Mechanisms and models of cardiac sodium channel inactivation

Identification of crucial inflammaging related risk factors in multiple sclerosis

Background

Multiple sclerosis (MS) is an immune-mediated disease characterized by inflammatory demyelinating lesions in the central nervous system. Studies have shown that the inflammation is vital to both the onset and progression of MS, where aging plays a key role in it. However, the potential mechanisms on how aging-related inflammation (inflammaging) promotes MS have not been fully understood. Therefore, there is an urgent need to integrate the underlying mechanisms between inflammaging and MS, where meaningful prediction models are needed.

Methods

First, both aging and disease models were developed using machine learning methods, respectively. Then, an integrated inflammaging model was used to identify relative risk factors, by identifying essential "aging-inflammation-disease" triples. Finally, a series of bioinformatics analyses (including network analysis, enrichment analysis, sensitivity analysis, and pan-cancer analysis) were further used to explore the potential mechanisms between inflammaging and MS.

Results

A series of risk factors were identified, such as the protein homeostasis, cellular homeostasis, neurodevelopment and energy metabolism. The inflammaging indices were further validated in different cancer types. Therefore, various risk factors were integrated, and even both the theories of inflammaging and immunosenescence were further confirmed.

Conclusion

In conclusion, our study systematically investigated the potential relationships between inflammaging and MS through a series of computational approaches, and could present a novel thought for other aging-related diseases.

Kir2.1-NaV1.5 channelosome and its role in arrhythmias in inheritable cardiac diseases

Sudden cardiac death in children and young adults is a relatively rare but tragic event whose pathophysiology is unknown at the molecular level. Evidence indicates that the main cardiac sodium channel (NaV1.5) and the strong inward rectifier potassium channel (Kir2.1) physically interact and form macromolecular complexes (channelosomes) with common partners, including adapter, scaffolding, and regulatory proteins that help them traffic together to their eventual membrane microdomains. Most important, dysfunction of either or both ion channels has direct links to hereditary human diseases. For example, certain mutations in the KCNJ2 gene encoding the Kir2.1 protein result in Andersen-Tawil syndrome type 1 and alter both inward rectifier potassium and sodium inward currents. Similarly, trafficking-deficient mutations in the gene encoding the NaV1.5 protein (SCN5A) result in Brugada syndrome and may also disturb both inward rectifier potassium and sodium inward currents. Moreover, gain-of-function mutations in KCNJ2 result in short QT syndrome type 3, which is extremely rare but highly arrhythmogenic, and can modify Kir2.1-NaV1.5 interactions in a mutation-specific way, further highlighting the relevance of channelosomes in ion channel diseases. By expressing mutant proteins that interrupt or modify Kir2.1 or NaV1.5 function in animal models and patient-specific pluripotent stem cell-derived cardiomyocytes, investigators are defining for the first time the mechanistic framework of how mutation-induced dysregulation of the Kir2.1-NaV1.5 channelosome affects cardiac excitability, resulting in arrhythmias and sudden death in different cardiac diseases.

Selective Inhibition of Cardiac Late Na+ Current Is Based on Fast Offset Kinetics of the Inhibitor

The present study was designed to test the hypothesis that the selectivity of blocking the late Na+ current (INaL) over the peak Na+ current (INaP) is related to the fast offset kinetics of the Na+ channel inhibitor. Therefore, the effects of 1 µM GS967 (INaL inhibitor), 20 µM mexiletine (I/B antiarrhythmic) and 10 µM quinidine (I/A antiarrhythmic) on INaL and INaP were compared in canine ventricular myocardium. INaP was estimated as the maximum velocity of action potential upstroke (V+max). Equal amounts of INaL were dissected by the applied drug concentrations under APVC conditions. The inhibition of INaL by mexiletine and quinidine was comparable under a conventional voltage clamp, while both were smaller than the inhibitory effect of GS967. Under steady-state conditions, the V+max block at the physiological cycle length of 700 ms was 2.3% for GS967, 11.4% for mexiletine and 26.2% for quinidine. The respective offset time constants were 110 ± 6 ms, 456 ± 284 ms and 7.2 ± 0.9 s. These results reveal an inverse relationship between the offset time constant and the selectivity of INaL over INaP inhibition without any influence of the onset rate constant. It is concluded that the selective inhibition of INaL over INaP is related to the fast offset kinetics of the Na+ channel inhibitor.

Bacterial toxins and heart function: heat-labile Escherichia coli enterotoxin B promotes changes in cardiac function with possible relevance for sudden cardiac death

Bacterial toxins can cause cardiomyopathy, though it is not its most common cause. Some bacterial toxins can form pores in the membrane of cardiomyocytes, while others can bind to membrane receptors. Enterotoxigenic E. coli can secrete enterotoxins, including heat-resistant (ST) or labile (LT) enterotoxins. LT is an AB5-type toxin that can bind to specific cell receptors and disrupt essential host functions, causing several common conditions, such as certain diarrhea. The pentameric B subunit of LT, without A subunit (LTB), binds specifically to certain plasma membrane ganglioside receptors, found in lipid rafts of cardiomyocytes. Isolated guinea pig hearts and cardiomyocytes were exposed to different concentrations of purified LTB. In isolated hearts, mechanical and electrical alternans and an increment of heart rate variability, with an IC50 of ~0.2 μg/ml LTB, were observed. In isolated cardiomyocytes, LTB promoted significant decreases in the amplitude and the duration of action potentials. Na+ currents were inhibited whereas L-type Ca2+ currents were augmented at their peak and their fast inactivation was promoted. Delayed rectifier K+ currents decreased. Measurements of basal Ca2+ or Ca2+ release events in cells exposed to LTB suggest that LTB impairs Ca2+ homeostasis. Impaired calcium homeostasis is linked to sudden cardiac death. The results are consistent with the recent view that the B subunit is not merely a carrier of the A subunit, having a role explaining sudden cardiac death in children (SIDS) infected with enterotoxigenic E. coli, explaining several epidemiological findings that establish a strong relationship between SIDS and ETEC E. coli.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-023-01100-6.

Differential regulation of cardiac sodium channels by intracellular fibroblast growth factors

Voltage-gated sodium (NaV) channels are responsible for the initiation and propagation of action potentials. In the heart, the predominant NaV1.5 α subunit is composed of four homologous repeats (I-IV) and forms a macromolecular complex with multiple accessory proteins, including intracellular fibroblast growth factors (iFGF). In spite of high homology, each of the iFGFs, iFGF11-iFGF14, as well as the individual iFGF splice variants, differentially regulates NaV channel gating, and the mechanisms underlying these differential effects remain elusive. Much of the work exploring iFGF regulation of NaV1.5 has been performed in mouse and rat ventricular myocytes in which iFGF13VY is the predominant iFGF expressed, whereas investigation into NaV1.5 regulation by the human heart-dominant iFGF12B is lacking. In this study, we used a mouse model with cardiac-specific Fgf13 deletion to study the consequences of iFGF13VY and iFGF12B expression. We observed distinct effects on the voltage-dependences of activation and inactivation of the sodium currents (INa), as well as on the kinetics of peak INa decay. Results in native myocytes were recapitulated with human NaV1.5 heterologously expressed in Xenopus oocytes, and additional experiments using voltage-clamp fluorometry (VCF) revealed iFGF-specific effects on the activation of the NaV1.5 voltage sensor domain in repeat IV (VSD-IV). iFGF chimeras further unveiled roles for all three iFGF domains (i.e., the N-terminus, core, and C-terminus) on the regulation of VSD-IV, and a slower time domain of inactivation. We present here a novel mechanism of iFGF regulation that is specific to individual iFGF isoforms and that leads to distinct functional effects on NaV channel/current kinetics.

Emerging methods to model cardiac ion channel and myocyte electrophysiology

In the field of cardiac electrophysiology, modeling has played a central role for many decades. However, even though the effort is well-established, it has recently seen a rapid and sustained evolution in the complexity and predictive power of the models being created. In particular, new approaches to modeling have allowed the tracking of parallel and interconnected processes that span from the nanometers and femtoseconds that determine ion channel gating to the centimeters and minutes needed to describe an arrhythmia. The connection between scales has brought unprecedented insight into cardiac arrhythmia mechanisms and drug therapies. This review focuses on the generation of these models from first principles, generation of detailed models to describe ion channel kinetics, algorithms to create and numerically solve kinetic models, and new approaches toward data gathering that parameterize these models. While we focus on application of these models for cardiac arrhythmia, these concepts are widely applicable to model the physiology and pathophysiology of any excitable cell.

Pacing Dynamics Determines the Arrhythmogenic Mechanism of the CPVT2-Causing CASQ2G112+5X Mutation in a Guinea Pig Ventricular Myocyte Computational Model

Calsequestrin Type 2 (CASQ2) is a high-capacity, low-affinity, Ca2+-binding protein expressed in the sarcoplasmic reticulum (SR) of the cardiac myocyte. Mutations in CASQ2 have been linked to the arrhythmia catecholaminergic polymorphic ventricular tachycardia (CPVT2) that occurs with acute emotional stress or exercise can result in sudden cardiac death (SCD). CASQ2G112+5X is a 16 bp (339-354) deletion CASQ2 mutation that prevents the protein expression due to premature stop codon. Understanding the subcellular mechanisms of CPVT2 is experimentally challenging because the occurrence of arrhythmia is rare. To obtain an insight into the characteristics of this rare disease, simulation studies using a local control stochastic computational model of the Guinea pig ventricular myocyte investigated how the mutant CASQ2s may be responsible for the development of an arrhythmogenic episode under the condition of β-adrenergic stimulation or in the slowing of heart rate afterward once β-adrenergic stimulation ceases. Adjustment of the computational model parameters based upon recent experiments explore the functional changes caused by the CASQ2 mutation. In the simulation studies under rapid pacing (6 Hz), electromechanically concordant cellular alternans appeared under β-adrenergic stimulation in the CPVT mutant but not in the wild-type nor in the non-β-stimulated mutant. Similarly, the simulations of accelerating pacing from slow to rapid and back to the slow pacing did not display alternans but did generate early afterdepolarizations (EADs) during the period of second slow pacing subsequent acceleration of rapid pacing.

Genomic and Non-Genomic Regulatory Mechanisms of the Cardiac Sodium Channel in Cardiac Arrhythmias

Nav1.5 is the predominant cardiac sodium channel subtype, encoded by the SCN5A gene, which is involved in the initiation and conduction of action potentials throughout the heart. Along its biosynthesis process, Nav1.5 undergoes strict genomic and non-genomic regulatory and quality control steps that allow only newly synthesized channels to reach their final membrane destination and carry out their electrophysiological role. These regulatory pathways are ensured by distinct interacting proteins that accompany the nascent Nav1.5 protein along with different subcellular organelles. Defects on a large number of these pathways have a tremendous impact on Nav1.5 functionality and are thus intimately linked to cardiac arrhythmias. In the present review, we provide current state-of-the-art information on the molecular events that regulate SCN5A/Nav1.5 and the cardiac channelopathies associated with defects in these pathways.

High-Throughput Analysis of Drug Safety Responses in Induced Pluripotent Stem Cell-Derived Cardiomyocytes Using Multielectrode Array

Microelectrode array (MEA) is an electrophysiological instrument used to track activities of ion channels in excitable cells. Neurons and cardiomyocytes are seeded to form a cell monolayer on a field of sensors able to detect electrical signals, called extracellular field potentials (EFPs). This noninvasive tool allows researchers to investigate key parameters such as EFP amplitude, duration, and arrhythmias. MEA is progressively considered the gold standard for high-throughput in vitro electrophysiological evaluation, particularly for cardiac disease modeling and cardiac toxicity assessment.

Late sodium current and calcium homeostasis in arrhythmogenesis

The cardiac late sodium current (INa,late) is the small sustained component of the sodium current active during the plateau phase of the action potential. Several studies demonstrated that augmentation of the current can lead to cardiac arrhythmias; therefore, INa,late is considered as a promising antiarrhythmic target. Fundamentally, enlarged INa,late increases Na+ influx into the cell, which, in turn, is converted to elevated intracellular Ca2+ concentration through the Na+/Ca2+ exchanger. The excessive Ca2+ load is known to be proarrhythmic. This review describes the behavior of the voltage-gated Na+ channels generating INa,late in health and disease and aims to discuss the physiology and pathophysiology of Na+ and Ca2+ homeostasis in context with the enhanced INa,late demonstrating also the currently accessible antiarrhythmic choices.

Conformations of voltage-sensing domain III differentially define NaV channel closed- and open-state inactivation

Voltage-gated Na⁺ (Na_V) channels underlie the initiation and propagation of action potentials (APs). Rapid inactivation after Na_V channel opening, known as open-state inactivation, plays a critical role in limiting the AP duration. However, Na_V channel inactivation can also occur before opening, namely closed-state inactivation, to tune the cellular excitability. The voltage-sensing domain (VSD) within repeat IV (VSD-IV) of the pseudotetrameric Na_V channel α-subunit is known to be a critical regulator of Na_V channel inactivation. Yet, the two processes of open- and closed-state inactivation predominate at different voltage ranges and feature distinct kinetics. How inactivation occurs over these different ranges to give rise to the complexity of Na_V channel dynamics is unclear. Past functional studies and recent cryo-electron microscopy structures, however, reveal significant inactivation regulation from other Na_V channel components. In this Hypothesis paper, we propose that the VSD of Na_V repeat III (VSD-III), together with VSD-IV, orchestrates the inactivation-state occupancy of Na_V channels by modulating the affinity of the intracellular binding site of the IFMT motif on the III-IV linker. We review and outline substantial evidence that VSD-III activates in two distinct steps, with the intermediate and fully activated conformation regulating closed- and open-state inactivation state occupancy by altering the formation and affinity of the IFMT crevice. A role of VSD-III in determining inactivation-state occupancy and recovery from inactivation suggests a regulatory mechanism for the state-dependent block by small-molecule anti-arrhythmic and anesthetic therapies.

Identification of structures for ion channel kinetic models

Markov models of ion channel dynamics have evolved as experimental advances have improved our understanding of channel function. Past studies have examined limited sets of various topologies for Markov models of channel dynamics. We present a systematic method for identification of all possible Markov model topologies using experimental data for two types of native voltage-gated ion channel currents: mouse atrial sodium currents and human left ventricular fast transient outward potassium currents. Successful models identified with this approach have certain characteristics in common, suggesting that aspects of the model topology are determined by the experimental data. Incorporating these channel models into cell and tissue simulations to assess model performance within protocols that were not used for training provided validation and further narrowing of the number of acceptable models. The success of this approach suggests a channel model creation pipeline may be feasible where the structure of the model is not specified a priori.

Markov models of ion channel dynamics have evolved as experimental advances have improved our understanding of channel function. Past studies have examined limited sets of various structures for Markov models of channel dynamics. Here, we present a computational routine designed to thoroughly search for Markov model topologies for simulating whole-cell currents. We tested this method on two distinct types of voltage-gated cardiac ion channels and found the number of states and connectivity required to recapitulate experimentally observed kinetics. Successful models identified with this approach have certain characteristics in common, suggesting that model structures are determined by the experimental data. Incorporation of these models into higher scale action potential and cable (an approximation of one-dimensional action potential propagation) simulations, identified key channel phenomena that were required for proper function. These methods provide a route to create functional channel models that can be used for action potential simulation without pre-defining their structure ahead of time.

Dual Mechanisms of Cardiac Action Potential Prolongation by 4-Oxo-Nonenal Increasing the Risk of Arrhythmia; Late Na+ Current Induction and hERG K+ Channel Inhibition

4-Oxo-nonenal (4-ONE) is an endogenous lipid peroxidation product that is more reactive than 4-hydroxy-nonenal (4-HNE). We previously reported the arrhythmic potential of 4-HNE by suppression of cardiac human Ether-a-go-go Related Gene (hERG) K⁺ channels with prolonged action potential duration (APD) in cardiomyocytes. Here, we illustrate the higher arrhythmic risk of 4-ONE by modulating the cardiac hNa_V1.5 channel currents (I_NaV). Although the peak amplitude of I_NaV was not significantly changed by 4-ONE up to 10 μM, the rate of I_NaV inactivation was slowed, and the late Na⁺ current (I_NaL) became larger by 10 μM 4-ONE. The chemical modification of specific residues in hNa_V1.5 by 4-ONE was identified using MS-fingerprinting analysis. In addition to the changes in I_NaV, 4-ONE decreased the delayed rectifier K⁺ channel currents including the hERG current. The L-type Ca²⁺ channel current was decreased, whereas its inactivation was slowed by 4-ONE. The APD prolongation by 10 μM of 4-ONE was more prominent than that by 100 μM of 4-HNE. In the computational in silico cardiomyocyte simulation analysis, the changes of I_NaL by 4-ONE significantly exacerbated the risk of arrhythmia exhibited by the TdP marker, qNet. Our study suggests an arrhythmogenic effect of 4-ONE on cardiac ion channels, especially hNa_V1.5.

Mexiletine-like cellular electrophysiological effects of GS967 in canine ventricular myocardium

Enhancement of the late Na⁺ current (I_NaL) increases arrhythmia propensity in the heart, while suppression of the current is antiarrhythmic. GS967 is an agent considered as a selective blocker of I_NaL. In the present study, effects of GS967 on I_NaL and action potential (AP) morphology were studied in canine ventricular myocytes by using conventional voltage clamp, action potential voltage clamp and sharp microelectrode techniques. The effects of GS967 (1 µM) were compared to those of the class I/B antiarrhythmic compound mexiletine (40 µM). Under conventional voltage clamp conditions, I_NaL was significantly suppressed by GS967 and mexiletine, causing 80.4 ± 2.2% and 59.1 ± 1.8% reduction of the densities of I_NaL measured at 50 ms of depolarization, and 79.0 ± 3.1% and 63.3 ± 2.7% reduction of the corresponding current integrals, respectively. Both drugs shifted the voltage dependence of the steady-state inactivation curve of I_NaL towards negative potentials. GS967 and mexiletine dissected inward I_NaL profiles under AP voltage clamp conditions having densities, measured at 50% of AP duration (APD), of −0.37 ± 0.07 and −0.28 ± 0.03 A/F, and current integrals of −56.7 ± 9.1 and −46.6 ± 5.5 mC/F, respectively. Drug effects on peak Na⁺ current (I_NaP) were assessed by recording the maximum velocity of AP upstroke (V⁺_max) in multicellular preparations. The offset time constant was threefold faster for GS967 than mexiletine (110 ms versus 289 ms), while the onset of the rate-dependent block was slower in the case of GS967. Effects on beat-to-beat variability of APD was studied in isolated myocytes. Beat-to-beat variability was significantly decreased by both GS967 and mexiletine (reduction of 42.1 ± 6.5% and 24.6 ± 12.8%, respectively) while their shortening effect on APD was comparable. It is concluded that the electrophysiological effects of GS967 are similar to those of mexiletine, but with somewhat faster offset kinetics of V⁺_max block. However, since GS967 depressed V⁺_max and I_NaL at the same concentration, the current view that GS967 represents a new class of drugs that selectively block I_NaL has to be questioned and it is suggested that GS967 should be classified as a class I/B antiarrhythmic agent.

The conduction velocity-potassium relationship in the heart is modulated by sodium and calcium

The relationship between cardiac conduction velocity (CV) and extracellular potassium (K⁺) is biphasic, with modest hyperkalemia increasing CV and severe hyperkalemia slowing CV. Recent studies from our group suggest that elevating extracellular sodium (Na⁺) and calcium (Ca²⁺) can enhance CV by an extracellular pathway parallel to gap junctional coupling (GJC) called ephaptic coupling that can occur in the gap junction adjacent perinexus. However, it remains unknown whether these same interventions modulate CV as a function of K⁺. We hypothesize that Na⁺, Ca²⁺, and GJC can attenuate conduction slowing consequent to severe hyperkalemia. Elevating Ca²⁺ from 1.25 to 2.00 mM significantly narrowed perinexal width measured by transmission electron microscopy. Optically mapped, Langendorff-perfused guinea pig hearts perfused with increasing K⁺ revealed the expected biphasic CV-K⁺ relationship during perfusion with different Na⁺ and Ca²⁺ concentrations. Neither elevating Na⁺ nor Ca²⁺ alone consistently modulated the positive slope of CV-K⁺ or conduction slowing at 10-mM K⁺; however, combined Na⁺ and Ca²⁺ elevation significantly mitigated conduction slowing at 10-mM K⁺. Pharmacologic GJC inhibition with 30-μM carbenoxolone slowed CV without changing the shape of CV-K⁺ curves. A computational model of CV predicted that elevating Na⁺ and narrowing clefts between myocytes, as occur with perinexal narrowing, reduces the positive and negative slopes of the CV-K⁺ relationship but do not support a primary role of GJC or sodium channel conductance. These data demonstrate that combinatorial effects of Na⁺ and Ca²⁺ differentially modulate conduction during hyperkalemia, and enhancing determinants of ephaptic coupling may attenuate conduction changes in a variety of physiologic conditions.

Feeling the heat: source–sink mismatch as a mechanism underlying the failure of thermal tolerance

A mechanistic explanation for the tolerance limits of animals at high temperatures is still missing, but one potential target for thermal failure is the electrical signaling off cells and tissues. With this in mind, here I review the effects of high temperature on the electrical excitability of heart, muscle and nerves, and refine a hypothesis regarding high temperature-induced failure of electrical excitation and signal transfer [the temperature-dependent deterioration of electrical excitability (TDEE) hypothesis]. A central tenet of the hypothesis is temperature-dependent mismatch between the depolarizing ion current (i.e. source) of the signaling cell and the repolarizing ion current (i.e. sink) of the receiving cell, which prevents the generation of action potentials (APs) in the latter. A source–sink mismatch can develop in heart, muscles and nerves at high temperatures owing to opposite effects of temperature on source and sink currents. AP propagation is more likely to fail at the sites of structural discontinuities, including electrically coupled cells, synapses and branching points of nerves and muscle, which impose an increased demand of inward current. At these sites, temperature-induced source–sink mismatch can reduce AP frequency, resulting in low-pass filtering or a complete block of signal transmission. In principle, this hypothesis can explain a number of heat-induced effects, including reduced heart rate, reduced synaptic transmission between neurons and reduced impulse transfer from neurons to muscles. The hypothesis is equally valid for ectothermic and endothermic animals, and for both aquatic and terrestrial species. Importantly, the hypothesis is strictly mechanistic and lends itself to experimental falsification.

Combination of "generalized Trotter operator splitting" and "quadratic adaptive algorithm" method for tradeoff among speedup, stability, and accuracy in the Markov chain model of sodium ion channels in the ventricular cell model

The fast hybrid operator splitting (HOS) and stable uniformization (UNI) methods have been proposed to save computation cost and enhance stability for Markov chain model in cardiac cell simulations. Moreover, Chen-Chen-Luo's quadratic adaptive algorithm (CCL) combined with HOS or UNI was used to improve the tradeoff between speedup and stability, but without considering accuracy. To compromise among stability, acceleration, and accuracy, we propose a generalized Trotter operator splitting (GTOS) method combined with CCL independent of the asymptotic property of a particular ion-channel model. Due to the accuracy underestimation of the mixed root mean square error (MRMSE) method, threshold root mean square error (TRMSE) is proposed to evaluate computation accuracy. With the fixed time-step RK4 as a reference, the second-order GTOS combined with CCL (30.8-fold speedup) for the wild-type Markov chain model with nine states (WT-9 model) or (7.4-fold) for the wild-type Markov chain model with eight states (WT-8 model) is faster than UNI combined with CCL (15.6-fold) for WT-9 model or (1.2-fold) for WT-8 model, separately. Besides, the second-order GTOS combined with CCL has 3.81% TRMSE for WT-9 model or 4.32% TRMSE for WT-8 model more accurate than 72.43% TRMSE for WT-9 model or 136.17% TRMSE for WT-8 model of HOS combined with CCL. To compromise speedup and accuracy, low-order GTOS combined with CCL is suggested to have the advantages of high precision and low computation cost. For high-accuracy requirements, high-order GTOS combined with CCL is recommended. Graphical abstract.

A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms

Motivated by growing evidence for pathway heterogeneity and alternative functions of molecular machines, we demonstrate a computational approach for investigating two questions: (1) Are there multiple mechanisms (state-space pathways) by which a machine can perform a given function, such as cotransport across a membrane? (2) How can additional functionality, such as proofreading/error-correction, be built into machine function using standard biochemical processes? Answers to these questions will aid both the understanding of molecular-scale cell biology and the design of synthetic machines. Focusing on transport in this initial study, we sample a variety of mechanisms by employing Metropolis Markov chain Monte Carlo. Trial moves adjust transition rates among an automatically generated set of conformational and binding states while maintaining fidelity to thermodynamic principles and a user-supplied fitness/functionality goal. Each accepted move generates a new model. The simulations yield both single and mixed reaction pathways for cotransport in a simple environment with a single substrate along with a driving ion. In a “competitive” environment including an additional decoy substrate, several qualitatively distinct reaction pathways are found which are capable of extremely high discrimination coupled to a leak of the driving ion, akin to proofreading. The array of functional models would be difficult to find by intuition alone in the complex state-spaces of interest.

Molecular machines, which operate on the nanoscale, are proteins/complexes that perform remarkable tasks such as the selective absorption of nutrients into the cell by transporters. These complex machines are often described using a fairly simple set of states and transitions that may not account for the stochasticity and heterogeneity generally expected at the nanoscale at body temperature. New tools are needed to study the full array of possibilities. This study presents a novel in silico method to systematically generate testable molecular-machine kinetic models and explore alternative mechanisms, applied first to membrane transport proteins. Our initial results suggest these transport machines may contain mechanisms which ‘detoxify’ the cell of an unwanted toxin, as well as significantly discriminate against the import of the toxin. This novel approach should aid the experimental study of key physiological processes such as renal glucose re-absorption, rational drug design, and potentially the development of synthetic machines.

Conservation and divergence in NaChBac and NaV1.7 pharmacology reveals novel drug interaction mechanisms

Voltage-gated Na⁺ (Na_V) channels regulate homeostasis in bacteria and control membrane electrical excitability in mammals. Compared to their mammalian counterparts, bacterial Na_V channels possess a simpler, fourfold symmetric structure and have facilitated studies of the structural basis of channel gating. However, the pharmacology of bacterial Na_V remains largely unexplored. Here we systematically screened 39 Na_V modulators on a bacterial channel (NaChBac) and characterized a selection of compounds on NaChBac and a mammalian channel (human Na_V1.7). We found that while many compounds interact with both channels, they exhibit distinct functional effects. For example, the local anesthetics ambroxol and lidocaine block both Na_V1.7 and NaChBac but affect activation and inactivation of the two channels to different extents. The voltage-sensing domain targeting toxin BDS-I increases Na_V1.7 but decreases NaChBac peak currents. The pore binding toxins aconitine and veratridine block peak currents of Na_V1.7 and shift activation (aconitine) and inactivation (veratridine) respectively. In NaChBac, they block the peak current by binding to the pore residue F224. Nonetheless, aconitine has no effect on activation or inactivation, while veratridine only modulates activation of NaChBac. The conservation and divergence in the pharmacology of bacterial and mammalian Na_V channels provide insights into the molecular basis of channel gating and will facilitate organism-specific drug discovery.

Obtaining transition rates from single-channel data without initial parameter seeding

Background and Purpose: Ion-channels are membrane proteins that can adopt several distinct structural conformations. Some of the conformations are open and allow the passage of ions through the membrane; others are closed and hinder ion flow. Patch-clamp recordings of single ion-channels show if a channel is open or closed, but does not immediately reveal the underlying mechanism, which typically includes several open and closed conformations.With kinetic analysis of single-channel data, sequences of observed open and closed times are fitted to proposed schemes to deduct the underlying kinetics of the ion-channel. Current programs to perform kinetic analysis uses initial parameter guessing. Here an alternative approach that uses a global fitting procedure and no initial parameter seeding is developed and tested.Methods: Different fitting algorithms that use variations and combinations of Simplex-optimization, Genetic Algorithm and Particle Swarm are tested against simulated data with brief events removed as in real resolution limited data.Results: A two-step fitting algorithm that uses Particle Swarm optimization to find initial parameters and then a modified Simplex approach to fine-adjust the initial parameters successfully find the correct rates used for data simulation.Conclusions: SCAIM (Single Channel Analysis in MATLAB) facilitate the deduction of kinetic schemes underlying single-channel data.

Predicting Patient Response to the Antiarrhythmic Mexiletine Based on Genetic Variation

RATIONALE

Mutations in the SCN5A gene, encoding the α subunit of the Nav1.5 channel, cause a life-threatening form of cardiac arrhythmia, long QT syndrome type 3 (LQT3). Mexiletine, which is structurally related to the Na⁺ channel-blocking anesthetic lidocaine, is used to treat LQT3 patients. However, the patient response is variable, depending on the genetic mutation in SCN5A.

OBJECTIVE

The goal of this study is to understand the molecular basis of patients' variable responses and build a predictive statistical model that can be used to personalize mexiletine treatment based on patient's genetic variant.

METHODS AND RESULTS

We monitored the cardiac Na⁺ channel voltage-sensing domain (VSD) conformational dynamics simultaneously with other gating properties for the LQT3 variants. To systematically identify the relationship between mexiletine block and channel biophysical properties, we used a system-based statistical modeling approach to connect the multivariate properties to patient phenotype. We found that mexiletine altered the conformation of the Domain III VSD, which is the same VSD that many tested LQT3 mutations affect. Analysis of 15 LQT3 variants showed a strong correlation between the activation of the Domain III-VSD and the strength of the inhibition of the channel by mexiletine. Based on this improved molecular-level understanding, we generated a systems-based model based on a dataset of 32 LQT3 patients, which then successfully predicted the response of 7 out of 8 patients to mexiletine in a blinded, retrospective trial.

CONCLUSIONS

Our results imply that the modulated receptor theory of local anesthetic action, which confines local anesthetic binding effects to the channel pore, should be revised to include drug interaction with the Domain III-VSD. Using an algorithm that incorporates this mode of action, we can predict patient-specific responses to mexiletine, improving therapeutic decision making.

A Molecularly Detailed NaV1.5 Model Reveals a New Class I Antiarrhythmic Target

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Antiarrhythmic therapies remain suboptimal due to our inability to predict how drug interactions with ion channels will affect the ability of the tissue to initiate and sustain an arrhythmia.

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We built a computational framework that allows for in silico design of precision-targeted therapeutic agents that simultaneously assesses antiarrhythmic markers of success and failure at multiple spatial and time scales. Using this framework, a novel in silico mexiletine “booster” was designed that may dramatically improve the efficacy of mexiletine in suppression of arrhythmia triggers.

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These results provide a roadmap for the design of novel molecular-based therapy to treat myriad arrhythmia syndromes, including ventricular tachycardia, heart failure arrhythmias, and inherited arrhythmia syndromes.

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In summary, computational modeling approaches to drug discovery represent a novel tool to design and test precision-targeted therapeutic agents. By exploiting nontraditional ion channel drug targets, an entirely new dimension can be added to the wide parameter space of traditional antiarrhythmic drugs to develop more precision-targeted and potent Class I therapeutic agents.

Antiarrhythmic treatment strategies remain suboptimal due to our inability to predict how drug interactions with ion channels will affect the ability of the tissues to initiate and sustain an arrhythmia. We built a multiscale molecular model of the Na⁺ channel domain III (domain III voltage-sensing domain) to highlight the molecular underpinnings responsible for mexiletine drug efficacy. This model predicts that a hyperpolarizing shift in the domain III voltage-sensing domain is critical for drug efficacy and may be leveraged to design more potent Class I molecules. The model was therefore used to design, in silico, a theoretical mexiletine booster that can dramatically rescue a mutant resistant to the potent antiarrhythmic effects of mexiletine. Our framework provides a strategy for in silico design of precision-targeted therapeutic agents that simultaneously assesses antiarrhythmic markers of success and failure at multiple spatial and time scales. This approach provides a roadmap for the design of novel molecular-based therapy to treat myriad arrhythmia syndromes, including ventricular tachycardia, heart failure arrhythmias, and inherited arrhythmia syndromes.

Reduced hybrid/complex N-glycosylation disrupts cardiac electrical signaling and calcium handling in a model of dilated cardiomyopathy

Dilated cardiomyopathy (DCM) is the third most common cause of heart failure, with ~70% of DCM cases considered idiopathic. We showed recently, through genetic ablation of the MGAT1 gene, which encodes an essential glycosyltransferase (GlcNAcT1), that prevention of cardiomyocyte hybrid/complex N-glycosylation was sufficient to cause DCM that led to heart failure and early death. Our findings are consistent with increasing evidence suggesting a link between aberrant glycosylation and heart diseases of acquired and congenital etiologies. However, the mechanisms by which changes in glycosylation contribute to disease onset and progression remain largely unknown. Activity and gating of voltage-gated Na⁺ and K⁺ channels (Na_v and K_v respectively) play pivotal roles in the initiation, shaping and conduction of cardiomyocyte action potentials (APs) and aberrant channel activity was shown to contribute to cardiac disease. We and others showed that glycosylation can impact Na_v and K_v function; therefore, here, we investigated the effects of reduced cardiomyocyte hybrid/complex N-glycosylation on channel activity to investigate whether chronic aberrant channel function can contribute to DCM. Ventricular cardiomyocytes from MGAT1 deficient (MGAT1KO) mice display prolonged APs and pacing-induced aberrant early re-activation that can be attributed to, at least in part, a significant reduction in K_v expression and activity that worsens over time suggesting heart disease-related remodeling. MGAT1KO Na_v demonstrate no change in expression or maximal conductance but show depolarizing shifts in voltage-dependent gating. Together, the changes in MGAT1KO Na_v and K_v function likely contribute to observed anomalous electrocardiograms and Ca²⁺ handling. These findings provide insight into mechanisms by which altered glycosylation contributes to DCM through changes in Na_v and K_v activity that impact conduction, Ca²⁺ handling and contraction. The MGAT1KO can also serve as a useful model to study the effects of aberrant electrical signaling on cardiac function and the remodeling events that can occur with heart disease progression.

Phosphorylation of cardiac voltage-gated sodium channel: Potential players with multiple dimensions

Cardiomyocytes are highly coordinated cells with multiple proteins organized in micro domains. Minor changes or interference in subcellular proteins can cause major disturbances in physiology. The cardiac sodium channel (Na_V1.5) is an important determinant of correct electrical activity in cardiomyocytes which are localized at intercalated discs, T‐tubules and lateral membranes in the form of a macromolecular complex with multiple interacting protein partners. The channel is tightly regulated by post‐translational modifications for smooth conduction and propagation of action potentials. Among regulatory mechanisms, phosphorylation is an enzymatic and reversible process which modulates Na_V1.5 channel function by attaching phosphate groups to serine, threonine or tyrosine residues. Phosphorylation of Na_V1.5 is implicated in both normal physiological and pathological processes and is carried out by multiple kinases. In this review, we discuss and summarize recent literature about the (a) structure of Na_V1.5 channel, (b) formation and subcellular localization of Na_V1.5 channel macromolecular complex, (c) post‐translational phosphorylation and regulation of Na_V1.5 channel, and (d) how these phosphorylation events of Na_V1.5 channel alter the biophysical properties and affect the channel during disease status. We expect, by reviewing these aspects will greatly improve our understanding of Na_V1.5 channel biology, physiology and pathology, which will also provide an insight into the mechanism of arrythmogenesis at molecular level.