Determining the molecular basis of voltage sensitivity in membrane proteins

Silencing of ATP1A1 attenuates cell membrane disruption by nanosecond electric pulses

This study explored the role of the Na/K-ATPase (NKA) in membrane permeabilization induced by nanosecond electric pulses. Using CRISPR/Cas9 and shRNA, we silenced the ATP1A1 gene, which encodes α1 NKA subunit in U937 human monocytes. Silencing reduced the rate and the cumulative uptake of YoPro-1 dye after electroporation by 300-ns, 7-10 kV/cm pulses, while ouabain, a specific NKA inhibitor, enhanced YoPro-1 entry. We conclude that the α1 subunit supports the electropermeabilized membrane state, by forming or stabilizing electropores or by hindering repair mechanisms, and this role is independent of NKA's ion pump function.

Mitochondrial sAC-cAMP-PKA Axis Modulates the ΔΨm-Dependent Control Coefficients of the Respiratory Chain Complexes: Evidence of Respirasome Plasticity

The current view of the mitochondrial respiratory chain complexes I, III and IV foresees the occurrence of their assembly in supercomplexes, providing additional functional properties when compared with randomly colliding isolated complexes. According to the plasticity model, the two structural states of the respiratory chain may interconvert, influenced by the intracellular prevailing conditions. In previous studies, we suggested the mitochondrial membrane potential as a factor for controlling their dynamic balance. Here, we investigated if and how the cAMP/PKA-mediated signalling influences the aggregation state of the respiratory complexes. An analysis of the inhibitory titration profiles of the endogenous oxygen consumption rates in intact HepG2 cells with specific inhibitors of the respiratory complexes was performed to quantify, in the framework of the metabolic flux theory, the corresponding control coefficients. The attained results, pharmacologically inhibiting either PKA or sAC, indicated that the reversible phosphorylation of the respiratory chain complexes/supercomplexes influenced their assembly state in response to the membrane potential. This conclusion was supported by the scrutiny of the available structure of the CI/CIII2/CIV respirasome, enabling us to map several PKA-targeted serine residues exposed to the matrix side of the complexes I, III and IV at the contact interfaces of the three complexes.

Domain- and state-specific shape of the electric field tunes voltage sensing in voltage-gated sodium channels

The ability to sense transmembrane voltage underlies most physiological roles of voltage-gated sodium (Nav) channels. Whereas the key role of their voltage-sensing domains (VSDs) in channel activation is well established, the molecular underpinnings of voltage coupling remain incompletely understood. Voltage-dependent energetics of the activation process can be described in terms of the gating charge that is defined by coupling of charged residues to the external electric field. The shape of the electric field within VSDs is therefore crucial for the activation of voltage-gated ion channels. Here, we employed molecular dynamics simulations of cardiac Nav1.5 and bacterial NavAb, together with our recently developed tool g_elpot, to gain insights into the voltage-sensing mechanisms of Nav channels via high-resolution quantification of VSD electrostatics. In contrast to earlier low-resolution studies, we found that the electric field within VSDs of Nav channels has a complex isoform- and domain-specific shape, which prominently depends on the activation state of a VSD. Different VSDs vary not only in the length of the region where the electric field is focused but also differ in their overall electrostatics, with possible implications in the diverse ion selectivity of their gating pores. Due to state-dependent field reshaping, not only translocated basic but also relatively immobile acidic residues contribute significantly to the gating charge. In the case of NavAb, we found that the transition between structurally resolved activated and resting states results in a gating charge of 8e, which is noticeably lower than experimental estimates. Based on the analysis of VSD electrostatics in the two activation states, we propose that the VSD likely adopts a deeper resting state upon hyperpolarization. In conclusion, our results provide an atomic-level description of the gating charge, demonstrate diversity in VSD electrostatics, and reveal the importance of electric-field reshaping for voltage sensing in Nav channels.

Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine

Voltage-gated potassium channels of the Kv7.x family are involved in a plethora of biological processes across many tissues in animals, and their misfunctioning could lead to several pathologies ranging from diseases caused by neuronal hyperexcitability, such as epilepsy, or traumatic injuries and painful diabetic neuropathy to autoimmune disorders. Among the members of this family, the Kv7.2 channel can form hetero-tetramers together with Kv7.3, forming the so-called M-channels, which are primary regulators of intrinsic electrical properties of neurons and of their responsiveness to synaptic inputs. Here, prompted by the similarity between the M-current and that in Kv7.2 alone, we perform a computational-based characterization of this channel in its different conformational states and in complex with the modulator retigabine. After validation of the structural models of the channel by comparison with experimental data, we investigate the effect of retigabine binding on the two extreme states of Kv7.2 (resting-closed and activated-open). Our results suggest that binding, so far structurally characterized only in the intermediate activated-closed state, is possible also in the other two functional states. Moreover, we show that some effects of this binding, such as increased flexibility of voltage sensing domains and propensity of the pore for open conformations, are virtually independent on the conformational state of the protein. Overall, our results provide new structural and dynamic insights into the functioning and the modulation of Kv7.2 and related channels.

A novel theoretical framework reveals more than one voltage-sensing pathway in the lateral membrane of outer hair cells

Outer hair cell (OHC) electromotility amplifies acoustic vibrations throughout the frequency range of hearing. Electromotility requires that the lateral membrane protein prestin undergo a conformational change upon changes in the membrane potential to produce an associated displacement charge. The magnitude of the charge displaced and the mid-reaction potential (when one half of the charge is displaced) reflects whether the cells will produce sufficient gain at the resting membrane potential to boost sound in vivo. Voltage clamp measurements performed under near-identical conditions ex vivo show the charge density and mid-reaction potential are not always the same, confounding interpretation of the results. We compare the displacement charge measurements in OHCs from rodents with a theory shown to exhibit good agreement with in silico simulations of voltage-sensing reactions in membranes. This model equates the charge density to the potential difference between two pseudo-equilibrium states of the sensors when they are in a stable conformation and not contributing to the displacement current. The model predicts this potential difference to be one half of its value midway into the reaction, when one equilibrium conformation transforms to the other pseudo-state. In agreement with the model, we find the measured mid-reaction potential to increase as the charge density decreases to exhibit a negative slope of ∼1/2. This relationship suggests that the prestin sensors exhibit more than one stable hyperpolarized state and that voltage sensing occurs by more than one pathway. We determine the electric parameters for prestin sensors and use the analytical expressions of the theory to estimate the energy barriers for the two voltage-dependent pathways. This analysis explains the experimental results, supports the theoretical approach, and suggests that voltage sensing occurs by more than one pathway to enable amplification throughout the frequency range of hearing.

g_elpot: A Tool for Quantifying Biomolecular Electrostatics from Molecular Dynamics Trajectories

Electrostatic forces drive a wide variety of biomolecular processes by defining the energetics of the interaction between biomolecules and charged substances. Molecular dynamics (MD) simulations provide trajectories that contain ensembles of structural configurations sampled by biomolecules and their environment. Although this information can be used for high-resolution characterization of biomolecular electrostatics, it has not yet been possible to calculate electrostatic potentials from MD trajectories in a way allowing for quantitative connection to energetics. Here, we present g_elpot, a GROMACS-based tool that utilizes the smooth particle mesh Ewald method to quantify the electrostatics of biomolecules by calculating potential within water molecules that are explicitly present in biomolecular MD simulations. g_elpot can extract the global distribution of the electrostatic potential from MD trajectories and measure its time course in functionally important regions of a biomolecule. To demonstrate that g_elpot can be used to gain biophysical insights into various biomolecular processes, we applied the tool to MD trajectories of the P2X3 receptor, TMEM16 lipid scramblases, the secondary-active transporter Glt_Ph, and DNA complexed with cationic polymers. Our results indicate that g_elpot is well suited for quantifying electrostatics in biomolecular systems to provide a deeper understanding of its role in biomolecular processes.

Structural Pharmacology of Voltage-Gated Sodium Channels

Voltage-gated sodium (Na_V) channels initiate and propagate action potentials in excitable tissues to mediate key physiological processes including heart contraction and nervous system function. Accordingly, Na_V channels are major targets for drugs, toxins and disease-causing mutations. Recent breakthroughs in cryo-electron microscopy have led to the visualization of human Na_V1.1, Na_V1.2, Na_V1.4, Na_V1.5 and Na_V1.7 channel subtypes at high-resolution. These landmark studies have greatly advanced our structural understanding of channel architecture, ion selectivity, voltage-sensing, electromechanical coupling, fast inactivation, and the molecular basis underlying Na_V channelopathies. Na_V channel structures have also been increasingly determined in complex with toxin and small molecule modulators that target either the pore module or voltage sensor domains. These structural studies have provided new insights into the mechanisms of pharmacological action and opportunities for subtype-selective Na_V channel drug design. This review will highlight the structural pharmacology of human Na_V channels as well as the potential use of engineered and chimeric channels in future drug discovery efforts.

Pulsed Electric Fields Can Create Pores in the Voltage Sensors of Voltage-Gated Ion Channels

Pulsed electric fields are increasingly used in medicine to transiently increase the cell membrane permeability via electroporation to deliver therapeutic molecules into the cell. One type of event that contributes to this increase in membrane permeability is the formation of pores in the membrane lipid bilayer. However, electrophysiological measurements suggest that membrane proteins are affected as well, particularly voltage-gated ion channels (VGICs). The molecular mechanisms by which the electric field could affects these molecules remain unidentified. In this study, we used molecular dynamics simulations to unravel the molecular events that take place in different VGICs when exposing them to electric fields mimicking electroporation conditions. We show that electric fields can induce pores in the voltage-sensor domains (VSDs) of different VGICs and that these pores form more easily in some channels than in others. We demonstrate that poration is more likely in VSDs that are more hydrated and are electrostatically more favorable for the entry of ions. We further show that pores in VSDs can expand into so-called complex pores, which become stabilized by lipid headgroups. Our results suggest that such complex pores are considerably more stable than conventional lipid pores, and their formation can lead to severe unfolding of VSDs from the channel. We anticipate that such VSDs become dysfunctional and unable to respond to changes in transmembrane voltage, which is in agreement with previous electrophysiological measurements showing a decrease in the voltage-dependent transmembrane ionic currents after pulse treatment. Finally, we discuss the possibility of activation of VGICs by submicrosecond-duration pulses. Overall, our study reveals a new, to our knowledge, mechanism of electroporation through membranes containing VGICs.

Molecular Insights from Conformational Ensembles via Machine Learning

Biomolecular simulations are intrinsically high dimensional and generate noisy data sets of ever-increasing size. Extracting important features from the data is crucial for understanding the biophysical properties of molecular processes, but remains a big challenge. Machine learning (ML) provides powerful dimensionality reduction tools. However, such methods are often criticized as resembling black boxes with limited human-interpretable insight. We use methods from supervised and unsupervised ML to efficiently create interpretable maps of important features from molecular simulations. We benchmark the performance of several methods, including neural networks, random forests, and principal component analysis, using a toy model with properties reminiscent of macromolecular behavior. We then analyze three diverse biological processes: conformational changes within the soluble protein calmodulin, ligand binding to a G protein-coupled receptor, and activation of an ion channel voltage-sensor domain, unraveling features critical for signal transduction, ligand binding, and voltage sensing. This work demonstrates the usefulness of ML in understanding biomolecular states and demystifying complex simulations.

Structural basis of temperature sensation by the TRP channel TRPV3

We present structures of mouse TRPV3 in temperature-dependent open, closed and intermediate states that suggest two-step activation of TRPV3 by heat. During the strongly temperature-dependent first step, sensitization, the channel pore remains closed while S6 helices undergoe α-to-π transitions. During the weakly temperature-dependent second step, channel opening, tight association of the S1–S4 and pore domains is stabilized by changes in the C-terminal and linker domains.

Predicting voltage sensing

New method predicts the molecular basis of membrane proteins’ voltage sensitivity.

New method predicts the molecular basis of membrane proteins’ voltage sensitivity.