), as were all spectra in Figure 1E. We now indicate this clearly in the methods section and in the figure legend. Fluorescence was measured from the membrane region as indicated by mCherry fluorescence and as illustrated in Figure 2-Supplement 1. We did not explore this mutant further and we cannot answer the question of whether a depolarizing potential might produce a red shift of the spectrum.

   1. In Figure 3E, spectra are shown as normalized signals for different voltages, but an amplitude change should also be demonstrated by providing raw spectra at different voltages.

   We have changed figure 3E to show non-normalized data that now show the increase in fluorescence intensity and no wavelength shift in the fluorescence spectrum of Anap (see also response to point 5).

   1. In Figure 4, spectra are compared between A197Anap and F150A-A197Anap, showing increase of fluorescence in F150A-A197Anap. Were these obtained at a negative membrane voltage? How do these spectra change when membrane potential is changed?

   See response to point 4 of "Revisions essential for endorsement" section.

   Additional suggestions for the authors to consider:

   1. The authors propose that Anap fluorescence tracks an S4 movement involved in the opening of the channel. They also argue that the existence of more than one open state could explain why the increase in florescence upon depolarization lags the proton current in most cases. While they convincingly show that Anap is not pH sensitive per se, when incorporated into the protein, the fluorescence efficiency of the fluorophore could still be affected by protonation of channel residues in the immediate environment when the channel opens, even after S4 has completed its movement. To address this alternative explanation, the authors could use Hv1 mutants with strongly reduced proton conductance. Channels bearing mutations corresponding to N214R or D112N were used successfully to isolate Hv1 gating currents from the much larger proton currents (De La Rosa & Ramsey, Biophys. J. 2018 114:2844-2854; Carmona et al. PNAS 2018 115:9240-9245; Carmona et al. PNAS 2021 118: e2025556118). Perhaps, they could be used with patch clamp fluorometry as well?

   This is an interesting suggestion that could be explored in a follow up study.

   1. The data showing that Hv1-197Anap is quenched by Phe at position 150 are very nice. Yet, it would be useful to show that the quenching is specific to F150 using a negative control. F149, for instance, is just next to F150 but points in a different direction, so its mutation to alanine should not affect Hv1-197Anap fluorescence.

   This is an interesting suggestion, but, as suggested by reviewers, we think there is a possibility that other aromatic residues could contribute to quenching. Given the absence of a reliable structure for Hv1, prediction of the relative positions of any resides is very difficult and thus we did not attempt the suggested experiment.

   1. A major finding of this work is the identification of a slow kinetic component that is highly sensitive to ΔpH. Earlier studies found that the ability of Hv1 to sense ΔpH is altered by some channel modifications, e.g., in the loop between TMH2 and TMH3 (Cherny et al. J. Gen. Physiol. 2018 150:851-862). Did the authors check whether any of these modifications alter the transition responsible for the slow kinetic component? For instance, a suppression of the transition resulting from a H168X mutation would help tighten the link to ΔpH sensing.

   We did not carry out any of these experiments.

   1. We understand that it is difficult to tightly control intracellular and extracellular pH when Hv1 is heterologously expressed in mammalian cells. The G-V relation is not always reliable because accumulation of protons or depletion of protons upon Hv channel activity will alter gating, as the authors have previously published (De La Rosa et al., J. Gen. Physiol. 2016 147:127-136). Could the kinetic analysis of Anap fluorescence be affected by similar alterations to proton concentration in the vicinity of Hv1? It would be helpful for the authors to comment on this specifically.

   Thanks for this suggestion. Yes, we think that the kinetics, specially of ionic currents can be affected by even small changes in the pH gradient, for this reason we did not attempt a systematic kinetic analysis. We mention this in the text where we compare the voltage dependence of current and fluorescence activation for construct A197Anap (line 223).

   1. Quenching of Anap by Phe could be verified in cell free conditions using a spectrophotometer with different concentrations of Phe, or citing the literature if it has already been reported.

   We attempted this experiment but were unsuccessful in observing Anap quenching by phenylalanine at the concentrations of phenylalanine that can be attained in aqueous solution. We suspect that Phe quenching of Anap could happen by electron transfer or ground-state complex formation, in which case near proximity is necessary and higher concentrations of Phe would be required to detect quenching in solution. However, we measured the absorbance of Anap in the absence and presence of phenylalanine (Phe) (and tyrosine (Tyr)) at the concentrations that can be achieved in aqueous solution (8 mM and 1mM, respectively). Absorbance measurements can detect ground-state complex formation even at relatively low concentrations (J.R. Lakowicz, 1999, Principles of Fluorescence Spectroscopy). We observed that the absorbance of Anap is modified by the presence of Tyr or Phe, indicating that these amino acids indeed interact with Anap, possibly through ground-state complex formation. We include this data for the reviewers to inspect.

   1. The authors did not cite any example of Anap incorporation into S4 helices, but there are several recent papers where Anap was utilized to probe motion of S4 in other channels. Examples include Dai et al., Nat. Commun. 2021 12:2802 and Mizutani et al. PNAS 2022 119:e2200364119.

   Thanks for this observation, we have included these important results in the discussion.

   1. In the Anap-free negative control (with only A197TAG plasmid transfection), the mCherry signal seems positive (Supplementary Figure 1, left row, second from the top). Is this due to unexpected skipping of the TAG codon to make mCherry-containing partial polypeptides? It would seem like an explanation is needed.

   Thanks for bringing this up. We do not know the exact origin of these leak expression of red fluorescence. We think that, as suggested, there is a possibility that skipping of the Amber codon can lead to a methionine at the end of S4 acting as a second translation initiation site, giving rise to truncated channels that would express mCherry but not currents. This is consistent with the fact that we cannot detect currents in the absence of Anap but we see a small number of red cells.

   1. The data of Figure 3E are shown as data with different membrane voltages. But there is no information about membrane voltage for Fig. 1E and Fig. 2A and Fig. 4B. Are these from unpatched cells? Please clarify.

   See response to point 4 of "Revisions essential for endorsement" section.

   1. G-V relations are shown for F150A-A197Anap, but current traces of F150A-A197Anap are missing.

   We have modified the figure to include current and fluorescence traces.

   1. On Page 11, Line 303 says "experimental F-V relationship is positively shifted by 10 mV with respect to the G-V curve". But looking at the data Fig5D, the shift at ΔpH=2 seems the opposite. Perhaps "positively" should be "negatively" in this sentence?

   Thanks for pointing out this mistake. We have found that this misunderstanding was provoked because of a mistake with the image labeling of F-V and G-V curves for the ΔpH=2 data, we have now corrected the figure. The shift of F-V is indeed positive to G-V as stated before.

   (This is a response to peer review conducted by Biophysics Colab on version 1 of this preprint.)

   Read the original source
4. 

   Version published to 10.1101/2022.06.30.498345v2 on bioRxiv

   Nov 29, 2022
5. 

   Biophysics Colab

   Sep 27, 2022

   Consolidated peer review report (9 September 2022)

   GENERAL ASSESSMENT

   This interesting preprint by Suárez-Delgado et al. explores the mechanism by which activation of the Hv1 voltage-activated proton channel is dependent upon both the voltage and pH difference across the membrane. The authors are the first to incorporate the fluorescent unnatural amino acid, Anap, into the extracellular regions of the S4 helix of human Hv1 to monitor transitions of S4 upon changes in voltage or pH. The authors first checked that Anap is pH insensitive for practical use in Hv1, where changes in local pH are known to occur when the voltage sensor activates and the proton pore opens. Anap was incorporated at positions throughout the S3-S4 linker and the extracellular end of S4 (up to the 202nd residue) of hHv1 and some positions showed clear …

   Consolidated peer review report (9 September 2022)

   GENERAL ASSESSMENT

   This interesting preprint by Suárez-Delgado et al. explores the mechanism by which activation of the Hv1 voltage-activated proton channel is dependent upon both the voltage and pH difference across the membrane. The authors are the first to incorporate the fluorescent unnatural amino acid, Anap, into the extracellular regions of the S4 helix of human Hv1 to monitor transitions of S4 upon changes in voltage or pH. The authors first checked that Anap is pH insensitive for practical use in Hv1, where changes in local pH are known to occur when the voltage sensor activates and the proton pore opens. Anap was incorporated at positions throughout the S3-S4 linker and the extracellular end of S4 (up to the 202nd residue) of hHv1 and some positions showed clear voltage-dependent changes in fluorescence intensity. The authors also obtained fluorescence spectra at different voltages and observed no spectral shifts, raising the possibility that voltage dependent changes in fluorescence intensity could primarily be due to fluorescence quenching. Upon mutation of F150, the Anap signal at the resting membrane voltage increased, suggesting dequenching upon removal of F150. The authors also discovered that the kinetics of Anap fluorescence upon membrane repolarization have two phases (rapid and slow) under certain pH conditions and that there is a pH- dependent negative shift of the conductance-voltage (G-V) relation compared with the fluorescence-voltage (F-V) relation in some mutants. The biphasic kinetics of the fluorescence decay upon repolarization were explained by modelling a slower transition of return from intermediate resting state to a resting state. The pH-dependent shift of the G-V relation from the F-V relation provides insight into mechanisms of ΔpH-dependent gating of Hv1, a longstanding enigma. Overall, the approaches are rigorous, the figures show important results, and this work paves the way for the use of Anap fluorescence to study Hv1 gating and modulation.

   RECOMMENDATIONS

   Revisions essential for endorsement:

   1. In its current form, the narrative of the preprint has two threads. One on the mechanisms of Anap fluorescence changes (mainly quenching) and another on a previously unappreciated transition of the voltage sensor, as revealed by Anap. Our impression is that the preprint suffers somewhat from this split focus, which could be resolved by explaining why Anap was used to explore voltage sensor activation in Hv1 in the introduction. Perhaps the authors could also explain the advantage of smaller sized fluorophores compared to other maleimide-based fluorophores earlier in the introduction, or the utility of being able to insert Anap into transmembrane segments. The authors should more clearly point out how they exploited the advantages of Anap as a tool in this study. It would furthermore be helpful to discuss previous studies using nongenetic tools for VCF and spell out how they have delineated key aspects of Hv1, which would help to emphasize how several positions studied here (for example, 201 and 202) could not be labelled with cysteine-based fluorophores.

   2. We think the authors should be cautious about understanding the physicochemical nature of Anap using prodan as a model. It would be helpful to discuss the possibility that undetected spectral shifts due to a nonquenching mechanism could be overlooked, even though major signal changes can be explained by fluorescence quenching in their data. Regarding the mechanisms of remaining voltage-dependent fluorescence changes of F150A-A197Anap, it would be helpful for the authors to suggest possible ideas about which residues might account for remaining signals.

   The beautiful spectral data for Anap is impressive. However, the physicochemical basis of the fluorescence change of Anap cannot be understood by simple extension of findings for prodan, which shows structural similarity to Anap. Our understanding is that changes in Anap fluorescence can only reveal a change in the structural relationship between Anap and one of its neighbors because the physicochemical basis of Anap fluorescence is complicated. For example, fluorescence could also be affected by the electrostatic environment, stretch of peptide bond, etc. Previous studies, including those of TRP channels, showed that the kind of environmental changes that Anap faces in ion channels do not necessarily induce large spectral shifts, unlike in cell-free spectral analyses using distinct solvents. Further, only minor shifts in spectra occur upon local structural change, as seen in previous work including Xu et al. Nat. Commun. 2020 11:3790. Such minor shifts could be perhaps overlooked even when Anap is incorporated into S4 and exposed to environmental change. Therefore, it is not easy to decode the physicochemical basis of Anap fluorescence changes. F150A-A197Anap has increased fluorescence and no change in spectral pattern, leading the authors to conclude that F150 quenches Anap fluorescence of A197 position. However, a significant amount of fluorescence change still occurs upon changes in membrane potential after F150 is changed to alanine (Figure 4). It is very likely that quenching is not the only mechanism underlying the observed voltage induced change of Anap fluorescence of Hv1. The authors suggest that remaining voltage-dependent fluorescence change of F150A-A197Anap could be due to interaction with other aromatic residues, but this has not been tested.

   1. The current version of the preprint is missing important control experiments, ideally performed using western blots to measure protein expression or, if that is not possible, proton current and fluorescence measurements, to demonstrate that protein expression or functional channels are not seen for all mutants in the absence of ANAP (but in the presence of the tRNA and Rs construct). A similar control for imaging would be to use ANAP alone without encoding.

   2. Aromatics in the S4 segment were ruled out as potential quenchers on the assumption that they would move together with Anap during gating. It should be noted, however, that Hv1 is a dimer and therefore a fluorophore attached to S4 in one subunit could be quenched by S4 aromatics in the neighboring subunit if were close to the dimer interface. In Fujiwara et al. J. Gen. Physiol. 2014 143:377-386, for example, W207 does not appear very far from labeled positions in the adjacent S4. This possibility should be mentioned in the discussion.

   3. It is not clear whether the Anap spectra purely represent Hv1 incorporated into the plasma membrane or perhaps include signals from the cytoplasm or channels in internal membranes (whether assembled or incompletely assembled). It would be helpful to provide a more complete presentation of the data obtained and to provide more information in the Methods Section. In the Methods section, it is stated “The spectra of both fluorophores (Anap and mCherry) were recorded by measuring line scans of the spectral image of the cell membrane, and the background fluorescence from a region of the image without cells was subtracted”. How are signals from cell membranes specified in this method being discriminated from those associated with the cytoplasm and intracellular membranes? If spectral data include signals from free Anap in the cytoplasm or Hv1 in intracellular membranes, spectral shifts upon membrane potential changes will be difficult to detect, even when Anap is incorporated into Hv1 and senses environmental change by voltage-induced conformational change. In Figure 3E, wavelength spectra were shown as standardized signals for different voltages. Amplitude change would be demonstrated (spectrum at different voltages without standardization would be shown). In Figure 4, spectra were compared between A197Anap and F150A-A197Anap, showing increases of fluorescence in F150A-A197Anap. Was this signal measured at resting membrane potential? How does the spectrum change when the membrane potential is changed?

   Rationales for the confirmation of signals originating from the cell surface for Hv1 Anap might include the observations that: a) some mutants showed slightly different spectral patterns (in particular, Q191Anap showed a small hump at longer wavelengths, which is proposed to represent FRET between mCherry and Anap) and b) signal intensity was voltage dependent (if signals originate from endomembranes, they should not be voltage dependent). Mentioning these two points earlier in the text might help to alleviate concerns about the location of the protein that contributes to the measured signals.

   1. In Fig 5, the fluorescence kinetics do not really match the current activation kinetics for panels A, B, and C. Is there an explanation for this mismatch? It would be helpful to have the fitted data in the figure. A more thorough comparison of the kinetics of currents and fluorescence would be helpful throughout the study.

   2. Which construct of hHv1 was used to obtain the data in Figure 6? Unless we missed it, this information is not provided in the text or figure legend. Is it for L201Anap? This figure also shows an intriguing finding that the G-V relationship is negatively shifted from the F-V relationship at pHo7-pHi7 but not at pHo5.5-pHi5.5. A shifted G-V relation with the same ΔpH contrasts with what has been reported in other papers. However, the authors did not really discuss this surprising finding in the light of previous references. Could the shift of the G-V relation between two pH conditions with the same ΔpH be due to any position-specific effect of Anap? If Figure 6 represents L201Anap mutant, the presence of Anap at L201 probably makes such shift of G-V curve in Figure 6C? The authors should openly discuss this finding in relation to what has been reported in the literature.

   3. The authors suggest that the small hump near 600 nm in Figure 1E represents FRET between Anap and mCherry. It is surprising that FRET can take place across the membrane. Can the authors point to another case of FRET taking place across a cell membrane? One possibility might be that misfolded proteins place mCherry and Anap close to each other. It is also curious that only A191Anap did not show such a FRET-like signal. Also, if there is FRET, why wouldn’t this also contribute to the voltage-dependent changes in fluorescence?

   4. F150A-A197Anap shows a leftward shift of the F-V relation compared with the G-V relation only when ΔpH=1. Another unusual finding with F150A-A197Anap is the very small shift of the G-V relation between ΔpH=0 and ΔpH=1, when other reports in the literature suggest it should be 40 mV or more. Are these peculiar properties simply due to the absence of Phe at position 150, which might play a critical role in gating as one of the hydrophobic plugs of Hv1? To address this possibility, it would be ideal to compare different ΔpH values with and without F150 when Anap is incorporated at a different position (such as L201Anap). Regardless, it would be helpful to discuss this point.

   5. In Figure 1E, I202Anap exhibits a blue shift in its spectrum suggesting the environment of Anap on I202 is more hydrophobic than the other sites. We presume these spectra were obtained at a negative membrane voltage, but the text or legend should clearly state how these were obtained. The authors should also explain whether the whole cell or edge was imaged. If these are at negative membrane voltages, might the Anap spectrum shift to higher wavelengths (i.e. more hydrophilic) when the membrane is depolarized? Did the authors find any spectral shift for I202Anap when doing a similar test as depicted in Figure 3E?

   6. In Figure 3E, spectra are shown as normalized signals for different voltages, but an amplitude change should also be demonstrated by providing raw spectra at different voltages.

   7. In Figure 4, spectra are compared between A197Anap and F150A-A197Anap, showing increase of fluorescence in F150A-A197Anap. Were these obtained at a negative membrane voltage? How do these spectra change when membrane potential is changed?

   Additional suggestions for the authors to consider:

   1. The authors propose that Anap fluorescence tracks an S4 movement involved in the opening of the channel. They also argue that the existence of more than one open state could explain why the increase in florescence upon depolarization lags the proton current in most cases. While they convincingly show that Anap is not pH sensitive per se, when incorporated into the protein, the fluorescence efficiency of the fluorophore could still be affected by protonation of channel residues in the immediate environment when the channel opens, even after S4 has completed its movement. To address this alternative explanation, the authors could use Hv1 mutants with strongly reduced proton conductance. Channels bearing mutations corresponding to N214R or D112N were used successfully to isolate Hv1 gating currents from the much larger proton currents (De La Rosa & Ramsey, Biophys. J. 2018 114:2844-2854; Carmona et al. PNAS 2018 115:9240-9245; Carmona et al. PNAS 2021 118: e2025556118). Perhaps, they could be used with patch clamp fluorometry as well?

   2. The data showing that Hv1-197Anap is quenched by Phe at position 150 are very nice. Yet, it would be useful to show that the quenching is specific to F150 using a negative control. F149, for instance, is just next to F150 but points in a different direction, so its mutation to alanine should not affect Hv1-197Anap fluorescence.

   3. A major finding of this work is the identification of a slow kinetic component that is highly sensitive to ΔpH. Earlier studies found that the ability of Hv1 to sense ΔpH is altered by some channel modifications, e.g., in the loop between TMH2 and TMH3 (Cherny et al. J. Gen. Physiol. 2018 150:851-862). Did the authors check whether any of these modifications alter the transition responsible for the slow kinetic component? For instance, a suppression of the transition resulting from a H168X mutation would help tighten the link to ΔpH sensing.

   4. We understand that it is difficult to tightly control intracellular and extracellular pH when Hv1 is heterologously expressed in mammalian cells. The G-V relation is not always reliable because accumulation of protons or depletion of protons upon Hv channel activity will alter gating, as the authors have previously published (De La Rosa et al., J. Gen. Physiol. 2016 147:127-136). Could the kinetic analysis of Anap fluorescence be affected by similar alterations to proton concentration in the vicinity of Hv1? It would be helpful for the authors to comment on this specifically.

   5. Quenching of Anap by Phe could be verified in cell free conditions using a spectrophotometer with different concentrations of Phe, or citing the literature if it has already been reported.

   6. The authors did not cite any example of Anap incorporation into S4 helices, but there are several recent papers where Anap was utilized to probe motion of S4 in other channels. Examples include Dai et al., Nat. Commun. 2021 12:2802 and Mizutani et al. PNAS 2022 119:e2200364119.

   7. In the Anap-free negative control (with only A197TAG plasmid transfection), the mCherry signal seems positive (Supplementary Figure 1, left row, second from the top). Is this due to unexpected skipping of the TAG codon to make mCherry-containing partial polypeptides? It would seem like an explanation is needed.

   8. The data of Figure 3E are shown as data with different membrane voltages. But there is no information about membrane voltage for Fig. 1E and Fig. 2A and Fig. 4B. Are these from unpatched cells? Please clarify.

   9. G-V relations are shown for F150A-A197Anap, but current traces of F150A-A197Anap are missing.

   10. On Page 11, Line 303 says “experimental F-V relationship is positively shifted by 10 mV with respect to the G-V curve”. But looking at the data Fig5D, the shift at ΔpH=2 seems the opposite. Perhaps “positively” should be “negatively” in this sentence?

   REVIEWING TEAM

   Reviewed by:

   Yasushi Okamura, Professor, Osaka University, Japan: voltage-sensing proteins, electrophysiology and fluorescence spectroscopy

   Francesco Tombola, Associate Professor, University of California, Irvine, USA: ion channel mechanisms, electrophysiology and fluorescence spectroscopy

   Christopher A. Ahern, Professor, University of Iowa, USA: ion channel mechanisms, non-canonical amino acidic mutagenesis

   Curated by:

   Kenton J. Swartz, Senior Investigator, NINDS, NIH USA

   (This consolidated report is a result of peer review conducted by Biophysics Colab on version 1 of this preprint. Minor corrections and presentational issues have been omitted for brevity.)

   Read the original source
6. 

   Version published to 10.1101/2022.06.30.498345v1 on bioRxiv

   Jul 1, 2022