Lucie Delemotte

Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations

The response of a membrane-bound Kv1.2 ion channel to an applied transmembrane potential has been studied using molecular dynamics simulations. Channel deactivation is shown to involve three intermediate states of the voltage sensor domain (VSD), and concomitant movement of helix S4 charges 10–15 Å along the bilayer normal; the latter being enabled by zipper-like sequential pairing of S4 basic residues with neighboring VSD acidic residues and membrane-lipid head groups. During the observed sequential transitions S4 basic residues pass through the recently discovered charge transfer center with its conserved phenylalanine residue, F233. Analysis indicates that the local electric field within the VSD is focused near the F233 residue and that it remains essentially unaltered during the entire process. Overall, the present computations provide an atomistic description of VSD response to hyperpolarization, add support to the sliding helix model, and capture essential features inferred from a variety of recent experiments.

Molecular Dynamics Simulations of Lipid Membrane Electroporation

The permeability of cell membranes can be transiently increased following the application of external electric fields. Theoretical approaches such as molecular modeling provide a significant insight into the processes affecting, at the molecular level, the integrity of lipid cell membranes when these are subject to voltage gradients under similar conditions as those used in experiments. This article reports on the progress made so far using such simulations to model membrane—lipid bilayer—electroporation. We first describe the methods devised to perform in silico experiments of membranes subject to nanosecond, megavolt-per-meter pulsed electric fields and of membranes subject to charge imbalance, mimicking therefore the application of low-voltage, long-duration pulses. We show then that, at the molecular level, the two types of pulses produce similar effects: provided the TM voltage these pulses create are higher than a certain threshold, hydrophilic pores stabilized by the membrane lipid headgroups form within the nanosecond time scale across the lipid core. Similarly, when the pulses are switched off, the pores collapse (close) within similar time scales. It is shown that for similar TM voltages applied, both methods induce similar electric field distributions within the membrane core. The cascade of events following the application of the pulses, and taking place at the membrane, is a direct consequence of such an electric field distribution.

Modeling Membranes under a Transmembrane Potential

Accurate modeling of ion transport through synthetic and biological transmembrane channels has been so far a challenging problem. We introduce here a new method that allows one to study such transport under realistic biological conditions. We present results from molecular dynamics simulations of an ion channel formed by a peptide nanotube, embedded in a lipid bilayer, and subject to transmembrane potentials generated by asymmetric distributions of ions on both sides of the membrane. We show that the method is efficient for generating ionic currents and allows us to estimate the intrinsic conductance of the channel.

Transport of siRNA through lipid membranes driven by nanosecond electric pulses: an experimental and computational study.

The use of small interfering RNA (siRNA) is a blossoming technique for gene regulation. However, its therapeutic potential is today severely hampered by the lack of an efficient means of safely delivering these nucleic acids to the intracellular medium. We report here that a single 10 ns high-voltage electric pulse can permeabilize lipid vesicles and allow the delivery of siRNA to the cytoplasm. Combining experiments and molecular dynamics simulations has allowed us to provide the detailed molecular mechanisms of such transport and to give practical guidance for the design of protocols aimed at using nanosecond-pulse siRNA electro-delivery in medical and biotechnological applications.

Gating pore currents and the resting state of Nav1.4 voltage sensor domains

Mammalian voltage-gated sodium channels are composed of four homologous voltage sensor domains (VSDs; DI, DII, DIII, and DIV) in which their S4 segments contain a variable number of positively charged residues. We used single histidine (H) substitutions of these charged residues in the Nav1.4 channel to probe the positions of the S4 segments at hyperpolarized potentials. The substitutions led to the formation of gating pores that were detected as proton leak currents through the VSDs. The leak currents indicated that the mutated residues are accessible from both sides of the membrane. Leak currents of different magnitudes appeared in the DI/R1H, DII/R1H, and DIII/R2H mutants, suggesting that the resting state position of S4 varies depending on the domain. Here, DI/R1H indicates the first arginine R1, in domain DI, has been mutated to histidine. The single R1H, R2H, and R3H mutations in DIV did not produce appreciable proton currents, indicating that the VSDs had different topologies. A structural model of the resting states of the four VSDs of Nav1.4 relaxed in their membrane/solution environment using molecular dynamics simulations is proposed based on the recent NavAb sodium channel X-ray structure. The model shows that the hydrophobic septa that isolate the intracellular and the extracellular media within the DI, DII, and DIII VSDs are ∼2 Å long, similar to those of Kv channels. However, the septum of DIV is longer, which prevents water molecules from hydrating the center of the VSD, thus breaking the proton conduction pathway. This structural model rationalizes the activation sequence of the different VSDs of the Nav1.4 channel.

Conduction in a biological sodium selective channel.

The crystal structure of NavAb, a bacterial voltage gated Na(+) channel, exhibits a selectivity filter (SF) wider than that of K(+) channels. This new structure provides the opportunity to explore the mechanism of conduction and help rationalize its selectivity for sodium. Recent molecular dynamics (MD) simulations of single- and two-ion permeation processes have revealed that a partially hydrated Na(+) permeates the channel by exploring three SF binding sites while being loosely coupled to other ions and/or water molecules; a finding that differs significantly from the behavior of K(+) selective channels. Herein, we present results derived from a combination of metadynamics and voltage-biased MD simulations that throws more light on the nature of the Na(+) conduction mechanism. Conduction under 0 mV bias explores several distinct pathways involving the binding of two ions to three possible SF sites. While these pathways are very similar to those observed in the presence of a negative potential (inward conduction), a completely different mechanism operates for outward conduction at positive potentials.

Understanding TRPV1 activation by ligands: Insights from the binding modes of capsaicin and resiniferatoxin

Significance Using computational methodologies, we refined the binding modes of the transient receptor potential cation channel subfamily V member 1 (TRPV1) modulators, capsaicin and resiniferatoxin, provided by the recent experimental cryo-electron microscopy electron density. The resulting insights enable us to predict the binding pose of 96 additional TRPV1 agonists, which we compare with reported mutagenesis studies. Specifically, we characterize the response of five previously unidentified mutants to capsaicin and resiniferatoxin. Analysis of the amino acids engaged in favorable ligand–channel interactions defines the key structural determinants of the TRPV1 vanilloid binding site. The transient receptor potential cation channel subfamily V member 1 (TRPV1) or vanilloid receptor 1 is a nonselective cation channel that is involved in the detection and transduction of nociceptive stimuli. Inflammation and nerve damage result in the up-regulation of TRPV1 transcription, and, therefore, modulators of TRPV1 channels are potentially useful in the treatment of inflammatory and neuropathic pain. Understanding the binding modes of known ligands would significantly contribute to the success of TRPV1 modulator drug design programs. The recent cryo-electron microscopy structure of TRPV1 only provides a coarse characterization of the location of capsaicin (CAPS) and resiniferatoxin (RTX). Herein, we use the information contained in the experimental electron density maps to accurately determine the binding mode of CAPS and RTX and experimentally validate the computational results by mutagenesis. On the basis of these results, we perform a detailed analysis of TRPV1–ligand interactions, characterizing the protein ligand contacts and the role of individual water molecules. Importantly, our results provide a rational explanation and suggestion of TRPV1 ligand modifications that should improve binding affinity.

Evolutionary imprint of activation: The design principles of VSDs

Approaches from information theory and probabilistic modeling show that voltage-sensing domain sequences conform to a small set of rules.

Dual Effect of Phosphatidyl (4,5)-Bisphosphate PIP2 on Shaker K+ Channels

Background: Phosphatidylinositol (4,5)-bisphosphate (PIP2) regulates several voltage-gated K+ channels, but the molecular mechanism remains elusive. Results: PIP2 exerts on Shaker opposite effects on maximal current amplitude and activation voltage dependence. Conclusion: PIP2 stabilizes the gate in the open state and the voltage sensor in the resting state. Significance: This is the first description of an effect of PIP2 on voltage sensor movement. Phosphatidylinositol (4,5)-bisphosphate (PIP2) is a phospholipid of the plasma membrane that has been shown to be a key regulator of several ion channels. Functional studies and more recently structural studies of Kir channels have revealed the major impact of PIP2 on the open state stabilization. A similar effect of PIP2 on the delayed rectifiers Kv7.1 and Kv11.1, two voltage-gated K+ channels, has been suggested, but the molecular mechanism remains elusive and nothing is known on PIP2 effect on other Kv such as those of the Shaker family. By combining giant-patch ionic and gating current recordings in COS-7 cells, and voltage-clamp fluorimetry in Xenopus oocytes, both heterologously expressing the voltage-dependent Shaker channel, we show that PIP2 exerts 1) a gain-of-function effect on the maximal current amplitude, consistent with a stabilization of the open state and 2) a loss-of-function effect by positive-shifting the activation voltage dependence, most likely through a direct effect on the voltage sensor movement, as illustrated by molecular dynamics simulations.

Dual effect of PIP2 on Shaker potassium channels

Background: Phosphatidylinositol (4,5)-bisphosphate (PIP2) regulates several voltage-gated K+ channels, but the molecular mechanism remains elusive. Results: PIP2 exerts on Shaker opposite effects on maximal current amplitude and activation voltage dependence. Conclusion: PIP2 stabilizes the gate in the open state and the voltage sensor in the resting state. Significance: This is the first description of an effect of PIP2 on voltage sensor movement. Phosphatidylinositol (4,5)-bisphosphate (PIP2) is a phospholipid of the plasma membrane that has been shown to be a key regulator of several ion channels. Functional studies and more recently structural studies of Kir channels have revealed the major impact of PIP2 on the open state stabilization. A similar effect of PIP2 on the delayed rectifiers Kv7.1 and Kv11.1, two voltage-gated K+ channels, has been suggested, but the molecular mechanism remains elusive and nothing is known on PIP2 effect on other Kv such as those of the Shaker family. By combining giant-patch ionic and gating current recordings in COS-7 cells, and voltage-clamp fluorimetry in Xenopus oocytes, both heterologously expressing the voltage-dependent Shaker channel, we show that PIP2 exerts 1) a gain-of-function effect on the maximal current amplitude, consistent with a stabilization of the open state and 2) a loss-of-function effect by positive-shifting the activation voltage dependence, most likely through a direct effect on the voltage sensor movement, as illustrated by molecular dynamics simulations.