Self-organized Models of Selectivity in Ca and Na Channels (original) (raw)
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Biochimica et Biophysica Acta (BBA) - Biomembranes, 2009
Calcium channels have highly charged selectivity filters (4 COO − groups) that attract cations in to balance this charge and minimize free energy, forcing the cations (Na + and Ca 2+ ) to compete for space in the filter. A reduced model was developed to better understand the mechanism of ion selectivity in calcium channels. The charge/space competition (CSC) mechanism implies that Ca 2+ is more efficient in balancing the charge of the filter because it provides twice the charge as Na + while occupying the same space. The CSC mechanism further implies that the main determinant of Ca 2+ vs. Na + selectivity is the density of charged particles in the selectivity filter, i.e., the volume of the filter (after fixing the number of charged groups in the filter). In this paper we test this hypothesis by changing filter length and/or radius (shape) of the cylindrical selectivity filter of our reduced model. We show that varying volume and shape together has substantially stronger effects than varying shape alone with volume fixed. Our simulations show the importance of depletion zones of ions in determining channel conductance calculated with the integrated Nernst-Planck equation. We show that confining the protein side chains with soft or hard walls does not influence selectivity.
Ionic selectivity in L-type calcium channels by electrostatics and hard-core repulsion
Journal of General Physiology, 2009
Voltage-dependent calcium channels relay electrical signals from the cell membrane to the cytoplasm by allowing extracellular Ca 2+ to flow into the cell, where Ca 2+ acts as a chemical signal . The Ca 2+ -conducting pore of these transmembrane proteins selects Ca 2+ over the much more abundant cations Na + and K + . Four amino acid residues bearing acidic side chains (the "EEEE" locus in L-type calcium channels) extend into this pore, and all cooperate in selecting Ca 2+ with high affinity for review see . Here, we compute consequences of a physical model of selectivity in which ions compete for interaction with negative structural charge and for restricted space in the EEEE locus.
Journal of Physical Chemistry B, 2001
Our earlier simulation (J. Phys. Chem. B 2000, 104, 8903) of the selectivity of a model calcium channel, where all ions were assumed to have the same diameter and the channel dimensions were fixed, is extended to allow for different ionic size and variable channel size. We find that for equal valence, the channel selects cations of the smallest size. If higher valence cations are present, the channel selects cations with the highest valence, and as a result, Ca ++ will replace monovalent cations. This replacement is more efficient for larger monovalent cations than for smaller ones. This is what would be expected on the basis of the charge/space competition mechanism that has been postulated earlier. Of course, if the size ratio is very large, size might be selected over valence. In addition, we consider the effect of the channel diameter and find that narrow channels are less Ca ++ selective. This suggests that the recent theory of Nonner et al. (Biophys. J. 2000(Biophys. J. , 79, 1976) is most useful for wide, but still microscopic, channels.
Selectivity sequences in a model calcium channel: role of electrostatic field strength
European Biophysics Journal, 2011
The energetics that give rise to selectivity sequences of ionic binding selectivity of Li + , Na + , K + , Rb + , and Cs + in a model of a calcium channel are considered. This work generalizes Eisenman's classical treatment (Biophys. J. 2 (Suppl. 2), 259) by including multiple, mobile binding site oxygens that coordinate many permeating ions (all modeled as charged, hard spheres). The selectivity filter of the model calcium channel allows the carboxyl terminal groups of glutamate and aspartate side chains to directly interact with and coordinate the permeating ions. Ion dehydration effects are represented with a Born energy between the dielectric coefficients of the selectivity filter and the bath. High oxygen concentration creates a high field strength site that prefers small ions, as in Eisenman's model. On the other hand, a low filter dielectric constant also creates a high field strength site, but this site prefers large ions, contrary to Eisenman's model. These results indicate that field strength does not have a unique effect on ionic binding selectivity sequences once entropic, electrostatic, and dehydration forces are included in the model. Thus, Eisenman's classical relationship between field strength and selectivity sequences must be supplemented with additional information in selectivity filters like the calcium channel that have amino acid side chains mixing with ions to make a crowded permeation pathway.
Structural basis for Ca2+ selectivity of a voltage-gated calcium channel
Nature, 2013
Voltage-gated calcium (Ca V ) channels catalyse rapid, highly selective influx of Ca 21 into cells despite a 70-fold higher extracellular concentration of Na 1 . How Ca V channels solve this fundamental biophysical problem remains unclear. Here we report physiological and crystallographic analyses of a calcium selectivity filter constructed in the homotetrameric bacterial Na V channel Na V Ab. Our results reveal interactions of hydrated Ca 21 with two high-affinity Ca 21 -binding sites followed by a third lower-affinity site that would coordinate Ca 21 as it moves inward. At the selectivity filter entry, Site 1 is formed by four carboxyl side chains, which have a critical role in determining Ca 21 selectivity. Four carboxyls plus four backbone carbonyls form Site 2, which is targeted by the blocking cations Cd 21 and Mn 21 , with single occupancy. The lower-affinity Site 3 is formed by four backbone carbonyls alone, which mediate exit into the central cavity. This pore architecture suggests a conduction pathway involving transitions between two main states with one or two hydrated Ca 21 ions bound in the selectivity filter and supports a 'knock-off' mechanism of ion permeation through a stepwisebinding process. The multi-ion selectivity filter of our Ca V Ab model establishes a structural framework for understanding the mechanisms of ion selectivity and conductance by vertebrate Ca V channels.
Mechanisms of Permeation and Selectivity in Calcium Channels
Biophysical Journal, 2001
The mechanisms underlying ion transport and selectivity in calcium channels are examined using electrostatic calculations and Brownian dynamics simulations. We model the channel as a rigid structure with fixed charges in the walls, representing glutamate residues thought to be responsible for ion selectivity. Potential energy profiles obtained from multi-ion electrostatic calculations provide insights into ion permeation and many other observed features of L-type calcium channels. These qualitative explanations are confirmed by the results of Brownian dynamics simulations, which closely reproduce several experimental observations. These include the current-voltage curves, current-concentration relationship, block of monovalent currents by divalent ions, the anomalous mole fraction effect between sodium and calcium ions, attenuation of calcium current by external sodium ions, and the effects of mutating glutamate residues in the amino acid sequence.
The Anomalous Mole Fraction Effect in Calcium Channels: A Measure of Preferential Selectivity
Biophysical Journal, 2008
The cause of the anomalous mole fraction effect (AMFE) in calcium-selective ion channels is studied. An AMFE occurs when the conductance through a channel is lower in a mixture of salts than in the pure salts at the same concentration. The textbook interpretation of the AMFE is that multiple ions move through the pore in coordinated, single-file motion. Instead of this, we find that at its most basic level an AMFE reflects a channel's preferential binding selectivity for one ion species over another. The AMFE is explained by considering the charged and uncharged regions of the pore as electrical resistors in series: the AMFE is produced by these regions of high and low ion concentration changing differently with mole fraction due to the preferential ion selectivity. This is demonstrated with simulations of a model L-type calcium channel and a mathematical analysis of a simplistic point-charge model. The particle simulations reproduce the experimental data of two L-type channel AMFEs. Conditions under which an AMFE may be found experimentally are discussed. The resistors-in-series model provides a fundamentally different explanation of the AMFE than the traditional theory and does not require single filing, multiple occupancy, or momentum-correlated ion motion.
Binding and Selectivity in L-Type Calcium Channels:A Mean Spherical Approximation
Biophysical Journal, 2000
L-type calcium channels are Ca 2ϩ binding proteins of great biological importance. They generate an essential intracellular signal of living cells by allowing Ca 2ϩ ions to move across the lipid membrane into the cell, thereby selecting an ion that is in low extracellular abundance. Their mechanism of selection involves four carboxylate groups, containing eight oxygen ions, that belong to the side chains of the "EEEE" locus of the channel protein, a setting similar to that found in many Ca 2ϩ -chelating molecules. This study examines the hypothesis that selectivity in this locus is determined by mutual electrostatic screening and volume exclusion between ions and carboxylate oxygens of finite diameters. In this model, the eight half-charged oxygens of the tethered carboxylate groups of the protein are confined to a subvolume of the pore (the "filter"), but interact spontaneously with their mobile counterions as ions interact in concentrated bulk solutions. The mean spherical approximation (MSA) is used to predict ion-specific excess chemical potentials in the filter and baths. The theory is calibrated using a single experimental observation, concerning the apparent dissociation constant of Ca 2ϩ in the presence of a physiological concentration of NaCl. When ions are assigned their independently known crystal diameters and the carboxylate oxygens are constrained, e.g., to a volume of 0.375 nm 3 in an environment with an effective dielectric coefficient of 63.5, the hypothesized selectivity filter produces the shape of the calcium binding curves observed in experiment, and it predicts Ba 2ϩ /Ca 2ϩ and Na ϩ /Li ϩ competition, and Cl Ϫ exclusion as observed. The selectivities for Na ϩ , Ca 2ϩ , Ba 2ϩ , other alkali metal ions, and Cl Ϫ thus can be predicted by volume exclusion and electrostatic screening alone. Spontaneous coordination of ions and carboxylates can produce a wide range of Ca 2ϩ selectivities, depending on the volume density of carboxylate groups and the permittivity in the locus. A specific three-dimensional structure of atoms at the binding site is not needed to explain Ca 2ϩ selectivity.
Computer Simulation Studies of the Selectivity and Conductance of A Model Calcium Channel
Some results of our simulation studies of selectivity and conductance of calcium ion channels in membranes are reported. Ion channels regulate many important physiological functions. To simulate the system we use periodic boundary conditions. We have noted previously that the use of such boundary conditions does not affect our results in any significant manner. The structure of the filter of a calcium channel is reasonably well understood. An important structural element is the set of four glutamate residues that are attached to the wall of the channel. Since the glutamates are long and flexible, Nonner and Eisenberg et al. have suggested that these glutamates can be modeled by eight half-charged oxygen ions that represent the carboxylates at the end of each residue. These oxygen ions are confined to the filter but otherwise are mobile. We have used this model in simulations of the selectivity and conductance of this model calcium channel filter. Our studies confirm that this model behaves as a calcium filter; calcium ions will drive sodium ions from the filter. In many of our simulations, explicit water molecules are used with water molecules in both the filter and bath.
The effect of protein dielectric coefficient on the ionic selectivity of a calcium channel
The Journal of Chemical Physics, 2006
Calcium-selective ion channels are known to have carboxylate-rich selectivity filters, a common motif that is primarily responsible for their high Ca 2+ affinity. Different Ca 2+ affinities ranging from micromolar ͑the L-type Ca channel͒ to millimolar ͑the ryanodine receptor channel͒ are closely related to the different physiological functions of these channels. To understand the physical mechanism for this range of affinities given similar amino acids in their selectivity filters, we use grand canonical Monte Carlo simulations to assess the binding of monovalent and divalent ions in the selectivity filter of a model Ca channel. We use a reduced model where the electolyte is modeled by hard-sphere ions embedded in a continuum dielectric solvent, while the interior of protein surrounding the channel is allowed to have a dielectric coefficient different from that of the electrolyte. The induced charges that appear on the protein/lumen interface are calculated by the induced charge computation method ͓Boda et al., Phys. Rev. E 69, 046702 ͑2004͔͒. It is shown that decreasing the dielectric coefficient of the protein attracts more cations into the pore because the protein's carboxyl groups induce negative charges on the dielectric boundary. As the density of the hard-sphere ions increases in the filter, Ca 2+ is absorbed into the filter with higher probability than Na + because Ca 2+ provides twice the charge to neutralize the negative charge of the pore ͑both structural carboxylate oxygens and induced charges͒ than Na + while occupying about the same space ͑the charge/space competition mechanism͒. As a result, Ca 2+ affinity is improved an order of magnitude by decreasing the protein dielectric coefficient from 80 to 5. Our results indicate that adjusting the dielectric properties of the protein surrounding the permeation pathway is a possible way for evolution to regulate the Ca 2+ affinity of the common four-carboxylate motif.