Structural basis for human Cav1.2 inhibition by multiple drugs and the neurotoxin calciseptine.

Cav1.2 channels play crucial roles in various neuronal and physiological processes. Here, we present cryo-EM structures of human Cav1.2, both in its apo form and in complex with several drugs, as well as the peptide neurotoxin calciseptine. Most structures, apo or bound to calciseptine, amlodipine, or a combination of amiodarone and sofosbuvir, exhibit a consistent inactivated conformation with a sealed gate, three up voltage-sensing domains (VSDs), and a down VSDII. Calciseptine sits on the shoulder of the pore domain, away from the permeation path. In contrast, when pinaverium bromide, an antispasmodic drug, is inserted into a cavity reminiscent of the IFM-binding site in Nav channels, a series of structural changes occur, including upward movement of VSDII coupled with dilation of the selectivity filter and its surrounding segments in repeat III. Meanwhile, S4-5III merges with S5III to become a single helix, resulting in a widened but still non-conductive intracellular gate.

Structural basis for the severe adverse interaction of sofosbuvir and amiodarone on L-type Cav channels.

Drug-drug interaction of the antiviral sofosbuvir and the antiarrhythmics amiodarone has been reported to cause fatal heartbeat slowing. Sofosbuvir and its analog, MNI-1, were reported to potentiate the inhibition of cardiomyocyte calcium handling by amiodarone, which functions as a multi-channel antagonist, and implicate its inhibitory effect on L-type Cav channels, but the molecular mechanism has remained unclear. Here we present systematic cryo-EM structural analysis of Cav1.1 and Cav1.3 treated with amiodarone or sofosbuvir alone, or sofosbuvir/MNI-1 combined with amiodarone. Whereas amiodarone alone occupies the dihydropyridine binding site, sofosbuvir is not found in the channel when applied on its own. In the presence of amiodarone, sofosbuvir/MNI-1 is anchored in the central cavity of the pore domain through specific interaction with amiodarone and directly obstructs the ion permeation path. Our study reveals the molecular basis for the physical, pharmacodynamic interaction of two drugs on the scaffold of Cav channels.

Dissection of the structure-function relationship of Nav channels.

Voltage-gated sodium channels (Nav) undergo conformational shifts in response to membrane potential changes, a mechanism known as the electromechanical coupling. To delineate the structure-function relationship of human Nav channels, we have performed systematic structural analysis using human Nav1.7 as a prototype. Guided by the structural differences between wild-type (WT) Nav1.7 and an eleven mutation-containing variant, designated Nav1.7-M11, we generated three additional intermediate mutants and solved their structures at overall resolutions of 2.9-3.4 Å. The mutant with nine-point mutations in the pore domain (PD), named Nav1.7-M9, has a reduced cavity volume and a sealed gate, with all voltage-sensing domains (VSDs) remaining up. Structural comparison of WT and Nav1.7-M9 pinpoints two residues that may be critical to the tightening of the PD. However, the variant containing these two mutations, Nav1.7-M2, or even in combination with two additional mutations in the VSDs, named Nav1.7-M4, failed to tighten the PD. Our structural analysis reveals a tendency of PD contraction correlated with the right shift of the static inactivation I-V curves. We predict that the channel in the resting state should have a "tight" PD with down VSDs.

Unwinding and spiral sliding of S4 and domain rotation of VSD during the electromechanical coupling in Nav1.7.

Voltage-gated sodium (Nav) channel Nav1.7 has been targeted for the development of nonaddictive pain killers. Structures of Nav1.7 in distinct functional states will offer an advanced mechanistic understanding and aid drug discovery. Here we report the cryoelectron microscopy analysis of a human Nav1.7 variant that, with 11 rationally introduced point mutations, has a markedly right-shifted activation voltage curve with V1/2 reaching 69 mV. The voltage-sensing domain in the first repeat (VSDI) in a 2.7-Å resolution structure displays a completely down (deactivated) conformation. Compared to the structure of WT Nav1.7, three gating charge (GC) residues in VSDI are transferred to the cytosolic side through a combination of helix unwinding and spiral sliding of S4I and ∼20° domain rotation. A conserved WNФФD motif on the cytoplasmic end of S3I stabilizes the down conformation of VSDI. One GC residue is transferred in VSDII mainly through helix sliding. Accompanying GC transfer in VSDI and VSDII, rearrangement and contraction of the intracellular gate is achieved through concerted movements of adjacent segments, including S4-5I, S4-5II, S5II, and all S6 segments. Our studies provide important insight into the electromechanical coupling mechanism of the single-chain voltage-gated ion channels and afford molecular interpretations for a number of pain-associated mutations whose pathogenic mechanism cannot be revealed from previously reported Nav structures.

Structural basis for high-voltage activation and subtype-specific inhibition of human Nav1.8.

The dorsal root ganglia-localized voltage-gated sodium (Nav) channel Nav1.8 represents a promising target for developing next-generation analgesics. A prominent characteristic of Nav1.8 is the requirement of more depolarized membrane potential for activation. Here we present the cryogenic electron microscopy structures of human Nav1.8 alone and bound to a selective pore blocker, A-803467, at overall resolutions of 2.7 to 3.2 Å. The first voltage-sensing domain (VSDI) displays three different conformations. Structure-guided mutagenesis identified the extracellular interface between VSDI and the pore domain (PD) to be a determinant for the high-voltage dependence of activation. A-803467 was clearly resolved in the central cavity of the PD, clenching S6IV. Our structure-guided functional characterizations show that two nonligand binding residues, Thr397 on S6I and Gly1406 on S6III, allosterically modulate the channel's sensitivity to A-803467. Comparison of available structures of human Nav channels suggests the extracellular loop region to be a potential site for developing subtype-specific pore-blocking biologics.

Structure of human Nav1.5 reveals the fast inactivation-related segments as a mutational hotspot for the long QT syndrome.

Nav1.5 is the primary voltage-gated Na+ (Nav) channel in the heart. Mutations of Nav1.5 are associated with various cardiac disorders exemplified by the type 3 long QT syndrome (LQT3) and Brugada syndrome (BrS). E1784K is a common mutation that has been found in both LQT3 and BrS patients. Here we present the cryo-EM structure of the human Nav1.5-E1784K variant at an overall resolution of 3.3 Å. The structure is nearly identical to that of the wild-type human Nav1.5 bound to quinidine. Structural mapping of 91- and 178-point mutations that are respectively associated with LQT3 and BrS reveals a unique distribution pattern for LQT3 mutations. Whereas the BrS mutations spread evenly on the structure, LQT3 mutations are clustered mainly to the segments in repeats III and IV that are involved in gating, voltage-sensing, and particularly inactivation. A mutational hotspot involving the fast inactivation segments is identified and can be mechanistically interpreted by our "door wedge" model for fast inactivation. The structural analysis presented here, with a focus on the impact of mutations on inactivation and late sodium current, establishes a structure-function relationship for the mechanistic understanding of Nav1.5 channelopathies.

Comparative structural analysis of human Nav1.1 and Nav1.5 reveals mutational hotspots for sodium channelopathies.

Among the nine subtypes of human voltage-gated sodium (Nav) channels, the brain and cardiac isoforms, Nav1.1 and Nav1.5, each carry more than 400 missense mutations respectively associated with epilepsy and cardiac disorders. High-resolution structures are required for structure-function relationship dissection of the disease variants. We report the cryo-EM structures of the full-length human Nav1.1-ß4 complex at 3.3 Å resolution here and the Nav1.5-E1784K variant in the accompanying paper. Up to 341 and 261 disease-related missense mutations in Nav1.1 and Nav1.5, respectively, are resolved. Comparative structural analysis reveals several clusters of disease mutations that are common to both Nav1.1 and Nav1.5. Among these, the majority of mutations on the extracellular loops above the pore domain and the supporting segments for the selectivity filter may impair structural integrity, while those on the pore domain and the voltage-sensing domains mostly interfere with electromechanical coupling and fast inactivation. Our systematic structural delineation of these mutations provides important insight into their pathogenic mechanism, which will facilitate the development of precise therapeutic interventions against various sodium channelopathies.

Structure of the voltage-gated calcium channel Ca(v)1.1 at 3.6 Å resolution.

The voltage-gated calcium (Cav) channels convert membrane electrical signals to intracellular Ca2+-mediated events. Among the ten subtypes of Cav channel in mammals, Cav1.1 is specified for the excitation-contraction coupling of skeletal muscles. Here we present the cryo-electron microscopy structure of the rabbit Cav1.1 complex at a nominal resolution of 3.6 Å. The inner gate of the ion-conducting α1-subunit is closed and all four voltage-sensing domains adopt an 'up' conformation, suggesting a potentially inactivated state. The extended extracellular loops of the pore domain, which are stabilized by multiple disulfide bonds, form a windowed dome above the selectivity filter. One side of the dome provides the docking site for the α2δ-1-subunit, while the other side may attract cations through its negative surface potential. The intracellular I-II and III-IV linker helices interact with the ß1a-subunit and the carboxy-terminal domain of α1, respectively. Classification of the particles yielded two additional reconstructions that reveal pronounced displacement of ß1a and adjacent elements in α1. The atomic model of the Cav1.1 complex establishes a foundation for mechanistic understanding of excitation-contraction coupling and provides a three-dimensional template for molecular interpretations of the functions and disease mechanisms of Cav and Nav channels.

Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution.

The ryanodine receptors (RyRs) are high-conductance intracellular Ca(2+) channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest known ion channels, with a homotetrameric organization and approximately 5,000 residues in each protomer. Here we report the structure of the rabbit RyR1 in complex with its modulator FKBP12 at an overall resolution of 3.8 Å, determined by single-particle electron cryomicroscopy. Three previously uncharacterized domains, named central, handle and helical domains, display the armadillo repeat fold. These domains, together with the amino-terminal domain, constitute a network of superhelical scaffold for binding and propagation of conformational changes. The channel domain exhibits the voltage-gated ion channel superfamily fold with distinct features. A negative-charge-enriched hairpin loop connecting S5 and the pore helix is positioned above the entrance to the selectivity-filter vestibule. The four elongated S6 segments form a right-handed helical bundle that closes the pore at the cytoplasmic border of the membrane. Allosteric regulation of the pore by the cytoplasmic domains is mediated through extensive interactions between the central domains and the channel domain. These structural features explain high ion conductance by RyRs and the long-range allosteric regulation of channel activities.

Structural Basis for Pore Blockade of the Human Cardiac Sodium Channel Nav 1.5 by the Antiarrhythmic Drug Quinidine*.

Nav 1.5, the primary voltage-gated Na+ (Nav ) channel in heart, is a major target for class I antiarrhythmic agents. Here we present the cryo-EM structure of full-length human Nav 1.5 bound to quinidine, a class Ia antiarrhythmic drug, at 3.3 Šresolution. Quinidine is positioned right beneath the selectivity filter in the pore domain and coordinated by residues from repeats I, III, and IV. Pore blockade by quinidine is achieved through both direct obstruction of the ion permeation path and induced rotation of an invariant Tyr residue that tightens the intracellular gate. Structural comparison with a truncated rat Nav 1.5 in the presence of flecainide, a class Ic agent, reveals distinct binding poses for the two antiarrhythmics within the pore domain. Our work reported here, along with previous studies, reveals the molecular basis for the mechanism of action of class I antiarrhythmic drugs.

Prevalence of fluoroquinolone, macrolide and sulfonamide-related resistance genes in landfills from East China, mainly driven by MGEs.

Landfills are one of the most important reservoirs of antibiotic resistance genes (ARGs), and ARG pollution in landfills has been well investigated. However, the various factors contributing to the widespread prevalence of ARGs in landfills have rarely been explored. Here, we quantified three classes of antibiotics, six kinds of heavy metals, eight types of ARGs, and five varieties of mobile genetic elements (MGEs) in refuse samples from 10 landfills in Zhejiang Province, China. Compared with sulfonamides and macrolides, fluoroquinolones were present at much higher concentrations in all refuse samples, reaching a concentration of 1406.85 µg/kg in the Jiaxing region. The relative abundances of qnrD, qnrS, mexF, ermA, ermB, mefA, sul1, and sul2 in most landfills were >10-4 copies per 16S rRNA, suggesting the presence of highly contaminated ARGs. No significant correlations between most target antibiotics and their corresponding ARGs were found. Variation partitioning analysis indicated that MGEs could be the determining factor in the spread of ARGs in landfills. This research not only reveals high levels of ARGs and the ubiquitous presence of antibiotics in refuse, but also provides guidance for controlling the spread of ARGs in landfills.

A structural atlas of druggable sites on Nav channels.

Voltage-gated sodium (Nav) channels govern membrane excitability by initiating and propagating action potentials. Consistent with their physiological significance, dysfunction, or mutations in these channels are associated with various channelopathies. Nav channels are thereby major targets for various clinical and investigational drugs. In addition, a large number of natural toxins, both small molecules and peptides, can bind to Nav channels and modulate their functions. Technological breakthrough in cryo-electron microscopy (cryo-EM) has enabled the determination of high-resolution structures of eukaryotic and eventually human Nav channels, alone or in complex with auxiliary subunits, toxins, and drugs. These studies have not only advanced our comprehension of channel architecture and working mechanisms but also afforded unprecedented clarity to the molecular basis for the binding and mechanism of action (MOA) of prototypical drugs and toxins. In this review, we will provide an overview of the recent advances in structural pharmacology of Nav channels, encompassing the structural map for ligand binding on Nav channels. These findings have established a vital groundwork for future drug development.

Extremely Enhanced Photoluminescence in MoS2-Derived Quantum Sheets.

Molybdenum disulfide (MoS2) quantum sheets (QSs) are attractive for applications due to their tunable energy band structures and optical and electronic properties. The photoluminescence quantum yield (PLQY) of MoS2 QSs achieved by mechanical and liquid exfoliation and chemical vapor deposition is low. Some studies have reported that chemical treatment and elemental doping can improve the PLQY of transition metal dichalcogenides (TMDs), but this is limited by complex instruments and reactions. In this study, a heat treatment method based on a polar solvent is reported to improve the PLQY and photoluminescence (PL) intensity of MoS2 QSs at room temperature. The absolute PLQY of treated MoS2 QSs is increased to 18.5%, and the PL intensity is increased by a factor of 64. This method is also effective for tungsten disulfide (WS2) QSs. The PL enhancement of QSs is attributed to oxidation of the edges. Such passivation/deformation of MoS2 QSs facilitates the radiative route rather than the nonradiative route, resulting in extreme enhancement of the PL. Our work could provide novel insights/routes toward the PL enhancement of TMD QSs.

Tailoring Graphite into Subnanometer Graphene.

Within the intersection of materials science and nanoscience/technology, extremely downsized (including quantum-sized and subnanometer-sized) materials attract increasing interest. However, the effective and controllable production of extremely downsized materials through physical strategies remains a great challenge. Herein, an all-physical top-down method for the production of sub-1 nm graphene with completely broken lattice is reported. The graphene subnanometer materials (GSNs) with monolayer structures and lateral sizes of ≈0.5 nm are obtained. Compared with their bulk, nanosheets, and quantum sheets, the intrinsic GSNs present extremely enhanced photoluminescence and nonlinear saturation absorption performances, as well as unique carrier behavior. The non-equilibrium states induced by the entirely exposed and broken, intrinsic lattices in sub-1 nm graphene can be determinative to their extreme performances. This work shows the great potential of broken lattice and provides new insights toward subnanometer materials.

Platinum Nanoparticles Prevent the Resistance of Pseudomonas aeruginosa to Ciprofloxacin and Imipenem: Mechanism Insights.

Metal nanoparticles (MNPs) have recently gained extensive attention due to their broad-spectrum prospect, particularly in biomedical application. Here, we reveal that long-term exposure to platinum nanoparticles (Pt NPs) increases the susceptibility of Pseudomonas aeruginosa PAO1 to imipenem and ciprofloxacin. We exposed PAO1 to Pt NPs (a series of doses, varying from 0.125 to 35 µg/mL) for 60 days and characterized the evolved strains (ES) and compared with wild type (WT) to understand the mechanism of heightened sensitivity. We found that overexpression of oprD and downregulation of mexEF-oprN facilitate the intracellular accumulation of antibiotic, thus increasing susceptibility. Furthermore, loss-of-function mutations were discovered in regulators lasR and mexT. Cloning intact lasR from wild-type (WT) into ES slightly improves imipenem resistance. Strikingly, cloning mexT from WT into ES reverts the imipenem and ciprofloxacin resistance to the original level. Briefly, the increase of membrane permeability controlled by mexT made PAO1 greatly susceptible to imipenem and ciprofloxacin, and the decrease of quorum sensing mediated by lasR made PAO1 slightly susceptible to imipenem. Overall, these results reveal an antibiotic susceptibility mechanism from prolonged exposure to MNPs, which provides a promising approach to prevent antibiotic resistance.

Quantum-sized topological insulators/semimetals enable ultrahigh and broadband saturable absorption.

Two-dimensional topological insulators/semimetals have recently attracted much attention. However, quantum-sized topological insulators/semimetals with intrinsic characteristics have never been reported before. Herein, we report the high-yield production of topological insulator (i.e., Bi2Se3 and Sb2Te3) and semimetal (i.e., TiS2) quantum sheets (QSs) with monolayer structures and sub-4 nm lateral sizes. Both linear and nonlinear optical performances of the QSs are investigated. The QS dispersions present remarkable photoluminescence with excitation wavelength-, concentration-, and solvent-dependence. The solution-processed QSs-poly(methyl methacrylate) (PMMA) hybrid thin films demonstrate exceptional nonlinear saturation absorption (NSA). Particularly, Bi2Se3 QSs-PMMA enables record-high NSA performance with a broadband feature. Specifically, the (absolute) modulation depths up to 71.6 and 72.4% and saturation intensities down to 1.52 and 0.49 MW cm-2 are achieved at 532 and 800 nm, respectively. Such a phenomenal NSA performance would greatly facilitate their applications in mode-locked lasers and related fields.

Interaction with teichoic acids contributes to highly effective antibacterial activity of graphene oxide on Gram-positive bacteria.

Graphene oxide (GO) has high-efficient antibacterial activity to diverse pathogenic bacteria. However, the detailed antibacterial mechanism of GO is not fully clear. Herein the antibacterial properties of GO against model Gram-positive (Gram+) (Staphylococcus aureus and Staphylococcus epidermidis) and Gram-negative (Gram-) bacteria (Pseudomonas aeruginosa and Escherichia coli) were compared by plate count method. Results showed that 4 mg/L of GO induced the mortality of Gram+ and Gram- bacteria by > 99% and < 25%, respectively. GO had greater adsorption affinity to teichoic acids, the unique components existing in the cell wall of Gram+ bacteria, mainly via π-π interaction. The adsorption efficiency of teichoic acids was 27 times higher than that of peptidoglycan when they were simultaneously exposed to 100 mg/L GO. The superior adsorption of teichoic acids onto GO increased one order of magnitude of atlA expression, the autolysin related gene. As a result, these accelerated bacterial death by hydrolyzing peptidoglycan in cell walls. Exogenous addition of 50 mg/L teichoic acids could impair 4-5 fold of antibacterial activity of GO against S. aureus. These new findings illuminate the antibacterial mechanism of GO against Gram+ bacteria, which paves the way for the further application of graphene-based materials in water disinfection and pathogen control.

Through quorum sensing, Pseudomonas aeruginosa resists noble metal-based nanomaterials toxicity.

Noble metal-based nanomaterials (NMNs), such as platinum nanoparticles (Pt@NPs) and palladium nanoparticles (Pd@NPs), are increasingly being used as antibacterial agents. However, little information is available on bacterial resistance to NMNs. In this study, owing to their oxidase-like and peroxidase-like properties, both Pt@NPs and Pd@NPs induce reactive oxygen species (ROS) and manifest antibacterial activities: 6.25 µg/mL of either Pt@NPs or Pd@NPs killed >50% of Staphylococcus aureus strain ATCC29213. However, Pseudomonas aeruginosa strain PAO1 completely resisted 12.5 µg/mL of Pt@NPs and 6.25 µg/mL of Pd@NPs. Compared to the non-NMN groups, these NMNs promoted 2-3-fold upregulation of the quorum sensing (QS) gene lasR in strain PAO1. In fact, the lasR gene upregulation induced a 1.5-fold reduction in ROS production and increased biofilm formation by 11% (Pt@NPs) and 27% (Pd@NPs) in strain PAO1. The ΔlasR mutants (lasR gene knock out in strain PAO1), became sensitive to NMNs. The survival rates of ΔlasR mutants at 12.5 µg/mL Pt@NPs and Pd@NPs treatments were only 77% and 58%, respectively. This is the first report indicating that bacteria can resist NMNs through QS. Based on these results, evaluation of the ecological risks of using NMNs as antibacterial agents is necessary.

Molecular basis for pore blockade of human Na+ channel Nav1.2 by the µ-conotoxin KIIIA.

The voltage-gated sodium channel Nav1.2 is responsible for the initiation and propagation of action potentials in the central nervous system. We report the cryo-electron microscopy structure of human Nav1.2 bound to a peptidic pore blocker, the µ-conotoxin KIIIA, in the presence of an auxiliary subunit, ß2, to an overall resolution of 3.0 angstroms. The immunoglobulin domain of ß2 interacts with the shoulder of the pore domain through a disulfide bond. The 16-residue KIIIA interacts with the extracellular segments in repeats I to III, placing Lys7 at the entrance to the selectivity filter. Many interacting residues are specific to Nav1.2, revealing a molecular basis for KIIIA specificity. The structure establishes a framework for the rational design of subtype-specific blockers for Nav channels.