Structural dynamics determine voltage and pH gating in human voltage-gated proton channel

  1. Shuo Han
  2. Sophia Peng
  3. Joshua Vance
  4. Kimberly Tran
  5. Nhu Do
  6. Nauy Bui
  7. Zhenhua Gui
  8. Shizhen Wang  Is a corresponding author
  1. University of Missouri-Kansas City, United States

Abstract

Voltage-gated ion channels are key players of electrical signaling in cells. As a unique subfamily, voltage-gated proton (Hv) channels are standalone voltage sensors without separate ion conductive pores. Hv channels are gated by both voltage and transmembrane proton gradient (i.e ∆pH), serving as acid extruders in most cells. Amongst their many functions, Hv channels are known for regulating the intracellular pH of human spermatozoa and compensating for the charge and pH imbalances caused by NADPH oxidases in phagocytes. Like the canonical voltage sensors, Hv channels are a bundle of 4 helices (named S1 through S4), with the S4 segment carrying 3 positively charged Arg residues. Extensive structural and electrophysiological studies on voltage-gated ion channels, in general, agree on an outwards movement of the S4 segment upon activating voltage, but the real-time conformational transitions are still unattainable. With purified human voltage-gated proton (hHv1) channels reconstituted in liposomes, we have examined its conformational dynamics, including the S4 segment at different voltage and pHs using single-molecule fluorescence resonance energy transfer (smFRET). Here, we provide the first glimpse of real-time conformational trajectories of the hHv1 voltage sensor and show that both voltage and pH gradient shift the conformational dynamics of the S4 segment to control channel gating. Our results indicate that the S4 segment transits among 3 major conformational states and kinetic analysis suggest that only the transitions between the inward and outward conformations are highly dependent on voltage and pH changes. Our smFRET studies uncover the stochastic conformational dynamics of S4 and demonstrate how voltage and pH shift its conformational distributions to regulate channel gating. Altogether, we propose a kinetic model that explains the mechanisms underlying voltage and pH gating in Hv channels, which may also serve as a general framework for understanding the voltage sensing and gating in other voltage-gated ion channels.

Data availability

The source data of all smFRET traces, contour maps, histograms, as well as liposome flux assay data is deposited in Dryad (Dryad Digital Repository, doi:10.5061/dryad.dv41ns1zs), including Fig 1b, c, d, e, g, h; Fig 2; Fig 3a and b; Fig 4a, b; Fig 5a, Fig 1-figure supplement1a and c, Fig1-figure supplement 2a, b, c; Fig1-figure supplement 3a, b; Fig1-figure supplement 4a and b.

The following data sets were generated

Article and author information

Author details

  1. Shuo Han

    Department of Cell Biology and Biophysics, University of Missouri-Kansas City, Kansas City, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Sophia Peng

    Department of Cell Biology and Biophysics, University of Missouri-Kansas City, Kansas City, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7434-5445
  3. Joshua Vance

    Department of Cell Biology and Biophysics, University of Missouri-Kansas City, Kansas City, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Kimberly Tran

    Department of Cell Biology and Biophysics, University of Missouri-Kansas City, Kansas City, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Nhu Do

    Department of Cell Biology and Biophysics, University of Missouri-Kansas City, Kansas City, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Nauy Bui

    Department of Cell Biology and Biophysics, University of Missouri-Kansas City, Kansas City, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Zhenhua Gui

    Department of Cell Biology and Biophysics, University of Missouri-Kansas City, Kansas City, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Shizhen Wang

    Department of Cell Biology and Biophysics, University of Missouri-Kansas City, Kansas City, United States
    For correspondence
    wangshizhen@umkc.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1065-4756

Funding

NIH (1R15GM137215-01)

  • Shizhen Wang

University of Missouri-Kansas City (Startup fund)

  • Shizhen Wang

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2022, Han et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,667
    views
  • 302
    downloads
  • 10
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Shuo Han
  2. Sophia Peng
  3. Joshua Vance
  4. Kimberly Tran
  5. Nhu Do
  6. Nauy Bui
  7. Zhenhua Gui
  8. Shizhen Wang
(2022)
Structural dynamics determine voltage and pH gating in human voltage-gated proton channel
eLife 11:e73093.
https://doi.org/10.7554/eLife.73093

Share this article

https://doi.org/10.7554/eLife.73093

Further reading

    1. Structural Biology and Molecular Biophysics
    Johannes Elferich, Lingli Kong ... Nikolaus Grigorieff
    Research Advance

    Images taken by transmission electron microscopes are usually affected by lens aberrations and image defocus, among other factors. These distortions can be modeled in reciprocal space using the contrast transfer function (CTF). Accurate estimation and correction of the CTF is essential for restoring the high-resolution signal in cryogenic electron microscopy (cryoEM). Previously, we described the implementation of algorithms for this task in the cisTEM software package (Grant et al., 2018). Here we show that taking sample characteristics, such as thickness and tilt, into account can improve CTF estimation. This is particularly important when imaging cellular samples, where measurement of sample thickness and geometry derived from accurate modeling of the Thon ring pattern helps judging the quality of the sample. This improved CTF estimation has been implemented in CTFFIND5, a new version of the cisTEM program CTFFIND. We evaluated the accuracy of these estimates using images of tilted aquaporin crystals and eukaryotic cells thinned by focused ion beam milling. We estimate that with micrographs of sufficient quality CTFFIND5 can measure sample tilt with an accuracy of 3° and sample thickness with an accuracy of 5 nm.

    1. Structural Biology and Molecular Biophysics
    Mrityunjay Singh, Dinesh C Indurthi ... Shailendra Asthana
    Research Advance

    Agonists enhance receptor activity by providing net-favorable binding energy to active over resting conformations, with efficiency (η) linking binding energy to gating. Previously, we showed that in nicotinic receptors, η-values are grouped into five structural pairs, correlating efficacy and affinity within each class, uniting binding with allosteric activation (Indurthi and Auerbach, 2023). Here, we use molecular dynamics (MD) simulations to investigate the low-to-high affinity transition (L→H) at the Torpedo α−δ nicotinic acetylcholine receptor neurotransmitter site. Using four agonists spanning three η-classes, the simulations reveal the structural basis of the L→H transition where: the agonist pivots around its cationic center (‘flip’), loop C undergoes staged downward displacement (‘flop’), and a compact, stable high-affinity pocket forms (‘fix’). The η derived from binding energies calculated in silico matched exact values measured experimentally in vitro. Intermediate states of the orthosteric site during receptor activation are apparent only in simulations, but could potentially be observed experimentally via time-resolved structural studies.