共查询到20条相似文献,搜索用时 15 毫秒
1.
Juliane Zimmermann Ryan?L. Hayes Markus Basan José?N. Onuchic Wouter-Jan Rappel Herbert Levine 《Biophysical journal》2014,106(3):548-555
The open gate of the Kv1.2 voltage-gated potassium channel can just hold a hydrated K+ ion. Quantum calculations starting from the x-ray coordinates of the channel confirm this, showing little change from the x-ray coordinates for the protein. Water molecules not in the x-ray coordinates, and the ion itself, are placed by the calculation. The water molecules, including their orientation and hydrogen bonding, with and without an ion, are critical for the path of the ion, from the solution to the gate. A sequence of steps is postulated in which the potential experienced by the ion in the pore is influenced by the position of the ion. The gate structure, with and without the ion, has been optimized. The charges on the atoms and bond lengths have been calculated using natural bond orbital calculations, giving K+ ∼0.77 charges, rather than 1.0. The PVPV hinge sequence has been mutated in silico to PVVV (P407V in the 2A79 numbering). The water structure around the ion becomes discontinuous, separated into two sections, above and below the ion. PVPV conservation closely relates to maintaining the water structure. Finally, these results have implications concerning gating. 相似文献
2.
Alisher M. Kariev 《生物化学与生物物理学报:生物膜》2007,1768(5):1218-1229
A series of ab initio (density functional) calculations were carried out on side chains of a set of amino acids, plus water, from the (intracellular) gating region of the KcsA K+ channel. Their atomic coordinates, except hydrogen, are known from X-ray structures [D.A. Doyle, J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, R. MacKinnon, The structure of the potassium channel: molecular basis of K+ conduction and selectivity, Science 280 (1998) 69-77; R. MacKinnon, S.L. Cohen, A. Kuo, A. Lee, B.T. Chait, Structural conservation in prokaryotic and eukaryotic potassium channels, Science 280 (1998) 106-109; Y. Jiang, A. Lee, J. Chen, M. Cadene, B.T. Chait, R. MacKinnon, The open pore conformation of potassium channels. Nature 417 (2001) 523-526], as are the coordinates of some water oxygen atoms. The 1k4c structure is used for the starting coordinates. Quantum mechanical optimization, in spite of the starting configuration, places the atoms in positions much closer to the 1j95, more tightly closed, configuration. This state shows four water molecules forming a “basket” under the Q119 side chains, blocking the channel. When a hydrated K+ approaches this “basket”, the optimized system shows a strong set of hydrogen bonds with the K+ at defined positions, preventing further approach of the K+ to the basket. This optimized structure with hydrated K+ added shows an ice-like 12 molecule nanocrystal of water. If the water molecules exchange, unless they do it as a group, the channel will remain blocked. The “basket” itself appears to be very stable, although it is possible that the K+ with its hydrating water molecules may be more mobile, capable of withdrawing from the gate. It is also not surprising that water essentially freezes, or forms a kind of glue, in a nanometer space; this agrees with experimental results on a rather different, but similarly sized (nm dimensions) system [K.B. Jinesh, J.W.M. Frenken, Capillary condensation in atomic scale friction: how water acts like a glue, Phys. Rev. Lett. 96 (2006) 166103/1-4]. It also agrees qualitatively with simulations on channels [A. Anishkin, S. Sukharev, Water dynamics and dewetting transitions in the small mechanosensitive channel MscS, Biophys. J. 86 (2004) 2883-2895; O. Beckstein, M.S.P. Sansom, Liquid-vapor oscillations of water in hydrophobic nanopores, Proc. Natl Acad. Sci. U. S. A. 100 (2003) 7063-7068] and on featureless channel-like systems [J. Lu, M.E. Green, Simulation of water in a pore with charges: application to a gating mechanism for ion channels, Prog. Colloid Polym. Sci. 103 (1997) 121-129], in that it forms a boundary on water that is not obvious from the liquid state. The idea that a structure is stable, even if individual molecules exchange, is well known, for example from the hydration shell of ions. We show that when charges are added in the form of protons to the domains (one proton per domain), the optimized structure is open. No stable water hydrogen bonds hold it together; an opening of 11.0 Å appears, measured diagonally between non-neighboring domains as glutamine 119 carbonyl O-O distance. This is comparable to the opening in the MthK potassium channel structure that is generally agreed to be open. The appearance of the opening is in rather good agreement with that found by Perozo and coworkers. In contrast, in the uncharged structure this diagonal distance is 6.5 Å, and the water “basket” constricts the uncharged opening still further, with the ice-like structure that couples the K+ ion to the gating region freezing the entrance to the channel. Comparison with our earlier model for voltage gated channels suggests that a similar mechanism may apply in those channels. 相似文献
3.
The stability of the KcsA channel accommodating more than one ion in the pore has been studied with molecular dynamics. We have used the very last X-ray structure of the KcsA channel at 2.0-Å resolution determined by Zhou et al. [Nature 414 (2001) 43]. In this channel, six of the seven experimentally evidenced sites have been considered. We show that the protein remains very stable in the presence of four K+ ions (three in the selectivity filter and one in the cavity). The locations and the respective distances of the different K+ ions and water molecules (W), calculated within our KWKWKK sequence, also fits well with the experimental observations. The analysis of the K+ ions and water molecules displacements shows concerted file motions on the simulated time scale (≈1 ns), which could act as precursor to the diffusion of K+ ions inside the channel. A simple one-dimensional dynamical model is used to interpret the concerted motions of the ions and water molecules in the pore leading ultimately to ion transfer. 相似文献
4.
Alisher Kariev 《生物化学与生物物理学报:生物膜》2009,1788(5):1188-3792
Different ions in the pore of the KcsA channel behave differently, and we relate this to their solvation. We show that the selectivity is dependent, in part, on the solvation in the cavity (sometimes referred to as the vestibule, it is the region containing water molecules between the intracellular gate and the selectivity filter at the extracellular end of the pore). We have shown earlier that potassium is more dependent at the upper end of the cavity region on solvation by the threonines there, while sodium ion has more water molecules as ligands. In addition, sodium ion is placed asymmetrically, while potassium is nearly exactly symmetric with respect to the four-fold symmetry of the channel. We have now extended these calculations to rubidium and cesium ions, and find that rubidium solvation resembles that of potassium (and both are permeant ions), while cesium resembles sodium (and both are non-permeant), in terms of the geometry of up to eight hydrating, and four non-hydrating, water molecules. In each case, a maximum of 12 water molecules are relevant to the calculation. The placement of the water molecules in the two cases is essentially the same as found from the electron density in the X-ray structure of Zhou and MacKinnon. For Na+ and K+, we show that energy decreases from bulk to the cavity to the lowest position in the selectivity filter (accurate energy could not be calculated for the heavier ions). A separate calculation shows that fixing the Na+ ion at the position of the K+ minimum, followed by re-optimization produced a significantly modified system, not something that could be produced by thermal fluctuations. Moving the K+ into the Na+ position in the upper cavity led to a small increase in energy, ≈ 3 kBT, but was accompanied by large shifts in the positions of hydrating waters, which would create a major kinetic barrier. Therefore, thermal fluctuations could not invalidate the conclusions of the main calculations. 相似文献
5.
Sönke Hornig Phanindra Velisetty Vitya Vardanyan Karin Giller Iris Ohmert Stefan Becker Olaf Pongs Marc Baldus 《The EMBO journal》2009,28(18):2825-2834
Potassium (K+)‐channel gating is choreographed by a complex interplay between external stimuli, K+ concentration and lipidic environment. We combined solid‐state NMR and electrophysiological experiments on a chimeric KcsA–Kv1.3 channel to delineate K+, pH and blocker effects on channel structure and function in a membrane setting. Our data show that pH‐induced activation is correlated with protonation of glutamate residues at or near the activation gate. Moreover, K+ and channel blockers distinctly affect the open probability of both the inactivation gate comprising the selectivity filter of the channel and the activation gate. The results indicate that the two gates are coupled and that effects of the permeant K+ ion on the inactivation gate modulate activation‐gate opening. Our data suggest a mechanism for controlling coordinated and sequential opening and closing of activation and inactivation gates in the K+‐channel pore. 相似文献
6.
The NaK channel is a cation selective channel with similar permeability for K+ and Na+. The available crystallographic structure of wild-type (WT) NaK is usually associated with a conductive state of the channel. Here, potential of mean force for complete conduction events of Na+ and K+ ions through NaK show that: i), large energy barriers prevent the passage of ions through the WT NaK structure, ii), the barriers are correlated to the presence of a hydrogen bond between Asp-66 and Asn-68, and iii), the structure of NaK mutated to mimic cyclic nucleotide-gated channels conducts Na+ and K+. These results support the hypothesis that the filter of cation selective channels can adopt at least two different structures: a conductive one, represented by the x-ray structures of the NaK-CNG chimeras, and a closed one, represented by the x-ray structures of the WT NaK. 相似文献
7.
K Conduction in the Selectivity Filter of Potassium Channels Is Monitored by the Charge Distribution along Their Sequence
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Werner Treptow 《Biophysical journal》2006,91(10):L81
Potassium channels display a high conservation of sequence of the selectivity filter (SF), yet nature has designed a variety of channels that present a wide range of absolute rates of K+ permeation. In KcsA, the structural archetype for K channels, under physiological concentrations, two K+ ions reside in the SF in configurations 1,3 (up state) and 2,4 (down state) and ion conduction is believed to follow a throughput cycle involving a transition between these states. Using free-energy calculations of KcsA, Kv1.2, and mutant channels, we show that this transition is characterized by a channel-dependent energy barrier. This barrier is strongly influenced by the charges partitioned along the sequence of each channel. These results unveil therefore how, for similar structures of the SF, the rate of K+ turnover may be fine-tuned within the family of potassium channels. 相似文献
8.
The ion selectivity of the bacterial potassium channel KCSA is explained upon comparing the energy characteristics of the interaction of cations (Li+, Na+, K+) with atoms of the selectivity filter of the protein pore. Quantum-chemical calculations reveal a deeper potential well for potassium ions, which accounts for preferred K+ permeation. It is shown that the conventional methods with AMBER, CHARMM, OPLS force fields in standard parametrization as well as partial re-parametrization give incorrect estimates of ion energy distribution in the channel. 相似文献
9.
Gastric H,K-ATPase is an electroneutral transmembrane pump that moves protons from the cytoplasm of the parietal cell into the gastric lumen in exchange for potassium ions. The mechanism of transport against the established electrochemical gradients includes intermediate conformations in which the transferred ions are trapped (occluded) within the membrane domain of the pump. The pump cycle involves switching between the E1 and E2P states. Molecular dynamics simulations on homology models of the E2P and E1 states were performed to investigate the mechanism of K+ movement in this enzyme. We performed separate E2P simulations with one K+ in the luminal channel, one K+ ion in the occlusion site, two K+ ions in the occlusion site, and targeted molecular dynamics from E2P to E1 with two K+ ions in the occlusion site. The models were inserted into a lipid bilayer system and were stable over the time course of the simulations, and K+ ions in the channel moved to a consistent location near the center of the membrane domain, thus defining the occlusion site. The backbone carbonyl oxygen from residues 337 through 342 on the nonhelical turn of M4, as well as side-chain oxygen from E343, E795, and E820, participated in the ion occlusion. A single water molecule was stably bound between the two K+ ions in the occlusion site, providing an additional ligand and partial shielding the positive charges from one another. Targeted molecular dynamics was used to transform the protein from the E2P to the E1 state (two K+ ions to the cytoplasm). This simulation identified the separation of the water column in the entry channel as the likely gating mechanism on the luminal side. A hydrated exit channel also formed on the cytoplasmic side of the occlusion site during this simulation. Hence, water molecules became available to hydrate the ions. The movement of the M1M2 transmembrane segments, and the displacement of residues Q159, E160, Q110, and T152 during the conformational change, as well as the motions of E343 and L346, acted as the cytoplasmic-side gate. 相似文献
10.
Steve W. Lockless 《The Journal of general physiology》2015,146(1):3-13
ConclusionThe equilibrium ion-binding properties of ion channels and transporters can be difficult to discern from crystal structures alone, as proteins often adopt different lowest energy states depending on the ions bound. In cases where transport is slow, their inherent ion-binding preferences can be used to infer their transport preferences. However, in cases where transport is fast, the transport selectivity can hide their equilibrium preferences by accentuating the kinetics of ions hopping through a channel over its inherent ion-binding preferences. Thus, depending on the arrangement of ion-binding sites in a channel’s selectivity filter, one can achieve either selective or nonselective ion transport.The equilibrium K+ selectivity of some nonselective channels suggests a potential mechanism whereby they could evolve into a fast K+-selective channel. K+ channels and nonselective channels like CNG and HCN are related to one another in both sequence and structure, suggesting an evolutionary link between them. Swap experiments show that only a few mutations separate a nonselective channel from a K+-selective channel. One might imagine an evolutionary path between these channels in which the equilibrium preference for a K+ ion in a nonselective channel evolves into a K+-selective channel through these few mutations to create the selective ion queue. Alternatively, a slow single-ion channel with an equilibrium and transport preference for K+ ions could be transformed into a fast multi-ion channel through mutations that create a queue of K+-selective ion-binding sites, as is seen in most K+ channels studied to date.In the case of multi-ion selectivity filters, such as those found in K+ channels, the selectivity filter can be viewed as the active site that interacts with different queues of ions and water molecules. At least three properties emerge from multi-ion queues: (1) high conductance by reducing the affinity of multiple bound ions versus single ions; (2) high selectivity by allowing disfavored ions time to dissociate back into solution; and, consequently, (3) robust selectivity in an environment where ion concentrations can change. For transporters and carriers, the equilibrium preference and slow transport naturally create robust selectivity. In all these cases, equilibrium-based ion selectivity is achieved by slowing transport enough so that the disfavored ion is able to dissociate back into solution before transport takes place. 相似文献
11.
The Na+ and K+ channels are essential to neural signaling, but our current knowledge at the atomic level is mainly limited to the conducting mechanism of K+. Unlike a K+ channel having four equivalent K+-binding sites in its selectivity filter, a NaK channel has a vestibule in the middle part of its selectivity filter, and can conduct both Na+ and K+ ions. However, the underlying mechanism for non-selective ion conduction in NaK remains elusive. Here we find four small grottos connecting with the vestibule of the NaK selectivity filter, which form a vestibule-grotto complex perpendicular to the filter pore with a few water molecules within it. It is shown that two or more of the water molecules coming to the vestibule to coordinate the cation are necessary for conducting both Na+ and K+ ions, while only one water molecule in the vestibule will obstruct ion permeation. Thus, the complex with the aid of interior water movement forms a dynamic hydration valve which is flexible in conveying different cations through the vestibule. Similar exquisite hydration valve mechanisms are expected to be utilized by other non-selective cation channels, and the results should shed new light on the importance of water in neural signaling. 相似文献
12.
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. 相似文献
13.
This study presents what is, to our knowledge, a novel technique by means of which the ratio of the single gating charges of voltage-gated rat brain IIA (rBIIA) sodium and Shaker potassium ion channels was estimated. In the experiment, multiple tandems of enhanced green fluorescent protein were constructed and inserted into the C-terminals of Na+ and K+ ion channels. cRNA of Na+ and K+ ion channels was injected and expressed in Xenopus laevis oocytes. The two electrode voltage-clamp technique allowed us to determine the total gating charge of sodium and potassium ion channels, while a relative measure of the amount of expressed channels could be established on the basis of the quantification of the fluorescence intensity of membrane-bound channels marked by enhanced green fluorescent proteins. As a result, gating charge and fluorescence intensity were found to be positively correlated. A relative comparison of the single gating charges of voltage-gated sodium and potassium ion channels could thus be established: the ratio of the single gating charges of the Shaker potassium channel and the rBIIA sodium channel was found to be 2.5 ± 0.4. Assuming the single channel gating charge of the Shaker K+ channel to be ∼13 elementary charges (well supported by other studies), this leads to approximately six elementary charges for the rBIIA sodium channel, which includes a fraction of gating charge that is missed during inactivation. 相似文献
14.
On the Theory of Ion Transport across the Nerve Membrane: V. Two Models for the Cole-Moore K+ Hyperpolarization Delay 总被引:2,自引:1,他引:1
Two illustrative molecular models, designed to explain the Cole-Moore K+ hyperpolarization delay, are proposed and analyzed. Both introduce a process supplementary to the usual Hodgkin-Huxley (HH) one for a K+ channel. In both cases the new process becomes involved as a consequence of the conditioning hyperpolarization of the membrane and would account for the observed delay time in the K+ current after depolarization to near ENa. The first model uses adsorption or desorption of phospholipid molecules on the surface of the assumed protein K+ channel or gate. The second model involves the translocation of the charged subunits of the channel in the hyperpolarizing electric field. 相似文献
15.
Miller C 《Genome biology》2000,1(4):reviews0004.1-reviews00045
Potassium channels, tetrameric integral membrane proteins that form aqueous pores through which K+ can flow, are found in virtually all organisms; the genomes of humans, Drosophila, and Caenorhabditis elegans contain 30-100 K+ channel genes each. The structure of a bacterial K+ channel, sequence comparisons with other channels and electrophysiological measurements have enabled conclusions about the mechanism of gating and ion flow to be drawn for many other channels. 相似文献
16.
Electrokinetic measurements, of streaming potential, were carried out on an excised inside-out patch of the vacuolar membrane of Chara corallina. A water activity gradient was imposed across the patch membrane containing a single K+ channel by addition of sorbitol to one side. Two different K+ channels were found in the tonoplast. Their open channel conductance was investigated as a function of KCl concentration. They had a maximal open channel conductance of 247 and 173 pS, and an apparent affinity (KM) of 116 and 92 mM, respectively. Single-channel zero-current potentials were determined in the presence of an osmotic gradient, and dilution artifacts were corrected for by addition of valinomycin to the bath. Our results suggest that 29 water molecules were coupled to the transport of one K+ ion in the large conductance K+ channel which has a pore radius of ~1.5 nm. 相似文献
17.
The N-terminus of the Na+,K+-ATPase α-subunit shows some homology to that of Shaker-B K+ channels; the latter has been shown to mediate the N-type channel inactivation in a ball-and-chain mechanism. When the Torpedo Na+,K+-ATPase is expressed in Xenopus oocytes and the pump is transformed into an ion channel with palytoxin (PTX), the channel exhibits a time-dependent inactivation gating at positive potentials. The inactivation gating is eliminated when the N-terminus is truncated by deleting the first 35 amino acids after the initial methionine. The inactivation gating is restored when a synthetic N-terminal peptide is applied to the truncated pumps at the intracellular surface. Truncated pumps generate no electrogenic current and exhibit an altered stoichiometry for active transport. Thus, the N-terminus of the α-subunit appears to act like an inactivation gate and performs a critical step in the Na+,K+-ATPase pumping function. 相似文献
18.
Doyle DA 《European biophysics journal : EBJ》2004,33(3):175-179
The recent crystal structure of the prokaryotic inwardly rectifying potassium channel, KirBac1.1, revealed for the first time the structure of a K+ channel in the closed state plus the location of the activation gate. Comparison of the KirBac1.1 structure with other known ion channels reveals a number of common structural features. These common characteristics include the formation of the ion conduction pathway at the interface between adjacent subunits, non-fixed charges forming part of the ion pathway, electrostatic sinks drawing ions into the channel, helix dipoles, and hydrophobic gates that ultimately prevent ion movement. This review describes in detail common structural themes present in ion channels.Presented at the Biophysical Society Meeting on Ion channels – from structure to disease held in May 2003, Rennes, France 相似文献
19.
Li Hong Wang Na Jiang Bo Zhao Xiao Dong Li Tian Hong Lu Xiao Lan Ding Xiao Hua Huang 《Journal of biological inorganic chemistry》2010,15(7):989-993
The current of the outward K+ channel in the cell of horseradish treated with La3+ and the direct interaction between La3+ and the K+ channel protein were investigated using the whole-cell patch-clamp technique, molecular dynamics simulation, and quantum
chemistry calculation methods. It was found for the first time that La3+ decreases the current of the K+ channel in the horseradish mesophyll cell. The decrease results from the formation of a coordination bond and hydrogen bond
between La3+ and the K+ channel protein in the plasma membrane. The direct interaction destroys the native structure of the K+ channel protein, disturbing the function of the K+ channel protein in the cells. The results can provide the theoretical foundation for understanding the interaction between
metal ions (especially high-valence metal ions) and the channel protein in organisms, including animal and plant cells. 相似文献
20.
H. Lühring 《Protoplasma》1986,133(1):19-28
Summary The cytoplasmic drop formed of effused cytoplasm fromChara internodes is enclosed by a membrane. Patch clamp experiments have been carried out on this membrane, revealing a K+ channel as the most frequently detected ion translocator. The K+ channel is saturated at a level of about 20 pA inward and 10 pA outward current. The channel conductance is dependent on the accessability of K+ ions, its maximum value amounts to about 165 pS. The discrimination of Na+ and Cl– is significant, permeability ratios PNa/PK and PCl/PK were estimated to be 0.01 either. Binding experiments with the fluorescent probe concanavalin A/FITC suggest that the membrane is derived from the tonoplast.Abbreviations EK
K+ equilibrium potential
- FITC
fluorescein isothiocyanat
- Vm
membrane voltage
- Vpip
pipette clamp voltage
- Vr
reversal voltage 相似文献