K+ and Na+ Conduction in Selective and Nonselective Ion Channels Via Molecular Dynamics Simulations

Generations of scientists have been captivated by ion channels and how they control the workings of the cell by admitting ions from one side of the cell membrane to the other. Elucidating the molecular determinants of ion conduction and selectivity are two of the most fundamental issues in the field of biophysics. Combined with ongoing progress in structural studies, modeling and simulation have been an integral part of the development of the field. As of this writing, the relentless growth in computational power, the development of new algorithms to tackle the so-called rare events, improved force-field parameters, and the concomitant increasing availability of membrane protein structures, allow simulations to contribute even further, providing more-complete models of ion conduction and selectivity in ion channels. In this report, we give an overview of the recent progress made by simulation studies on the understanding of ion permeation in selective and nonselective ion channels.     

Ion channels: from conductance to structure

In this perspective I tell the story (albeit a clearly abridged version) of how our knowledge of ion conduction through ion channels has evolved from a purely electrical concept to a structural dynamics view of ions interacting with a membrane protein. Our progress in this field has shown steady growth over the years but has also been interspersed with sudden jumps of discovery. These leaps have normally been associated with the introduction of a new technical advance or the development of a new biological preparation; therefore, it is quite certain that we have not seen them all.     

植物细胞质膜离子通道研究进展

多种有机和无机离子作为重要的营养物质、渗透物质、辅酶和信号分子, 参与植物生殖、生长发育和逆境反应等多种生物学过程。离子通道是离子跨质膜和内膜运动的重要渠道和动态调控因子, 直接影响和调控细胞内离子浓度及亚细胞分布的动态变化。目前, 植物尤其是模式植物拟南芥(Arabidopsis thaliana)的多个离子通道家族被先后鉴定出来, 其中部分离子通道蛋白定位在细胞质膜上, 其基本生物学功能, 诸如蛋白结构、离子选择性和通透性、门控特点、活性调控机理以及不同离子通道之间的协同关系等均取得重要进展。该文概要介绍近年来植物细胞质膜离子通道方面的研究进展。     

Solid-state NMR study and assignments of the KcsA potassium ion channel of S. lividans

The extraordinary efficiency and selectivity of potassium channels have made them ideal systems for biophysical and functional studies of ion conduction. We carried out solid-state NMR studies of the selectivity filter region of the protein. Partial site-specific assignments of the NMR signals were obtained based on high field multidimensional solid-state NMR spectra of uniformly (13)C, (15)N enriched KcsA potassium channel from Streptomyces lividans. Both backbone and sidechain atoms were assigned for residues V76-D80 and P83-L90, in and near the selectivity filter region of the protein; this region exhibits good dispersion and useful chemical shift fingerprints. This study will enable structure, dynamic and mechanistic studies of ion conduction by NMR.     

Anti-tumoral effect of scorpion peptides: Emerging new cellular targets and signaling pathways

Scorpion toxins have been the subject of many studies exploring their pharmacological potential. The high affinity and the overall selectivity to various types of ionic channels endowed scorpion toxins with a potential therapeutic effect against many channelopathies. These are diseases in which ionic channels play an important role in their development. Cancer is considered as a channelopathy since overexpression of some ionic channels was highlighted in many tumor cells and was linked to the pathology progression.Interestingly, an increasing number of studies have shown that scorpion venoms and toxins can decrease cancer growth in vitro and in vivo. Furthermore through their ability to penetrate the cell plasma membrane, certain scorpion toxins are able to enhance the efficiency of some clinical chemotherapies. These observations back-up the applicability of scorpion toxins as potential cancer therapeutics.In this review, we focused on the anti-cancer activity of scorpion toxins and their effect on the multiple hallmarks of cancer. We also shed light on effectors and receptors involved in signaling pathways in response to scorpion toxins effect. Until now, the anticancer mechanisms described for scorpion peptides consist on targeting ion channels to (i) inhibit cell proliferation and metastasis; and (ii) induce cell cycle arrest and/or apoptosis through membrane depolarization leading to hemostasis deregulation and caspase activation. Putative targets such as metalloproteinases, integrins and/or growth factor receptors, beside ion channels, have been unveiled to be affected by scorpion peptides.     

Simple model of ion transport through alamethicin channels in lipid membranes

The electrical characteristics of wide membrane channels such as those induced in lipid membranes by alamethicin have been analyzed using an electrodiffusion model. The channel is considered to be a water filled cylinder in which the potential energy barrier is a result of the difference in polarization energy of the ion environment when the ion is located inside as compared to outside of the channel. In addition, an electric field related to the channel structure is assumed. It is shown that without postulating any specific chemical ion-channel interaction one can reproduce experimental membrane potentials for NaCl, KCl, and CaCl₂ concentration gradients with a single set of channel parameters. The calculations also yield experimental J-V characteristics of discrete conduction states. In addition, a simple mechanism of interchannel coupling based on the above model is discussed. The model suggests a unifying approach to the problem of the origin of interionic selectivity of membrane channels induced by polyene antibiotics.     

Insights into the biophysical properties of GABA(A) ion channels: modulation of ion permeation by drugs and protein interactions

The fundamental properties of ion channels assure their selectivity for a particular ion, its rapid permeation through a central pore and that such electrical activity is modulated by factors that control the opening and closing (gating) of the channel. All cell types possess ion channels and their regulated flux of ions across the membrane play critical roles in all steps of life. An ion channel does not act alone to control cell excitability but rather forms part of larger protein complexes. The identification of protein interaction partners of ion channels and their influence on both the fundamental biophysical properties of the channel and its expression in the membrane are revealing the many ways in which electrical activity may be regulated. Highlighted here is the novel use of the patch clamp method to dissect out the influence of protein interactions on the activity of individual GABA(A) receptors. The studies demonstrate that ion conduction is a dynamic property of a channel and that protein interactions in a cytoplasmic domain underlie the channel's ability to alter ion permeation. A structural model describing a reorganisation of the conserved cytoplasmic gondola domain and the influence of drugs on this process are presented.     

Simulation of the effect of an external GHz electric field on the potential energy profile of Ca2+ ions in the selectivity filter of the CaVAb channel

Ca_V channels are transmembrane proteins that mediate and regulate ion fluxes across cell membranes, and they are activated in response to action potentials to allow Ca²⁺ influx. Since ion channels are composed of charge or polar groups, an external alternating electric field may affect the ion‐selective membrane transport and the performance of the channel. In this article, we have investigated the effect of an external GHz electric field on the dynamics of calcium ions in the selectivity filter of the Ca_VAb channel. Molecular dynamics (MD) simulations and the potential of mean force (PMF) calculations were carried out, via the umbrella sampling method, to determine the free energy profile of Ca²⁺ ions in the Ca_VAb channels in presence and absence of an external field. Exposing Ca_VAb channel to 1, 2, 3, 4, and 5 GHz electric fields increases the depth of the potential energy well and this may result in an increase in the affinity and strength of Ca²⁺ ions to binding sites in the selectivity filter the channel. This increase of strength of Ca²⁺ ions binding in the selectivity filter may interrupt the mechanism of Ca²⁺ ion conduction, and leads to a reduction of Ca²⁺ ion permeation through the Ca_VAb channel.     

Plants do it differently. A new basis for potassium/sodium selectivity in the pore of an ion channel

Understanding of the molecular architecture necessary for selective K(+) permeation through the pore of ion channels is based primarily on analysis of the crystal structure of the bacterial K(+) channel KcsA, and structure:function studies of cloned animal K(+) channels. Little is known about the conduction properties of a large family of plant proteins with structural similarities to cloned animal cyclic nucleotide-gated channels (CNGCs). Animal CNGCs are nonselective cation channels that do not discriminate between Na(+) and K(+) permeation. These channels all have the same triplet of amino acids in the channel pore ion selectivity filter, and this sequence is different from that of the selectivity filter found in K(+)-selective channels. Plant CNGCs have unique pore selectivity filters; unlike those found in any other family of channels. At present, the significance of the unique pore selectivity filters of plant CNGCs, with regard to discrimination between Na(+) and K(+) permeation is unresolved. Here, we present an electrophysiological analysis of several members of this protein family; identifying the first cloned plant channel (AtCNGC1) that conducts Na(+). Another member of this ion channel family (AtCNGC2) is shown to have a selectivity filter that provides a heretofore unknown molecular basis for discrimination between K(+) and Na(+) permeation. Specific amino acids within the AtCNGC2 pore selectivity filter (Asn-416, Asp-417) are demonstrated to facilitate K(+) over Na(+) conductance. The selectivity filter of AtCNGC2 represents an alternative mechanism to the well-known GYG amino acid triplet of K(+) channels that has been identified as the critical basis for K(+) over Na(+) permeation through the pore of ion channels.     

Role of ion channels during cell division

Ion channels are transmembrane proteins whose canonical function is the transport of ions across the plasma membrane to regulate cell membrane potential and play an essential role in neural communication, nerve conduction, and muscle contraction. However, over the last few years, non-canonical functions have been identified for many channels, having active roles in phagocytosis, invasiveness, proliferation, among others. The participation of some channels in cell proliferation has raised the question of whether they may play an active role in mitosis. There are several reports showing the participation of channels during interphase, however, the direct participation of ion channels in mitosis has received less attention. In this article, we summarize the current evidence on the participation of ion channels in mitosis. We also summarize some tools that would allow the study of ion channels and cell cycle regulatory molecules in individual cells during mitosis.     

Molecular simulation approaches to membrane proteins

Molecular simulations are an invaluable tool for understanding membrane proteins. Improvements to both hardware and simulation methods have allowed access to physiologically relevant timescales and have permitted the simulation of large multimeric complexes. This, coupled to the recent expansion in membrane protein structures, provides a means to elucidate the relationship between protein structure and function. In this review, we discuss the progress in using simulations to understand the complex processes that occur at the boundary of a cell, ranging from the transport of solutes and the interactions of ligands with ion channels to the conformational rearrangements required for gating of channels and the signaling by membrane-associated complexes.     

Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels

Ion channels catalyze the permeation of charged molecules across cell membranes and are essential for many vital physiological functions, including nerve and muscle activity. To understand better the mechanisms underlying ion conduction and valence selectivity of narrow ion channels, we have employed free energy techniques to calculate the potential of mean force (PMF) for ion movement through the prototypical gramicidin A channel. Employing modern all-atom molecular dynamics (MD) force fields with umbrella sampling methods that incorporate one hundred 1-2 ns trajectories, we find that it is possible to achieve semi-quantitative agreement with experimental binding and conductance measurements. We also examine the sensitivity of the MD-PMF results to the choice of MD force field and compare PMFs for potassium, calcium and chloride ions to explore the basis for the valence selectivity of this narrow and uncharged ion channel. A large central barrier is observed for both anions and divalent ions, consistent with lack of experimental conductance. Neither anion or divalent cation is seen to be stabilized inside the channel relative to the bulk electrolyte and each leads to large disruptions to the protein and membrane structure when held deep inside the channel. Weak binding of calcium ions outside the channel corresponds to a free energy well that is too shallow to demonstrate channel blocking. Our findings emphasize the success of the MD-PMF approach and the sensitivity of ion energetics to the choice of biomolecular force field.     

Ion Channels and Cancer

Membrane ion channels are essential for cell proliferation and appear to have a role in the development of cancer. This has initially been demonstrated for potassium channels and is meanwhile also suggested for other cation channels and Cl⁻ channels. For some of these channels, like voltage-gated ether à go-go and Ca²⁺-dependent potassium channels as well as calcium and chloride channels, a cell cycle-dependent function has been demonstrated. Along with other membrane conductances, these channels control the membrane voltage and Ca²⁺ signaling in proliferating cells. Homeostatic parameters, such as the intracellular ion concentration, cytosolic pH and cell volume, are also governed by the activity of ion channels. Thus it will be an essential task for future studies to unravel cell cycle-specific effects of ion channels and non-specific homeostatic functions. When studying the role of ion channels in cancer cells, it is indispensable to choose experimental conditions that come close to the in vivo situation. Thus, environmental parameters, such as low oxygen pressure, acidosis and exposure to serum proteins, have to be taken into account. In order to achieve clinical application, more studies on the original cancer tissue are required, and improved animal models. Finally, it will be essential to generate more potent and specific inhibitors of ion channels to overcome the shortcomings of some of the current approaches.     

Ion Conduction in Ligand-Gated Ion Channels: Brownian Dynamics Studies of Four Recent Crystal Structures

Four x-ray crystal structures of prokaryotic homologs of ligand-gated ion channels have recently been determined: ELIC from Erwinia chrysanthemi, two structures of a proton-activated channel from Gloebacter violaceus (GLIC1 and GLIC2) and that of the E221A mutant (GLIC1M). The availability of numerous structures of channels in this family allows for aspects of channel gating and ion conduction to be examined. Here, we determine the likely conduction states of the four structures as well as IV curves, ion selectivity, and steps involved in ion permeation by performing extensive Brownian dynamics simulations. Our results show that the ELIC structure is indeed nonconductive, but that GLIC1 and GLIC1M are both conductive of ions with properties different from those seen in experimental studies of the channel. GLIC2 appears to reflect an open state of the channel with a predicted conductance of 10.8-12.4 pS in 140 mM NaCl solution, which is comparable to the experimental value 8 ± 2 pS. The extracellular domain of the channel is shown to have an important influence on the channel current, but a less significant role in ion selectivity.     

Lipid regulation of cell membrane structure and function

Recent studies of structure-function relationships in biological membranes have revealed fundamental concepts concerning the regulation of cellular membrane function by membrane lipids. Considerable progress has been made in understanding the roles played by two membrane lipids: cholesterol and phosphatidyl-ethanolamine. Cholesterol has been shown to regulate ion pumps, which in some cases show an absolute dependence on cholesterol for activity. These studies suggest that an essential role that cholesterol plays in mammalian cell biology is to enable crucial membrane enzymes to provide function necessary for cell survival. Studies of phosphatidylethanolamine regulation of membrane protein activity and regulation of membrane morphology led to hypotheses concerning the roles for this particular lipid in biological membranes. New information on lipid-protein interactions and on the nature of the lipid head groups has permitted the development of mechanistic hypotheses for the regulation of membrane protein activity by phosphatidyl-ethanolamine. In addition, intermediates in the lamellar-nonlamellar phase transitions of membrane systems containing phosphatidylethanolamine, or other lipids with similar properties, have recently been implicated in facilitating membrane fusion. Finally, studies of transmembrane movement of lipids have provided new insight into the regulation of membrane lipid asymmetry and the biogenesis of cell membranes. These kinds of studies are harbingers of a new generation of progress in the field of cell membranes.     

Site-specific mutations in a minimal voltage-dependent K+ channel alter ion selectivity and open-channel block

MinK is a small membrane protein of 130 amino acids with a single potential membrane-spanning alpha-helical domain. Its expression in Xenopus oocytes induces voltage-dependent, K(+)-selective channels. Using site-directed mutagenesis of a synthetic gene, we have identified residues in the hydrophobic region of minK that influence both ion selectivity and open-channel block. Single amino acid changes increase the channel's relative permeability for NH4+ and Cs+ without affecting its ability to exclude Na+ and Li+. Blockade by two common K+ channel pore blockers, tetraethylammonium and Cs+, was also modified. These results suggest that an ion selectivity region and binding sites for the pore blockers within the conduction pathway have been modified. We conclude that the gene encoding minK is a structural gene for a K+ channel protein.     

Ion selectivity in potassium channels

Potassium channels are tetrameric membrane-spanning proteins that provide a selective pore for the conduction of K(+) across the cell membranes. One of the main physiological functions of potassium channels is efficient and very selective transport of K(+) ions through the membrane to the cell. Classical views of ion selectivity are summarized within a historical perspective, and contrasted with the molecular dynamics (MD) simulations free energy perturbation (FEP) performed on the basis of the crystallographic structure of the KcsA phospholipid membrane. The results show that the KcsA channel does not select for K(+) ions by providing a binding site of an appropriate (fixed) cavity size. Rather, selectivity for K(+) arises directly from the intrinsic local physical properties of the ligands coordinating the cation in the binding site, and is a robust feature of a pore symmetrically lined by backbone carbonyl groups. Further analysis reveals that it is the interplay between the attractive ion-ligand (favoring smaller cation) and repulsive ligand-ligand interactions (favoring larger cations) that is the basic element governing Na(+)/K(+) selectivity in flexible protein binding sites. Because the number and the type of ligands coordinating an ion directly modulate such local interactions, this provides a potent molecular mechanism to achieve and maintain a high selectivity in protein binding sites despite a significant conformational flexibility.     

Structural basis of TEA blockade in a model potassium channel

Potassium channels catalyze the selective transfer of potassium across the cell membrane and are essential for setting the resting potential in cells, controlling heart rate and modulating the firing pattern in neurons. Tetraethylammonium (TEA) blocks ion conduction through potassium channels in a voltage-dependent manner from both sides of the membrane. Here we show the structural basis of TEA blockade by cocrystallizing the prokaryotic potassium channel KcsA with two selective TEA analogs. TEA binding at both sites alters ion occupancy in the selectivity filter; these findings underlie the mutual destabilization and voltage-dependence of TEA blockade. We propose that TEA blocks potassium channels by acting as a potassium analog at the dehydration transition step during permeation.     

植物质膜钾离子转运体研究进展

近年,随着分子生物学技术的不断发展和广泛应用,有关植物质膜钾离子转运体的研究取得重要进展。目前已经克隆到多种质膜钾离子转运体基因并对钾离子转运体生化特性以及结构功能进行了广泛研究。研究认为,质膜钾离子转运体可分为钾离子载体和钾离子通道。钾离子通道又可分为内向性K+通道α亚基、K+通道β亚基及外向性K+通道等三类。本文对上述质膜钾离子转运体的生化特性以及结构功能研究的进展进行了综述。     

Ion binding affinity in the cavity of the KcsA potassium channel

The hydrophobic cell membrane interior presents a large energy barrier for ions to permeate. Potassium channels reduce this barrier by creating a water-filled cavity at the middle of their ion conduction pore to allow ion hydration and by directing the C-terminal "end charge" of four alpha-helices toward the water-filled cavity. Here we have studied the interaction of monovalent cations with the cavity of the KcsA K(+) channel using X-ray crystallography. In these studies, Tl(+) was used as an analogue for K(+) and the total ion-stabilization energy for Tl(+) in the cavity was estimated by measuring its binding affinity. Binding affinity for the Na(+) ion was also measured, revealing a weak selectivity ( approximately 7-fold) favoring Tl(+) over Na(+). The structures of the cavity containing Na(+), K(+), Tl(+), Rb(+), and Cs(+) are compared. These results are consistent with a fairly large (more negative than -100 mV) electrostatic potential inside the cavity, and they also imply the presence of a weak nonelectrostatic component to a cation's interaction with the cavity.