Activation and Inhibition of Histone Deacetylase 8 by Monovalent Cations

The metal-dependent histone deacetylases (HDACs) catalyze hydrolysis of acetyl groups from acetyllysine side chains and are targets of cancer therapeutics. Two bound monovalent cations (MVCs) of unknown function have been previously observed in crystal structures of HDAC8; site 1 is near the active site, whereas site 2 is located >20 Å from the catalytic metal ion. Here we demonstrate that one bound MVC activates catalytic activity (K_1/2 = 3.4 mm for K⁺), whereas the second, weaker-binding MVC (K_1/2 = 26 mm for K⁺) decreases catalytic activity by 11-fold. The weaker binding MVC also enhances the affinity of the HDAC inhibitor suberoylanilide hydroxamic acid by 5-fold. The site 1 MVC is coordinated by the side chain of Asp-176 that also forms a hydrogen bond with His-142, one of two histidines important for catalytic activity. The D176A and H142A mutants each increase the K_1/2 for potassium inhibition by ≥40-fold, demonstrating that the inhibitory cation binds to site 1. Furthermore, the MVC inhibition is mediated by His-142, suggesting that this residue is protonated for maximal HDAC8 activity. Therefore, His-142 functions either as an electrostatic catalyst or a general acid. The activating MVC binds in the distal site and causes a time-dependent increase in activity, suggesting that the site 2 MVC stabilizes an active conformation of the enzyme. Sodium binds more weakly to both sites and activates HDAC8 to a lesser extent than potassium. Therefore, it is likely that potassium is the predominant MVC bound to HDAC8 in vivo.     

Specific potassium ion interactions facilitate homocysteine binding to betaine‐homocysteine S‐methyltransferase

Betaine‐homocysteine S‐methyltransferase (BHMT) is a zinc‐dependent methyltransferase that uses betaine as the methyl donor for the remethylation of homocysteine to form methionine. This reaction supports S‐adenosylmethionine biosynthesis, which is required for hundreds of methylation reactions in humans. Herein we report that BHMT is activated by potassium ions with an apparent K_M for K⁺ of about 100 µM. The presence of potassium ions lowers the apparent K_M of the enzyme for homocysteine, but it does not affect the apparent K_M for betaine or the apparent k_cat for either substrate. We employed molecular dynamics (MD) simulations to theoretically predict and protein crystallography to experimentally localize the binding site(s) for potassium ion(s). Simulations predicted that K⁺ ion would interact with residues Asp26 and/or Glu159. Our crystal structure of BHMT bound to homocysteine confirms these sites of interaction and reveals further contacts between K⁺ ion and BHMT residues Gly27, Gln72, Gln247, and Gly298. The potassium binding residues in BHMT partially overlap with the previously identified DGG (Asp26‐Gly27‐Gly28) fingerprint in the Pfam 02574 group of methyltransferases. Subsequent biochemical characterization of several site‐specific BHMT mutants confirmed the results obtained by the MD simulations and crystallographic data. Together, the data herein indicate that the role of potassium ions in BHMT is structural and that potassium ion facilitates the specific binding of homocysteine to the active site of the enzyme. Proteins 2014; 82:2552–2564. © 2014 Wiley Periodicals, Inc.     

The Persistent Question of Potassium Channel Permeation Mechanisms

Potassium channels play critical roles in many physiological processes, providing a selective permeation route for K⁺ ions in and out of a cell, by employing a carefully designed selectivity filter, evolutionarily conserved from viruses to mammals. The structure of the selectivity filter was determined at atomic resolution by x-ray crystallography, showing a tight coordination of desolvated K⁺ ions by the channel. However, the molecular mechanism of K⁺ ions permeation through potassium channels remains unclear, with structural, functional and computational studies often providing conflicting data and interpretations. In this review, we will present the proposed mechanisms, discuss their origins, and will critically assess them against all available data. General properties shared by all potassium channels are introduced first, followed by the introduction of two main mechanisms of ion permeation: soft and direct knock-on. Then, we will discuss critical computational and experimental studies that shaped the field. We will especially focus on molecular dynamics (MD) simulations, that provided mechanistic and energetic aspects of K⁺ permeation, but at the same time created long-standing controversies. Further challenges and possible solutions are presented as well.     

钾肥及与秸秆配施对紫色土作物产量和微生物群落结构的影响

基于紫色菜园土壤莴笋-白菜-甜玉米轮作4年12季连续定位施钾肥试验,研究不同种类钾肥及用量对重庆地区紫色菜园土上作物产量和土壤微生物群落结构的影响,为该地区作物生产确定合理的施钾技术提供科学依据。结果表明,在施用氮磷肥基础上,不同钾肥处理莴笋、白菜、甜玉米产量均显著提高;从3种作物4年平均产量和钾肥效益看,以单施适量化学钾(K_2)、单施适量秸秆钾(M_2)和秸秆还田配施少量化学钾(K_1+M_1)的施钾肥模式对白菜的增产效果好,增产28.05%—30.27%;M_2和K_1+M_1施钾肥模式对莴笋的增产效果较好,增产13.89%和13.81%;K_1+M_1施钾肥模式对甜玉米的增产效果最好,增产15.10%,表明秸秆还田配施少量化学钾(K_1+M_1)模式在供试3种作物生产中具有很好的应用前景。不同施钾处理对土壤微生物群落结构及丰度均会产生一定影响,以秸秆还田配施少量化学钾肥(K_1+M_1)对提高土壤细菌、真菌、革兰氏阳性菌的作用较好,并显著增加土壤微生物总PLFA含量,缓解对土壤微生物生存环境的胁迫,说明K_1+M_1能为土壤微生物的生长繁育创造有利环境。莴笋、白菜、甜玉米3种作物4年平均产量与土壤细菌、真菌、革兰氏阳性菌和革兰氏阴性菌数量间存在显著相关性(P0.05),而不同钾肥处理对土壤微生物特征具有一定影响,说明施钾肥可能会调节土壤微生物特征,从而促进作物增产。     

Exploration of Novel Inhibitors for Class I Histone Deacetylase Isoforms by QSAR Modeling and Molecular Dynamics Simulation Assays

Histone deacetylases (HDAC) are metal-dependent enzymes and considered as important targets for cell functioning. Particularly, higher expression of class I HDACs is common in the onset of multiple malignancies which results in deregulation of many target genes involved in cell growth, differentiation and survival. Although substantial attempts have been made to control the irregular functioning of HDACs by employing various inhibitors with high sensitivity towards transformed cells, limited success has been achieved in epigenetic cancer therapy. Here in this study, we used ligand-based pharmacophore and 2-dimensional quantitative structure activity relationship (QSAR) modeling approaches for targeting class I HDAC isoforms. Pharmacophore models were generated by taking into account the known IC₅₀ values and experimental energy scores with extensive validations. The QSAR model having an external R² value of 0.93 was employed for virtual screening of compound libraries. 10 potential lead compounds (C1-C10) were short-listed having strong binding affinities for HDACs, out of which 2 compounds (C8 and C9) were able to interact with all members of class I HDACs. The potential binding modes of HDAC2 and HDAC8 to C8 were explored through molecular dynamics simulations. Overall, bioactivity and ligand efficiency (binding energy/non-hydrogen atoms) profiles suggested that proposed hits may be more effective inhibitors for cancer therapy.     

Role of Trace Elements,Oxidative Stress and Immune System: a Triad in Premature Ovarian Failure

Cadmium is an environmental pollutant closely linked with cardiovascular diseases that seems to involve endothelium dysfunction and reduced nitric oxide (NO) bioavailability. Knowing that NO causes dilatation through the activation of potassium channels and Na⁺/K⁺-ATPase, we aimed to determine whether acute cadmium administration (10 μM) alters the participation of K⁺ channels, voltage-activated calcium channel, and Na⁺/K⁺-ATPase activity in vascular function of isolated aortic rings of rats. Cadmium did not modify the acetylcholine-induced relaxation. After L-NAME addition, the relaxation induced by acetylcholine was abolished in presence or absence of cadmium, suggesting that acutely, this metal did not change NO release. However, tetraethylammonium (a nonselective K⁺ channels blocker) reduced acetylcholine-induced relaxation but this effect was lower in the preparations with cadmium, suggesting a decrease of K⁺ channels function in acetylcholine response after cadmium incubation. Apamin (a selective blocker of small Ca²⁺-activated K⁺ channels—SK_Ca), iberiotoxin (a selective blocker of large-conductance Ca²⁺-activated K⁺ channels—BK_Ca), and verapamil (a blocker of calcium channel) reduced the endothelium-dependent relaxation only in the absence of cadmium. Finally, cadmium decreases Na⁺/K⁺-ATPase activity. Our results provide evidence that the cadmium acute incubation unaffected the calcium-activated potassium channels (SK_Ca and BK_Ca) and voltage-calcium channels on the acetylcholine vasodilatation. In addition, acute cadmium incubation seems to reduce the Na⁺/K⁺-ATPase activity.     

Computational modeling and molecular dynamics simulations of mammalian cytoplasmic tyrosyl-tRNA synthetase and its complexes with substrates

Cytoplasmic tyrosyl-tRNA synthetase (TyrRS) is one of the key enzymes of protein biosynthesis. TyrRSs of pathogenic organisms have gained attention as potential targets for drug development. Identifying structural differences between various TyrRSs will facilitate the development of specific inhibitors for the TyrRSs of pathogenic organisms. However, there is a deficiency in structural data for mammalian cytoplasmic TyrRS in complexes with substrates. In this work, we constructed spatial structure of full-length Bos taurus TyrRS (BtTyrRS) and its complexes with substrates using the set of computational modeling techniques. Special attention was paid to BtTyrRS complexes with substrates [L-tyrosine, K⁺ and ATP:Mg²⁺] and intermediate products [tyrosyl-adenylate (Tyr-AMP), K⁺ and PP_i:Mg²⁺] with the different catalytic loop conformations. In order to analyze their dynamical properties, we performed 100 ns of molecular dynamics (MD) simulations. MD simulations revealed new structural data concerning the tyrosine activation reaction in mammalian TyrRS. Formation of strong interaction between Lys154 and γ-phosphate suggests the additional role of CP1 insertion as an important factor for ATP binding. The presence of a potassium-binding pocket within the active site of mammalian TyrRS compensates the absence of the second lysine in the KMSKS motif. Our data provide new details concerning a role of K⁺ ions at different stages of the first step of the tyrosylation reaction, including the coordination of substrates and involvement in the PP_i releasing. The results of this work suggest that differences between ATP-binding sites of mammalian and bacterial TyrRSs are meaningful and could be exploited in the drug design.     

K+-Dependent Selectivity and External Ca2+ Block of Shab K+ Channels

Potassium channels allow the selective flux of K⁺ excluding the smaller, and more abundant in the extracellular solution, Na⁺ ions. Here we show that Shab is a typical K⁺ channel that excludes Na⁺ under bi-ionic, Na_o/K_i or Na_o/Rb_i, conditions. However, when internal K⁺ is replaced by Cs⁺ (Na_o/Cs_i), stable inward Na⁺ and outward Cs⁺ currents are observed. These currents show that Shab selectivity is not accounted for by protein structural elements alone, as implicit in the snug-fit model of selectivity. Additionally, here we report the block of Shab channels by external Ca²⁺ ions, and compare the effect that internal K⁺ replacement exerts on both Ca²⁺ and TEA block. Our observations indicate that Ca²⁺ blocks the channels at a site located near the external TEA binding site, and that this pore region changes conformation under conditions that allow Na⁺ permeation. In contrast, the latter ion conditions do not significantly affect the binding of quinidine to the pore central cavity. Based on our observations and the structural information derived from the NaK bacterial channel, we hypothesize that Ca²⁺ is probably coordinated by main chain carbonyls of the pore´s first K⁺-binding site.     

Electrophysiology of human cardiac atrial and ventricular telocytes

Telocytes (TCs) with exceptionally long cellular processes of telopodes have been described in human epicardium to act as structural supporting cells in the heart. We examined myocardial chamber‐specific TCs identified in atrial and ventricular fibroblast culture using immunocytochemistry and studied their electrophysiological property by whole‐cell patch clamp. Atrial and ventricular TCs with extended telopodes and alternating podoms and podomers that expressed CD34, c‐Kit and PDGFR‐β were identified. These cells expressed large conductance Ca²⁺‐activated K⁺ current (BK_Ca) and inwardly rectifying K⁺ current (IK_ir), but not transient outward K⁺ current (I_to) and ATP‐sensitive potassium current (K_ATP). The active channels were functionally competent with demonstrated modulatory response to H₂S and transforming growth factor (TGF)‐β1 whereby H₂S significantly inhibited the stimulatory effect of TGF‐β1 on current density of both BK_Ca and IK_ir. Furthermore, H₂S attenuated TGF‐β1‐stimulated KCa1.1/Kv1.1 (encode BK_Ca) and Kir2.1 (encode IK_ir) expression in TCs. Our results show that functionally competent K⁺ channels are present in human atrial and ventricular TCs and their modulation may have significant implications in myocardial physiopathology.     

Surface Amorphization of Vanadium Dioxide (B) for K‐Ion Battery

Given the merits of low cost, fast ionic transport in electrolyte, and high operating voltage, potassium ion batteries (PIBs) are promising alternatives to lithium‐ion batteries. However, developing suitable electrode materials that can reversibly accommodate large potassium ions is a great challenge. Here, guided by density functional theory (DFT) calculations, it is demonstrated that the strategy of interfacial engineering via surface amorphization of VO₂ (B) nanorods (SA‐VO₂), which results in the formation of a crystalline core/amorphous shell heterostructure, enables superior K⁺ storage performance in terms of large capacity, outstanding rate capability, and long cycle stability working as an anode for PIBs. DFT calculations reveal that the created crystalline/amorphous heterointerface in SA‐VO₂ can substantially lower the surface energy, narrow the band gap, and reduce the K⁺ diffusion barrier of VO₂ (B). These conditions enable enhanced K⁺ storage capacity and rapid K⁺/electron transfer, which result in large capacity and outstanding rate capability. Using in situ X‐ray diffraction and in situ transmission electron microscopy complemented by ex situ microscopic and spectroscopic techniques, it is unveiled that the superior cycling stability originates from the excellent phase reversibility with negligible strain response and robust mechanical behavior of SA‐VO₂ upon (de)potassiation.     

Dynamics, Energetics, and Selectivity of the Low-K KcsA Channel Structure

Potassium channels are a diverse family of integral membrane proteins through which K⁺ can pass selectively. There is ongoing debate about the nature of conformational changes associated with the opening/closing and conductive/nonconductive states of potassium channels. The channels partly exert their function by varying their conductance through a mechanism known as C-type inactivation. Shortly after the activation of K⁺ channels, their selectivity filter stops conducting ions at a rate that depends on various stimuli. The molecular mechanism of C-type inactivation has not been fully understood yet. However, the X-ray structure of the KcsA channel obtained in the presence of low K⁺ concentration is thought to be representative of a K⁺ channel in the C-type inactivated state. Here, extensive, fully atomistic molecular dynamics and free-energy simulations of the low-K⁺ KcsA structure in an explicit lipid bilayer are performed to evaluate the stability of this structure and the selectivity of its binding sites. We find that the low-K⁺ KcsA structure is stable on the timescale of the molecular dynamics simulations performed, and that ions preferably remain in S1 and S4. In the absence of ions, the selectivity filter evolves toward an asymmetric architecture, as already observed in other computations of the high-K⁺ structure of KcsA and KirBac. The low-K⁺ KcsA structure is not permeable by Na⁺, K⁺, or Rb⁺, and the selectivity of its binding sites is different from that of the high-K⁺ structure.     

Effects of mono- and multi-valent cations on the inward-rectifying potassium channel in isolated protoplasts from maize roots

Transport properties mediated by ionic channels were studied by the patch-clamp technique in protoplasts from cortical parenchyma cells of maize roots (CPMR). While outward currents could be seen only occasionally, macroscopic voltage- and time-dependent potassium-selective inward currents (I_K+in) were frequently observed in the whole-cell configuration. These currents increased continuously as a function of K⁺ concentration (in the range 3 – 200 mm) and the slow-saturating macroscopic chord-conductance was fitted by a Michaelis-Menten function with K_m = 195 ± 39 mm. Other ions, like sodium and lithium, did not permeate at all through the maize root inward-channel, or like ammonium (P_NH4+/ P_K+ = 0.16 0.25) and rubidium (P_Rb+/P_K+≈ 0.10) displayed a very low permeability ratio. Up to 5 mm Rb⁺ did not induce any inhibition of the K⁺ inward current, whereas submillimolar concentrations of Cs⁺ were sufficient to block, in a voltage-dependent manner, the inward currents. A decrease of the external potassium concentration favoured Cs⁺ inhibition (K_m = 89 ± 6 μm and 26 ± 2 μm in 200 and 100 mm KCl, respectively). The potassium inward-currents were reversibly and consistently inhibited by submillimolar external concentrations of the metal ions Ni²⁺, Zn²⁺ and Co²⁺, while 1 mm La³⁺ only slightly decreased (≈10%) both the single channel conductance (9.2 ± 1.2 pS in 100 mm potassium) and the macroscopic current. In contrast to the case with Cs⁺, inhibition induced by other metal ions did not show any voltage dependence. These results suggest that, as with animal potassium channels, the inward channel of maize-root cortical cells has a narrow pore of permeation and metal ions decrease the K⁺ current, possibly by acting on binding sites located outside the pore. Received: 21 February 1997 / Accepted: 27 May 1997     

Chemically induced K+ conduction noise in squid axon

Internal perfusion of tetraethylammonium ions (TEA) in squid axons produces a significant high frequency noise component. Although internal TEA suppresses the potassium conductance (G _K) noise at relatively low frequencies, it induces high frequency noise which exceeds the intensity of the normal potassium and sodium noise. In addition, the induced noise is dependent on the presence of internal potassium ions (K⁺) suggesting that this source of noise arises from a modulation of the K⁺ conductance due to the blocking and unblocking of the K⁺ channel. The simplest model describing the TEA data is a two-step sequential pseudo-unimolecular reaction where TEA binds during an open conductance state. A unit channel conductance of 2 pS is estimated from the TEA data as well as noise induced by triethyldecylammonium (TEDA) ions. Thus, these data are consistent with the hypothesis that the channel is blocked whenever the quaternary ammonium ion binding site, located near or within the K⁺ channel, is occupied.     

Sodium-translocating adenosine triphosphatase inStreptococcus faecalis

Sodium-transloating ATPase in the fermentative bacteriumStreptococcus faecalis exchanges sodium for potassium ions. Sodium ions stimulate its activity, but K⁺ ions have no significant effect at present. Although the molecular nature of the sodium ATPase is not clear, the enzyme is distinct from other ion-motive ATPases (E₁E₂ type and F₁F₀ type) as judged by its resistance to vanadate as well as dicyclohexylcarbodiimde. The sodium ATPase is induced when cells are grown on media rich in sodium, particularly under conditions that limit the generation of a proton potential or block the constitutive sodium/proton antiporter, indicating that an increase in the cytoplasmic sodium level serves as the signal. The enzyme is not induced in response to K⁺ deprivation. The sodium ATPase may have evolved to cope with a sodium-rich environment under conditions that limit the magnitude of the proton potential.     

Effect of Antimicrobial Peptides Divergicin M35 and Nisin A on <Emphasis Type="Italic">Listeria monocytogenes</Emphasis> LSD530 Potassium Channels

The aim of this work was to study the effect of antimicrobial peptides: divergicin M35 and nisin A on Listeria monocytogenes LSD 530 potassium (K⁺) channels: ATP-sensitive (K_ATP), calcium-activated (BK_Ca), and depolarization-activated (K_v) types. Increase on K⁺ efflux and inhibition of cellular growth were observed after adding K⁺ channel activators pinacidil, NS1619, and cromakalim to divergicin M35. Increase in K⁺ efflux from log-phase cells was about 18 ± 1.1, 11 ± 0.63, and nmol mg⁻¹ of cell dry weight (CDW) for pinacidil and NS1619, respectively, over the efflux obtained with divergicin M35 alone. Increases in K⁺ efflux obtained by adding the same K⁺ channel activators to nisin A fit a completely different profile. Divergicin M35 activates K⁺ channels, particularly of the K_v and BK_Ca types and to a lesser extent the K_ATP type, causing K⁺ efflux and consequently cell death.     

Gill (Na+,K+)-ATPase from the blue crab Callinectes danae: modulation of K+-phosphatase activity by potassium and ammonium ions

The kinetic properties of a microsomal gill (Na⁺,K⁺)-ATPase from the blue crab Callinectes danae were analyzed using the substrate p-nitrophenylphosphate. The (Na⁺,K⁺)-ATPase hydrolyzed PNPP obeying cooperative kinetics (n=1.5) at a rate of V=125.4±7.5 U mg⁻¹ with K_0.5=1.2±0.1 mmol l⁻¹; stimulation by potassium (V=121.0±6.1 U mg⁻¹; K_0.5=2.1±0.1 mmol l⁻¹) and magnesium ions (V=125.3±6.3 U mg⁻¹; K_0.5=1.0±0.1 mmol l⁻¹) was cooperative. Ammonium ions also stimulated the enzyme through site–site interactions (n_H=2.7) to a rate of V=126.1±4.8 U mg⁻¹ with K_0.5=13.7±0.5 mmol l⁻¹. However, K⁺-phosphatase activity was not stimulated further by K⁺ plus NH₄⁺ ions. Sodium ions (K_I=36.7±1.7 mmol l⁻¹), ouabain (K_I=830.3±42.5 μmol l⁻¹) and orthovanadate (K_I=34.0±1.4 nmol l⁻¹) completely inhibited K⁺-phosphatase activity. The competitive inhibition by ATP (K_I=57.2±2.6 μmol l⁻¹) of PNPPase activity suggests that both substrates are hydrolyzed at the same site on the enzyme. These data reveal that the K⁺-phosphatase activity corresponds strictly to a (Na⁺,K⁺)-ATPase in C. danae gill tissue. This is the first known kinetic characterization of K⁺-phosphatase activity in the portunid crab C. danae and should provide a useful tool for comparative studies.     

Mechanism of Na+ Insertion in Alkali Vanadates and Its Influence on Battery Performance

Sodium‐ion batteries may become an alternative to the widespread lithium‐ion technology due to cost and kinetic advantages provided that cyclability is improved. For this purpose, the interplay between electrochemical and structural processes is key and is demonstrated in this work for Na_2.46V₆O₁₆ (NVO) and Li_2.55V₆O₁₆ employing operando synchrotron X‐ray diffraction. When NVO is cycled between 4.0 and 1.6 V, Na‐ions reversibly occupy two crystallographic sites, which results in remarkable cyclability. Upon discharge to 1.0 V, however, Na‐ions occupy also interstitial sites, inducing irreversible structural change with some loss of crystallinity concomitant with a decrease in capacity. Capacity fading increases with the ionic radius of the alkali ions (K⁺ > Na⁺ > Li⁺), suggesting that smaller ions stabilize the structure. This correlation of structural variation and electrochemical performance suggests a route toward improving cycling stability of a sodium‐ion battery. Its essence is a minor Li⁺‐retention in the A_2+xV₆O₁₆ structure. Even though the majority of Li‐ions are replaced by the abundant Na⁺, the residual Li‐ions (≈10%) are sufficient to stabilize the layered structure, diminishing the irreversible structural damage. These results pave the way for further exploitation of the role of small ions in lattice stabilization that increases cycling performance.     

Ion Conduction through the hERG Potassium Channel

The inward rectifier voltage-gated potassium channel hERG is of primary importance for the regulation of the membrane potential of cardiomyocytes. Unlike most voltage-gated K⁺-channels, hERG shows a low elementary conductance at physiological voltage and potassium concentration. To investigate the molecular features underlying this unusual behavior, we simulated the ion conduction through the selectivity filter at a fully atomistic level by means of molecular dynamics-based methods, using a homology-derived model. According to our calculations, permeation of potassium ions can occur along two pathways, one involving site vacancies inside the filter (showing an energy barrier of about 6 kcal mol⁻¹), and the other characterized by the presence of a knock-on intermediate (about 8 kcal mol⁻¹). These barriers are indeed in accordance with a low conductance behavior, and can be explained in terms of a series of distinctive structural features displayed by the hERG ion permeation pathway.     

A Nanosecond Molecular Dynamics Study of Antiparallel d(G)7 Quadruplex Structures: Effect of the Coordinated Cations

Abstract

Nanosecond scale molecular dynamics simulations have been performed on antiparallel Greek key type d(G₇) quadruplex structures with different coordinated ions, namely Na⁺ and K⁺ ion, water and Na⁺ counter ions, using the AMBER force field and Particle Mesh Ewald technique for electrostatic interactions. Antiparallel structures are stable during the simulation, with root mean square deviation values of ～ 1.5 Å from the initial structures. Hydrogen bonding patterns within the G-tetrads depend on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate different cations. However, alternating syn-anti arrangement of bases along a chain as well as in a quartet is maintained through out the MD simulation. Coordinated Na+ ions, within the quadruplex cavity are quite mobile within the central channel and can even enter or exit from the quadruplex core, whereas coordinated K⁺ ions are quite immobile. MD studies at 400K indicate that K⁺ ion cannot come out from the quadruplex core without breaking the terminal G-tetrads. Smaller grooves in antiparallel structures are better binding sites for hydrated counter ions, while a string of hydrogen bonded water molecules are observed within both the small and large grooves. The hydration free energy for the K⁺ ion coordinated structure is more favourable than that for the Na⁺ ion coordinated antiparallel quadruplex structure.     

Modulation of P2X4 pore closure by magnesium,potassium, and ATP

The P2X4 receptor plays a prominent role in cellular responses to extracellular ATP. Through classical all-atom molecular dynamics (MD) simulations totaling 24 μs we have investigated how metal-complexed ATP stabilizes the channel's open state and prevents its closing. We have identified two metal-binding sites, Mg²⁺ and potassium K⁺, one at the intersection of the three subunits in the ectodomain (MBS1) and the second one near the ATP-binding site (MBS2), similar to those characterized in Gulf Coast P2X. Our data indicate that when Mg²⁺ and K⁺ ions are complexed with ATP, the channel is locked into an open state. Interestingly, irrespective of the number of bound ATP molecules, Mg²⁺ ions bound to the MBS2 impeded the collapse of the open-state protein to a closed state by stabilizing the ATP-protein interactions. However, when Mg²⁺ in the MBS2 was replaced with K⁺ ions, as might be expected when in equilibrium with an extracellular solution, the interactions between the subunits were weakened and the pore collapsed. This collapse was apparent when fewer than two ATPs were bound to MBS2 in the presence of K⁺. Therefore, the different capacities of common cations to stabilize the channel may underlie a mechanism governing P2X4 channel gating in physiological systems. This study therefore provides structural insights into the differential modulation of ATP activation of P2X4 by Mg²⁺ and K⁺.