José D Faraldo-Gómez

Voltage-gated K ⁺ channels play central roles in human physiology, in health, and disease. A repertoire of inhibitors that are both potent and specific would, therefore, be of great value. RY785 has been described as promising in this regard, as it selectively inhibits channels in the Kv2 subfamily with high potency. Its mechanism of action has not yet been determined at the molecular level, but functional studies indicate it differs from those of less specific inhibitors, such as quaternary-ammonium compounds or aminopyridines. To examine this mechanism at the single-molecule level, we have carried out a series of all-atom molecular dynamics simulations based on the structure of the Kv2.1 channel in the ion-conducting state. The simulations demonstrate both RY785 and tetraethylammonium spontaneously enter the channel interior through the cytoplasmic gate, but with distinct effects. Tetraethylammonium binds to a site adjacent to the selectivity filter, on the pore axis, thus blocking the flow of K ⁺ ions. RY785, by contrast, binds to the channel walls, off-axis, and allows K ⁺ flow while the gate remains open. This observation indicates RY785 inhibits Kv2.1 by fostering the occlusion of the gate, through a network of hydrophobic interactions therein, explaining why it also modulates the voltage-sensing mechanism of the channel, 3 nanometers away.

Voltage-gated K+ channels play central roles in human physiology, both in health and disease. A repertoire of inhibitors that are both potent and specific would therefore be of great value, not only as pharmacological agents but also as research tools. The small molecule RY785 has been described as particularly promising in this regard, as it selectively inhibits channels in the Kv2 subfamily with high potency. Kv2 channels are expressed in multiple cell types in humans, and are of particular importance for neuronal function. The mechanism of action of RY785 has not yet been determined at the molecular level, but functional studies indicate it differs from that of less specific inhibitors, such as quaternary-ammonium compounds or aminopyridines; RY785 is distinct also in that it is electroneutral. To examine this mechanism at the single-molecule level, we have carried out a series of all-atom molecular dynamics simulations based on the experimental structure of the Kv2.1 channel in the activated, open state. First, we report a 25-microsecond trajectory calculated in the absence of any inhibitor, under an applied voltage of 100 mV, which demonstrates outward K+ flow under simulation conditions at rates comparable to experimental measurements. Additional simulations in which either RY785 or tetraethylammonium (TEA) is introduced in solution and allowed to interact with the pore domain show both inhibitors spontaneously enter the channel interior through the cytoplasmic gate, but with distinct effects. In agreement with prior structural studies, we observe that TEA binds to a site adjacent to the selectivity filter, on the pore axis, thereby blocking the flow of K+ ions. RY785, by contrast, binds to the channel walls, off-axis, and allows K+ flow while the cytoplasmic gate remains open. The observed mode of RY785 binding, however, indicates that its mechanism of action is to stabilize and occlude a semi-open state of the gate, by bridging hydrophobic protein-protein interactions therein; this hypothesis would explain the puzzling experimental observation that RY785 recognition influences the gating currents generated by the voltage sensors, 3 nm away.

A broad range of cellular functions involve transient or persistent changes in the morphology of lipid membranes, from the organellar to the molecular scale. By and large, the thermodynamics of these remodeling processes remain to be understood. Molecular Dynamics simulations enhanced by advanced sampling methods are uniquely suited to examine and quantitate these phenomena. Here, we focus on the cellular process known as mechanosensation and use the Multi-Map simulation method to quantify how applied lateral tension impacts the energetics of both global and localized membrane perturbations induced extrinsically. We also examine how tension impacts the dynamics of lipid molecules. We find that the conformational energetics of the membrane clearly differs when it is stretched, and that this difference increases with the magnitude of the applied tension. The reason is not that tension alters the mechanical properties of the lipid bilayer, such as its bending modulus, but rather that it opposes any reduction in the projected area of the membrane relative to that at rest, while the opposite is favored. It follows that tension may shift a conformational equilibrium of a protein that deforms the membrane differently in alternative functional states, if that difference also entails a change in the projected membrane area. Conversely, we find that stretch has little to no effect on the dynamics of lipids at the single-molecule level, implying it would also have no bearing on the lifetime of specific protein-lipid interactions. Finally, we show how changes in lipid composition that result in global membrane thinning can mimic the effect of lateral stretch without any applied tension. Statement of Significance: Cells have evolved the ability to sense mechanical forces, such as pressure or stretch, through specialized proteins embedded in their membranes. How exactly the membrane transduces these stimuli to the proteins therein has been unclear. Using state-of-the-art computer simulations, we show that stretching a membrane does not result in forces that pull or push on the individual lipid molecules that constitute the membrane. Instead, lateral tension alters the energetics of reshaping the membrane. This shift in plasticity explains why several well-known force-sensing proteins switch between active and inactive states at specific tension values observed experimentally. We also show that altering the lipid composition of the membrane can produce the same effect as lateral stretch, without any applied force.

The mechanism by which lipids regulate membrane proteins remains an open question. While many protein structures reveal associated lipids, neither binding nor regulatory mechanisms can be gleaned from frozen static snapshots, as these processes occur in the context of a dynamic membrane at equilibrium. In this study, we combine single-molecule experiments with computational analyses of lipid dynamics and lipid-solvation energetics to understand how changes in the lipid composition of the membrane influence the dimerization of the CLC-ec1 chloride/proton antiporter. We find this influence does not result from long-lived lipid binding at specific sites, but instead from an inherently dynamic effect known as preferential lipid solvation, which ultimately determines the relative thermodynamic stability of associated and dissociated dimers. This study provides a foundation for linking lipid composition to the modulation of membrane protein conformational equilibria and a framework for discriminating among different lipid regulation mechanisms in membranes.

Voltage-gated K⁺ channels play central roles in human physiology, both in health and disease. A repertoire of inhibitors that are both potent and specific would therefore be of great value, not only as pharmacological agents but also as research tools. The small molecule RY785 has been described as particularly promising in this regard, as it selectively inhibits channels in the Kv2 subfamily with high potency. Kv2 channels are expressed in multiple cell types in humans, and are of particular importance for neuronal function. The mechanism of action of RY785 has not yet been determined at the molecular level, but functional studies indicate it differs from that of less specific inhibitors, such as quaternary-ammonium compounds or aminopyridines; RY785 is distinct also in that it is electroneutral. To examine this mechanism at the single-molecule level, we have carried out a series of all-atom molecular dynamics simulations based on the experimental structure of the Kv2.1 channel in the activated, open state. First, we report a 25-microsecond trajectory calculated in the absence of any inhibitor, under an applied voltage of 100 mV, which demonstrates outward K⁺ flow under simulation conditions at rates comparable to experimental measurements. Additional simulations in which either RY785 or tetraethylammonium (TEA) is introduced in solution show both inhibitors spontaneously enter the channel through the cytoplasmic gate, with distinct effects. In agreement with prior structural studies, we observe that TEA binds to a site adjacent to the selectivity filter, on the pore axis, thereby blocking the flow of K⁺ ions. RY785, by contrast, binds to the channel walls, off-axis, and allows K⁺ flow while the cytoplasmic gate remains open. The observed mode of RY785 binding, however, indicates that its mechanism of action is to stabilize and occlude a semi-open state of the gate, by bridging hydrophobic protein-protein interactions therein; this hypothesis would explain the puzzling experimental observation that RY785 recognition influences the gating currents generated by the voltage sensors, 3 nm away.

Secondary-active transporters catalyze the movement of myriad substances across all cellular membranes, typically against opposing concentration gradients, and without consuming any ATP. To do so, these proteins employ an intriguing structural mechanism evolved to be activated only upon recognition or release of the transported species. We examine this self-regulated mechanism using a homolog of the cardiac Na ⁺ /Ca ²⁺ exchanger as a model system. Using advanced computer simulations, we map out the complete functional cycle of this transporter, including unknown conformations that we validate against existing experimental data. Calculated free-energy landscapes reveal why this transporter functions as an antiporter rather than a symporter, why it specifically exchanges Na ⁺ and Ca ²⁺ , and why the stoichiometry of this exchange is exactly 3:1. We also rationalize why the protein does not exchange H ⁺ for either Ca ²⁺ or Na ⁺ , despite being able to bind H ⁺ and its high similarity with H ⁺ /Ca ²⁺ exchangers. Interestingly, the nature of this transporter is not explained by its primary structural states, known as inward- and outward-open conformations; instead, the defining factor is the feasibility of conformational intermediates between those states, wherein access pathways leading to the substrate binding sites become simultaneously occluded from both sides of the membrane. This analysis offers a physically coherent, broadly transferable route to understand the emergence of function from structure among secondary-active membrane transporters.

Eukaryotic voltage-gated K ⁺ channels have been extensively studied, but the structural bases for some of their most salient functional features remain to be established. C-type inactivation, for example, is an auto-inhibitory mechanism that confers temporal resolution to their signal-firing activity. In a recent breakthrough, studies of a mutant of Shaker that is prone to inactivate indicated that this process entails a dilation of the selectivity filter, the narrowest part of the ion conduction pathway. Here, we report an atomic-resolution cryo–electron microscopy structure that demonstrates that the wild-type channel can also adopt this dilated state. All-atom simulations corroborate this conformation is congruent with the electrophysiological characteristics of the C-type inactivated state, namely, residual K ⁺ conductance and altered ion specificity, and help rationalize why inactivation is accelerated or impeded by certain mutations. In summary, this study establishes the molecular basis for an important self-regulatory mechanism in eukaryotic K ⁺ channels, laying a solid foundation for further studies.

Many ion channels are multisubunit complexes where oligomerization is an obligatory requirement for function as the binding axis forms the charged permeation pathway. However, the mechanisms of in-membrane assembly of thermodynamically stable channels are largely unknown. Here, we demonstrate a key advance by reporting the dimerization equilibrium reaction of an inverted-topology, homodimeric fluoride channel Fluc in lipid bilayers. While the wild-type channel is a long-lived dimer, we leverage a known mutation, N43S, that weakens Na ⁺ binding in a buried site at the interface, thereby unlocking the complex for reversible association in lipid bilayers. Single-channel recordings show that Na ⁺ binding is required for fluoride conduction while single-molecule microscopy experiments demonstrate that N43S Fluc exists in a dynamic monomer–dimer equilibrium in the membrane, even following removal of Na ⁺ . Quantifying the thermodynamic stability while titrating Na ⁺ indicates that dimerization occurs first, providing a membrane-embedded binding site where Na ⁺ binding weakly stabilizes the complex. To understand how these subunits form stable assemblies while presenting charged surfaces to the membrane, we carried out molecular dynamics simulations, which show the formation of a thinned membrane defect around the exposed dimerization interface. In simulations where subunits are permitted to encounter each other while preventing protein contacts, we observe spontaneous and selective association at the native interface, where stability is achieved by mitigation of the membrane defect. These results suggest a model wherein membrane-associated forces drive channel assembly in the native orientation while subsequent factors, such as Na ⁺ binding, result in channel activation.

Ca²⁺ is an important signaling messenger. In microorganisms, fungi, and plants, H⁺/Ca²⁺ antiporters (CAX) are known to play key roles in the homeostasis of intracellular Ca²⁺ by catalyzing its efflux across the cell membrane. Here, we reveal that the bacterial CAX homolog YfkE transports Ca²⁺ in two distinct modes: a low-flux H⁺/Ca²⁺ exchange mode and a high-flux mode in which Ca²⁺ and phosphate ions are co-transported (1:1) in exchange for H⁺. Coupling with phosphate greatly accelerates the Ca²⁺ efflux activity of YfkE. Our studies reveal that Ca²⁺ and phosphate bind to adjacent sites in a central translocation pathway and lead to mechanistic insights that explain how this CAX alters its conserved alpha-repeat motifs to adopt phosphate as a specific “transport chaperon” for Ca²⁺ translocation. This finding uncovers a co-transport mechanism within the CAX family that indicates this class of proteins contributes to the cellular homeostasis of both Ca²⁺ and phosphate.