Specific interactions between alkali metal cations and the KcsA channel studied using ATR-FTIR spectroscopy

Structural Insights and Influence of Terahertz Waves in Midinfrared Region on Kv1.2 Channel Selectivity Filter

Potassium ion channels are the structural basis for excitation transmission, heartbeat, and other biological processes. The selectivity filter is a critical structural component of potassium ion channels, whose structure is crucial to realizing their function. As biomolecules vibrate and rotate at frequencies in the terahertz band, potassium ion channels are sensitive to terahertz waves. Therefore, it is worthwhile to investigate how the terahertz wave influences the selectivity filter of the potassium channels. In this study, we investigate the structure of the selectivity filter of Kv1.2 potassium ion channels using molecular dynamics simulations. The effect of an electric field on the channel has been examined at four different resonant frequencies of the carbonyl group in SF: 36.75 37.06, 37.68, and 38.2 THz. As indicated by the results, 376GLY appears to be the critical residue in the selectivity filter of the Kv1.2 channel. Its dihedral angle torsion is detrimental to the channel structural stability and the transmembrane movement of potassium ions. 36.75 THz is the resonance frequency of the carbonyl group of 376GLY. Among all four frequencies explored, the applied terahertz electric field of this frequency has the most significant impact on the channel structure, negatively impacting the channel stability and reducing the ion permeability by 20.2% compared to the absence of fields. In this study, we simulate that terahertz waves in the mid-infrared frequency region can significantly alter the structure and function of potassium ion channels and that the effects of terahertz waves differ greatly based on frequency.

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.

Conductance selectivity of Na+ across the K+ channel via Na+ trapped in a tortuous trajectory

Ion selectivity of the potassium channel is crucial for regulating electrical activity in living cells; however, the mechanism underlying the potassium channel selectivity that favors large K⁺ over small Na⁺ remains unclear. Generally, Na⁺ is not completely excluded from permeation through potassium channels. Herein, the distinct nature of Na⁺ conduction through the prototypical KcsA potassium channel was examined. Single-channel current recordings revealed that, at a high Na⁺ concentration (200 mM), the channel was blocked by Na⁺, and this blocking was relieved at high membrane potentials, suggesting the passage of Na⁺ across the channel. At a 2,000 mM Na⁺ concentration, single-channel Na⁺ conductance was measured as one-eightieth of the K⁺ conductance, indicating that the selectivity filter allows substantial conduit of Na⁺ Molecular dynamics simulations revealed unprecedented atomic trajectories of Na⁺ permeation. In the selectivity filter having a series of carbonyl oxygen rings, a smaller Na⁺ was distributed off-center in eight carbonyl oxygen-coordinated sites as well as on-center in four carbonyl oxygen-coordinated sites. This amphipathic nature of Na⁺ coordination yielded a continuous but tortuous path along the filter. Trapping of Na⁺ in many deep free energy wells in the filter caused slow elution. Conversely, K⁺ is conducted via a straight path, and as the number of occupied K⁺ ions increased to three, the concerted conduction was accelerated dramatically, generating the conductance selectivity ratio of up to 80. The selectivity filter allows accommodation of different ion species, but the ion coordination and interactions between ions render contrast conduction rates, constituting the potassium channel conductance selectivity.

Two-dimensional adaptive membranes with programmable water and ionic channels

Membranes are ubiquitous in nature with primary functions that include adaptive filtering and selective transport of chemical/molecular species. Being critical to cellular functions, they are also fundamental in many areas of science and technology. Of particular importance are the adaptive and programmable membranes that can change their permeability or selectivity depending on the environment. Here, we explore implementation of such biological functions in artificial membranes and demonstrate two-dimensional self-assembled heterostructures of graphene oxide and polyamine macromolecules, forming a network of ionic channels that exhibit regulated permeability of water and monovalent ions. This permeability can be tuned by a change of pH or the presence of certain ions. Unlike traditional membranes, the regulation mechanism reported here relies on specific interactions between the membranes' internal components and ions. This allows fabrication of membranes with programmable, predetermined permeability and selectivity, governed by the choice of components, their conformation and their charging state.

Queueing arrival and release mechanism for K+ permeation through a potassium channel

The mechanism underlying ion permeation through potassium channels still remains controversial. K+ ions permeate across a narrow selectivity filter (SF) in a single file. Conventional scenarios assume that K+ ions are tightly bound in the SF, and, thus, they are displaced from their energy well by ion-ion repulsion with an incoming ion. This tight coupling between entering and exiting ions has been called the "knock-on" mechanism. However, this paradigm is contradicted by experimental data measuring the water-ion flux coupling ratio, demonstrating fewer ion occupancies. Here, the results of molecular dynamics simulations of permeation through the KcsA potassium channel revealed an alternative mechanism. In the aligned ions in the SF (an ion queue), the outermost K+ was readily and spontaneously released toward the extracellular space, and the affinity of the relevant ion was ~ 50 mM. Based on this low-affinity regime, a simple queueing mechanism described by loose coupling of entering and exiting ions is proposed.

Structural properties determining low K+ affinity of the selectivity filter in the TWIK1 K+ channel

Canonical K⁺ channels are tetrameric and highly K⁺-selective, whereas two-pore-domain K⁺ (K2P) channels form dimers, but with a similar pore architecture. A two-pore-domain potassium channel TWIK1 (KCNK1 or K2P1) allows permeation of Na⁺ and other monovalent ions, resulting mainly from the presence of Thr-118 in the P1 domain. However, the mechanistic basis for this reduced selectivity is unclear. Using ion-exchange-induced difference IR spectroscopy, we analyzed WT TWIK1 and T118I (highly K⁺-selective) and L228F (substitution in the P2 domain) TWIK1 variants and found that in the presence of K⁺ ions, WT and both variants exhibit an amide-I band at 1680 cm^-1 This band corresponds to interactions of the backbone carbonyls in the selectivity filter with K⁺, a feature very similar to that of the canonical K⁺ channel KcsA. Computational analysis indicated that the relatively high frequency for the amide-I band is well explained by impairment of hydrogen bond formation with water molecules. Moreover, concentration-dependent spectral changes indicated that the K⁺ affinity of the WT selectivity filter was much lower than those of the variants. Furthermore, only the variants displayed a higher frequency shift of the 1680-cm^-1 band upon changes from K⁺ to Rb⁺ or Cs⁺ conditions. High-speed atomic force microscopy disclosed that TWIK1's surface morphology largely does not change in K⁺ and Na⁺ solutions. Our results reveal the local conformational changes of the TWIK1 selectivity filter and suggest that the amide-I bands may be useful "molecular fingerprints" for assessing the properties of other K⁺ channels.

Ion-protein interactions of a potassium ion channel studied by attenuated total reflection Fourier transform infrared spectroscopy

An understanding of ion-protein interactions is key to a better understanding of the molecular mechanisms of proteins, such as enzymes, ion channels, and ion pumps. A potassium ion channel, KcsA, has been extensively studied in terms of ion selectivity. Alkali metal cations in the selectivity filter were visualized by X-ray crystallography. Infrared spectroscopy has an intrinsically higher structural sensitivity due to frequency changes in molecular vibrations interacting with different ions. In this review article, I attempt to summarize ion-exchange-induced differences in Fourier transform infrared spectroscopy, as applied to KcsA, to explain how this method can be utilized to study ion-protein interactions in the KcsA selectivity filter. A band at 1680 cm^-1 in the amide I region would be a marker band for the ion occupancy of K⁺, Rb⁺, and Cs⁺ in the filter. The band at 1627 cm^-1 observed in both Na⁺ and Li⁺ conditions suggests that the selectivity filter similarly interacts with these ions. In addition to the structural information, the results show that the titration of K⁺ ions provides quantitative information on the ion affinity of the selectivity filter.

Structural insights into the nucleotide base specificity of P2X receptors

P2X receptors are trimeric ATP-gated cation channels involved in diverse physiological processes, ranging from muscle contraction to nociception. Despite the recent structure determination of the ATP-bound P2X receptors, the molecular mechanism of the nucleotide base specificity has remained elusive. Here, we present the crystal structure of zebrafish P2X4 in complex with a weak affinity agonist, CTP, together with structure-based electrophysiological and spectroscopic analyses. The CTP-bound structure revealed a hydrogen bond, between the cytosine base and the side chain of the basic residue in the agonist binding site, which mediates the weak but significant affinity for CTP. The cytosine base is further recognized by two main chain atoms, as in the ATP-bound structure, but their bond lengths seem to be extended in the CTP-bound structure, also possibly contributing to the weaker affinity for CTP over ATP. This work provides the structural insights for the nucleotide base specificity of P2X receptors.

Solid-State Nuclear Magnetic Resonance Structural Study of the Retinal-Binding Pocket in Sodium Ion Pump Rhodopsin

The recently identified Krokinobacter rhodopsin 2 (KR2) functions as a light-driven sodium ion pump. The structure of the retinal-binding pocket of KR2 offers important insights into the mechanisms of KR2, which has motif of Asn112, Asp116, and Gln123 (NDQ) that is common among sodium ion pump rhodopsins but is unique among other microbial rhodopsins. Here we present solid-state nuclear magnetic resonance (NMR) characterization of retinal and functionally important residues in the vicinity of retinal in the ground state. We assigned chemical shifts of retinal C14 and C20 atoms, and Tyr218Cζ, Lys255Cε, and the protonated Schiff base of KR2 in lipid environments at acidic and neutral pH. ¹⁵N NMR signals of the protonated Schiff base showed a twist around the N-Cε bond under neutral conditions, compared with other microbial rhodopsins. These data indicated that the location of the counterion Asp116 is one helical pitch toward the cytoplasmic side. In acidic environments, the ¹⁵N Schiff base signal was shifted to a lower field, indicating that protonation of Asp116 induces reorientation during interactions between the Schiff base and Asp116. In addition, the Tyr218 residue in the vicinity of retinal formed a weak hydrogen bond with Asp251, a temporary Na⁺-binding site during the photocycle. These features may indicate unique mechanisms of sodium ion pumps.

New insights into metal ion–crown ether complexes revealed by SEIRA spectroscopy

We demonstrate the SEIRA spectroscopy of crown ether complexes for examining the relationship between the guest selectivity, structure, and solvent effect.