Zn2+-Binding to the Voltage-Gated Proton Channel Hv1/VSOP

Structural basis for ion selectivity in potassium-selective channelrhodopsins

KCR channelrhodopsins (K+-selective light-gated ion channels) have received attention as potential inhibitory optogenetic tools but more broadly pose a fundamental mystery regarding how their K+ selectivity is achieved. Here, we present 2.5-2.7 Å cryo-electron microscopy structures of HcKCR1 and HcKCR2 and of a structure-guided mutant with enhanced K+ selectivity. Structural, electrophysiological, computational, spectroscopic, and biochemical analyses reveal a distinctive mechanism for K+ selectivity; rather than forming the symmetrical filter of canonical K+ channels achieving both selectivity and dehydration, instead, three extracellular-vestibule residues within each monomer form a flexible asymmetric selectivity gate, while a distinct dehydration pathway extends intracellularly. Structural comparisons reveal a retinal-binding pocket that induces retinal rotation (accounting for HcKCR1/HcKCR2 spectral differences), and design of corresponding KCR variants with increased K+ selectivity (KALI-1/KALI-2) provides key advantages for optogenetic inhibition in vitro and in vivo. Thus, discovery of a mechanism for ion-channel K+ selectivity also provides a framework for next-generation optogenetics.

ATP modulates the activity of the voltage-gated proton channel through direct binding interaction

ATP is an important molecule implicated in diverse biochemical processes, including the modulation of ion channel and transporter activity. The voltage-gated proton channel (Hv1) controls proton flow through the transmembrane pathway in response to membrane potential, and various molecules regulate its activity. Although it is believed that ATP is not essential for Hv1 activity, a report has indicated that cytosolic ATP may modulate Hv1. However, the detailed molecular mechanism underlying the effect of ATP on Hv1 is unknown, and whether ATP is involved in the physiological regulation of Hv1 activity remains unclear. Here, we report that cytosolic ATP is required to maintain Hv1 activity. To gain insight into the underlying mechanism, we analysed the effects of ATP on the mouse Hv1 channel (mHv1) using electrophysiological and microscale thermophoresis (MST) methods. Intracellular ATP accelerated the activation kinetics of mHv1, thereby increasing the amplitude of the proton current within the physiological concentration range. The increase in proton current was reproduced with a non-hydrolysable ATP analogue, indicating that ATP directly influences Hv1 activity without an enzymatic reaction. The direct molecular interaction between the purified mHv1 protein and ATP was analysed and demonstrated through MST. In addition, ATP facilitation was observed for the endogenous proton current flowing through Hv1 in the physiological concentration range of ATP. These results suggest that ATP influences Hv1 activity via direct molecular interactions and is required for the physiological function of Hv1. KEY POINTS: We found that ATP is required to maintain the activity of voltage-gated proton channels (Hv1) and investigated the underlying molecular mechanism. Application of intracellular ATP increased the amplitude of the proton current flowing through Hv1, accompanied by an acceleration of activation kinetics. The direct interaction between purified Hv1 protein and ATP was quantitatively analysed using microscale thermophoresis. ATP enhanced endogenous proton currents in breast cancer cell lines. These results suggest that ATP influences Hv1 activity via direct molecular interactions and that its functional characteristics are required for the physiological activity of Hv1.

Specific zinc binding to heliorhodopsin

Heliorhodopsins (HeRs), a recently discovered family of rhodopsins, have an inverted membrane topology compared to animal and microbial rhodopsins. The slow photocycle of HeRs suggests a light-sensor function, although the actual function remains unknown. Although HeRs exhibit no specific binding of monovalent cations or anions, recent ATR-FTIR spectroscopy studies have demonstrated the binding of Zn²⁺ to HeR from Thermoplasmatales archaeon (TaHeR) and 48C12. Even though ion-specific FTIR spectra were observed for many divalent cations, only helical structural perturbations were observed for Zn²⁺-binding, suggesting a possible modification of the HeR function by Zn²⁺. The present study shows that Zn²⁺-binding lowers the thermal stability of TaHeR, and slows back proton transfer to the retinal Schiff base (M decay) during its photocycle. Zn²⁺-binding was similarly observed for a TaHeR opsin that lacks the retinal chromophore. We then studied the Zn²⁺-binding site by means of the ATR-FTIR spectroscopy of site-directed mutants. Among five and four mutants of His and Asp/Glu, respectively, only E150Q exhibited a completely different spectral feature of the α-helix (amide-I) in ATR-FTIR spectroscopy, suggesting that E150 is responsible for Zn²⁺-binding. Molecular dynamics (MD) simulations built a coordination structure of Zn²⁺-bound TaHeR, where E150 and protein bound water molecules participate in direct coordination. It was concluded that the specific binding site of Zn²⁺ is located at the cytoplasmic side of TaHeR, and that Zn²⁺-binding affects the structure and structural dynamics, possibly modifying the unknown function of TaHeR.

A Review on the Role of Bicarbonate and Proton Transporters during Sperm Capacitation in Mammals

Alkalinization of sperm cytosol is essential for plasma membrane hyperpolarization, hyperactivation of motility, and acrosomal exocytosis during sperm capacitation in mammals. The plasma membrane of sperm cells contains different ion channels implicated in the increase of internal pH (pH_i) by favoring either bicarbonate entrance or proton efflux. Bicarbonate transporters belong to the solute carrier families 4 (SLC4) and 26 (SLC26) and are currently grouped into Na⁺/HCO₃⁻ transporters and Cl⁻/HCO₃⁻ exchangers. Na⁺/HCO₃⁻ transporters are reported to be essential for the initial and fast entrance of HCO₃⁻ that triggers sperm capacitation, whereas Cl⁻/HCO₃⁻ exchangers are responsible for the sustained HCO₃⁻ entrance which orchestrates the sequence of changes associated with sperm capacitation. Proton efflux is required for the fast alkalinization of capacitated sperm cells and the activation of pH-dependent proteins; according to the species, this transport can be mediated by Na⁺/H⁺ exchangers (NHE) belonging to the SLC9 family and/or voltage-gated proton channels (HVCN1). Herein, we discuss the involvement of each of these channels in sperm capacitation and the acrosome reaction.

Zinc Binding to Heliorhodopsin

Heliorhodopsin (HeR), a recently discovered new rhodopsin family, has an inverted membrane topology compared to animal and microbial rhodopsins, and no ion-transport activity. The slow photocycle of HeRs suggests a light-sensor function, although the function remains unknown. HeRs exhibit no specific binding of monovalent cations or anions. Despite this, ATR-FTIR spectroscopy in the present study demonstrates binding of Zn²⁺ to HeR from Thermoplasmatales archaeon (TaHeR). The biding of Zn²⁺ to 0.2 mM K_d is accompanied by helical structural perturbations without altering its color. Even though ion-specific FTIR spectra were observed for many divalent cations, only helical structural perturbations were observed for Zn²⁺-binding. Similar results were obtained for HeR 48C12. These findings suggest a possible modification of HeR function by Zn²⁺.

Zinc modulation of proton currents in a new voltage-gated proton channel suggests a mechanism of inhibition

The H_V1 voltage‐gated proton (H_V1) channel is a key component of the cellular proton extrusion machinery and is pivotal for charge compensation during the respiratory burst of phagocytes. The best‐described physiological inhibitor of H_V1 is Zn²⁺. Externally applied ZnCl₂ drastically reduces proton currents reportedly recorded in Homo sapiens, Rattus norvegicus, Mus musculus, Oryctolagus cuniculus, Rana esculenta, Helix aspersa, Ciona intestinalis, Coccolithus pelagicus, Emiliania huxleyi, Danio rerio, Helisoma trivolvis, and Lingulodinium polyedrum, but with considerable species variability. Here, we report the effects of Zn²⁺ and Cd²⁺ on H_V1 from Nicoletia phytophila, NpH_V1. We introduced mutations at potential Zn²⁺ coordination sites and measured Zn²⁺ inhibition in different extracellular pH, with Zn²⁺ concentrations up to 1000 μm. Zn²⁺ inhibition in NpH_V1 was quantified by the slowing of the activation time constant and a positive shift of the conductance–voltage curve. Replacing aspartate in the S3‐S4 loop with histidine (D145H) enhanced both the slowing of activation kinetics and the shift in the voltage–conductance curve, such that Zn²⁺ inhibition closely resembled that of the human channel. Histidine is much more effective than aspartate in coordinating Zn²⁺ in the S3‐S4 linker. A simple Hodgkin Huxley model of NpH_V1 suggests a decrease in the opening rate if it is inhibited by zinc or cadmium. Limiting slope measurements and high‐resolution clear native gel electrophoresis (hrCNE) confirmed that NpH_V1 functions as a dimer. The data support the hypothesis that zinc is coordinated in between the dimer instead of the monomer. Zinc coordination sites may be potential targets for drug development.

Infrared Difference Spectroscopy of Proteins: From Bands to Bonds

Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.

Scorpion toxin inhibits the voltage-gated proton channel using a Zn2+ -like long-range conformational coupling mechanism

BACKGROUND AND PURPOSE

Blocking the voltage-gated proton channel H_V 1 is a promising strategy for the treatment of diseases like ischaemia stroke and cancer. However, few H_V 1 channel antagonists have been reported. Here, we have identified a novel H_V 1 channel antagonist from scorpion venom and have elucidated its action mechanism.

EXPERIMENTAL APPROACH

H_V 1 and NaV channels were heterologously expressed in mammalian cell lines and their currents recorded using whole-cell patch clamp. Site-directed mutagenesis was used to generate mutants. Toxins were recombinantly produced in Escherichia coli. AGAP/W38F-H_V 1 interaction was modelled by molecular dynamics simulations.

KEY RESULTS

The scorpion toxin AGAP (anti-tumour analgesic peptide) potently inhibited H_V 1 currents. One AGAP mutant has reduced Na_V channel activity but intact H_V 1 activity (AGAP/W38F). AGAP/W38F inhibited H_V 1 channel activation by trapping its S4 voltage sensor in a deactivated state and inhibited H_V 1 currents with less pH dependence than Zn²⁺ . Mutation analysis showed that the binding pockets of AGAP/W38F and Zn²⁺ in H_V 1 channel partly overlapped (common sites are His140 and His193). The E153A mutation at the intracellular Coulombic network (ICN) in H_V 1 channel markedly reduced AGAP/W38F inhibition, as observed for Zn²⁺ . Experimental data and MD simulations suggested that AGAP/W38F inhibited H_V 1 channel using a Zn²⁺ -like long-range conformational coupling mechanism.

CONCLUSION AND IMPLICATIONS

Our results suggest that the Zn²⁺ binding pocket in H_V 1 channel might be a hotspot for modulators and valuable for designing H_V 1 channel ligands. Moreover, AGAP/W38F is a useful molecular probe to study H_V 1 channel and a lead compound for drug development.

Structure-affinity insights into the Na+ and Ca2+ interactions with multiple sites of a sodium-calcium exchanger

Selective recognition and transport of Na⁺ and Ca²⁺ ions by sodium-calcium exchanger (NCX) proteins is a primary prerequisite for Ca²⁺ signaling and homeostasis. Twelve ion-coordinating residues are highly conserved among NCXs, and distinct NCX orthologs contain two or three carboxylates, while sharing a common ion-exchange stoichiometry (3Na⁺ :1Ca²⁺ ). How these structural differences affect the ion-binding affinity, selectivity, and transport rates remains unclear. Here, the mutational effects of three carboxylates (E54, E213, and D240) were analyzed on the ion-exchange rates in the archaeal NCX from Methanococcus jannaschii and ion-induced structure-affinity changes were monitored by attenuated total reflection-Fourier-transform infrared spectroscopy (ATR-FTIR). The D240N mutation elevated the ion-transport rates by twofold to threefold, meaning that the deprotonation of D240 is not essential for transport catalysis. In contrast, mutating E54 or E213 to A, D, N, or Q dramatically decreased the ion-transport rates. ATR-FTIR revealed high- and low-affinity binding of Na⁺ or Ca²⁺ with E54 and E213, but not with D240. These findings reveal distinct structure-affinity states at specific ion-binding sites in the inward-facing (IF) and outward-facing orientation. Collectively, two multidentate carboxylate counterparts (E54 and E213) play a critical role in determining the ion coordination/transport in prokaryotic and eukaryotic NCXs, whereas the ortholog substitutions in prokaryotes (aspartate) and eukaryotes (asparagine) at the 240 position affect the ion-transport rates differently (k_cat ), probably due to the structural differences in the transition state.

Assessing Structural Determinants of Zn2+ Binding to Human HV1 via Multiple MD Simulations

Voltage-gated proton channels (H_V1) are essential for various physiological tasks but are strongly inhibited by Zn²⁺ cations. Some determinants of Zn²⁺ binding have been elucidated experimentally and in computational studies. However, the results have always been interpreted under the assumption that Zn²⁺ binds to monomeric H_V1 despite evidence that H_V1 expresses as a dimer and that the dimer has a higher affinity for zinc than the monomer and experimental data that suggest coordination in the dimer interface. The results of former studies are also controversial, e.g., supporting either one single or two binding sites. Some structural determinants of the binding are still elusive. We performed a series of molecular dynamics simulations to address different structures of the human proton channel, the monomer and two plausible dimer conformations, to compare their respective potential to interact with and bind Zn²⁺ via the essential histidines. The series consisted of several copies of the system to generate independent trajectories and increase the significance compared to a single simulation. The amount of time simulated totals 29.9 μs for 126 simulations of systems comprising ∼59,000 to ∼187,000 atoms. Our approach confirms the existence of two binding sites in monomeric and dimeric human H_V1. The dimer interface is more efficient for attracting and binding Zn²⁺ via the essential histidines than the monomer or a dimer with the histidines in the periphery. The higher affinity is due to the residues in the dimer interface that create an attractive electrostatic potential funneling the zinc cations toward the binding sites.

Hydrophobic gasket mutation produces gating pore currents in closed human voltage-gated proton channels

A large family of membrane proteins, voltage-gated ion channels, regulate a vast array of physiological functions in essentially all life forms. How these molecules sense membrane potential and respond by creating ionic conduction is incompletely understood. The voltage sensors of these channels contain a “hydrophobic gasket,” a ring of hydrophobic amino acids near the center of the membrane, separating internal and external aqueous solutions. Although voltage-gated proton channels, H_V1, resemble voltage-sensing domains of other channels, they differ fundamentally. On depolarization, H_V1 conducts protons, whereas other voltage sensors open a physically distinct pore. We identify Val¹⁰⁹, Phe¹⁵⁰, Val¹⁷⁷, and Val¹⁷⁸ as the hH_V1 hydrophobic gasket. Replacement with less hydrophobic amino acids accelerated channel opening and caused proton-selective leak through closed channels.

The hydrophobic gasket (HG), a ring of hydrophobic amino acids in the voltage-sensing domain of most voltage-gated ion channels, forms a constriction between internal and external aqueous vestibules. Cationic Arg or Lys side chains lining the S4 helix move through this “gating pore” when the channel opens. S4 movement may occur during gating of the human voltage-gated proton channel, hH_V1, but proton current flows through the same pore in open channels. Here, we replaced putative HG residues with less hydrophobic residues or acidic Asp. Substitution of individuals, pairs, or all 3 HG positions did not impair proton selectivity. Evidently, the HG does not act as a secondary selectivity filter. However, 2 unexpected functions of the HG in H_V1 were discovered. Mutating HG residues independently accelerated channel opening and compromised the closed state. Mutants exhibited open–closed gating, but strikingly, at negative voltages where “normal” gating produces a nonconducting closed state, the channel leaked protons. Closed-channel proton current was smaller than open-channel current and was inhibited by 10 μM Zn²⁺. Extreme hyperpolarization produced a deeper closed state through a weakly voltage-dependent transition. We functionally identify the HG as Val¹⁰⁹, Phe¹⁵⁰, Val¹⁷⁷, and Val¹⁷⁸, which play a critical and exclusive role in preventing H⁺ influx through closed channels. Molecular dynamics simulations revealed enhanced mobility of Arg²⁰⁸ in mutants exhibiting H⁺ leak. Mutation of HG residues produces gating pore currents reminiscent of several channelopathies.

Molecular mechanisms of coupling to voltage sensors in voltage-evoked cellular signals

The voltage sensor domain (VSD) has long been studied as a unique domain intrinsic to voltage-gated ion channels (VGICs). Within VGICs, the VSD is tightly coupled to the pore-gate domain (PGD) in diverse ways suitable for its specific function in each physiological context, including action potential generation, muscle contraction and relaxation, hormone and neurotransmitter secretion, and cardiac pacemaking. However, some VSD-containing proteins lack a PGD. Voltage-sensing phosphatase contains a cytoplasmic phosphoinositide phosphatase with similarity to phosphatase and tensin homolog (PTEN). H_v1, a voltage-gated proton channel, also lacks a PGD. Within H_v1, the VSD operates as a voltage sensor, gate, and pore for both proton sensing and permeation. H_v1 has a C-terminal coiled coil that mediates dimerization for cooperative gating. Recent progress in the structural biology of VGICs and VSD proteins provides insights into the principles of VSD coupling conserved among these proteins as well as the hierarchy of protein organization for voltage-evoked cell signaling.

A Mechanism for the Adsorption of 2-(Hexadecanoylamino)Acetic Acid by Smithsonite: Surface Spectroscopy and Microflotation Experiments

Zinc is mostly extracted from oxidized zinc and zinc sulfide minerals, and this process involves flotation as a key step. While it is easier to float the sulfide mineral, its consumption and depletion has led to an increased reliance on oxidized zinc minerals, including smithsonite. Hence, the development of efficient ways of collecting smithsonite by flotation is an important objective. Herein, we describe the use of 2-(hexadecanoylamino)acetic acid (HAA), a novel surfactant, as a collector during smithsonite flotation. The mechanism and flotation performance of HAA during smithsonite flotation was investigated by total organic carbon (TOC) content studies, zeta potential measurements, Fourier-transform infrared (FTIR) spectroscopy, and X-ray photoelectron spectroscopy (XPS) analyses, combined with microflotation experiments. The flotation results revealed that HAA was an excellent collector in pulp over a wide pH range (9–12) and at a relatively low concentration (2 × 10−4 mol/L), at which a recovery of close to 90% of the smithsonite mineral was obtained. TOC content studies revealed that the good flotation recovery was ascribable to large amounts of collector molecule adsorbed on the smithsonite surface, while zeta potential measurements showed that the HAA was chemically adsorbed onto the smithsonite. FTIR and XPS analyses revealed that the HAA collector molecules adsorbed onto the smithsonite surface as zinc–HAA complexes involving carboxylate moieties and Zn sites on the smithsonite surface in alkaline solution.