Protein structure and ionic selectivity in calcium channels: selectivity filter size, not shape, matters

Unraveling the impact of ORF3a Q57H mutation on SARS-CoV-2: insights from molecular dynamics

ORF3a is a conserved accessory protein of SARS-CoV-2, linked to viral infection and pathogenesis, with acquired mutations at various locations. Previous studies have shown that the occurrence of the Q57H mutation is higher in comparison to other positions in ORF3a. This mutation is known to induce conformational changes, yet the extent of structural alteration and its role in the viral adaptation process remain unknown. Here we performed molecular dynamics (MD) simulations of wt-ORF3a, Q57H, and Q57A mutants to analyze structural changes caused by mutations compared to the native protein. The MD analysis revealed that Q57H and Q57A mutants show significant structural changes in the dimer conformation than the wt-ORF3a. This dimer conformer narrows down the ion channel cavity, which reduces Na + or K + permeability leading to decrease the antigenic response that can help the virus to escape the host immune system. Non-bonding interaction analysis shows the Q57H mutant has more interacting residues, resulting in more stability within dimer conformation than the wt-ORF3a and Q57A. Moreover, both mutant dimers (Q57H and Q57A) form a novel salt-bridge interaction at the same position between A:Asp142 and B:Lys61, whereas such an interaction is absent in the wt-ORF3a dimer. We have also noticed that the TM3 domain's flexibility in Q57H is increased because of strong inter-domain interactions of TM1 and TM2 within the dimer conformation. These unusual interactions and flexibility of Q57H mutant can have significant impacts on the SARS-CoV-2 adaptations, virulence, transmission, and immune system evasion. Our findings are consistent with the previous experimental data and provided details information on the structural perturbation in ORF3a caused by mutations, which can help better understand the structural change at the molecular level as well as the reason for the high virulence properties of this variant.Communicated by Ramaswamy H. Sarma.

New insights into the effects of small permanent charge on ionic flows: A higher order analysis

This study investigated how permanent charges influence the dynamics of ionic channels. Using a quasi-one-dimensional classical Poisson-Nernst-Planck (PNP) model, we investigated the behavior of two distinct ion species-one positively charged and the other negatively charged. The spatial distribution of permanent charges was characterized by zero values at the channel ends and a constant charge $ Q_0 $ within the central region. By treating the classical PNP model as a boundary value problem (BVP) for a singularly perturbed system, the singular orbit of the BVP depended on $ Q_0 $ in a regular way. We therefore explored the solution space in the presence of a small permanent charge, uncovering a systematic dependence on this parameter. Our analysis employed a rigorous perturbation approach to reveal higher-order effects originating from the permanent charges. Through this investigation, we shed light on the intricate interplay among boundary conditions and permanent charges, providing insights into their impact on the behavior of ionic current, fluxes, and flux ratios. We derived the quadratic solutions in terms of permanent charge, which were notably more intricate compared to the linear solutions. Through computational tools, we investigated the impact of these quadratic solutions on fluxes, current-voltage relations, and flux ratios, conducting a thorough analysis of the results. These novel findings contributed to a deeper comprehension of ionic flow dynamics and hold potential implications for enhancing the design and optimization of ion channel-based technologies.

Bound Ca2+ moves faster and farther from single open channels than free Ca2

A concept of Ca2+ nanodomains established in the cytoplasm after opening single-calcium channels helps mechanistically understand the physiological mechanisms of Ca2+ signaling. It predicts standing gradients of cytoplasmic free Ca2+ around single channels in the plasma membrane. The fate of bound Ca2+ attracted much less attention. This study aimed to examine the profiles of Ca2+ bound to low-mobility buffers such as bulky Ca2+-binding proteins. The solution of non-linear PDEs for an immobile buffer predicts fast decay of free [Ca2+] from the channel lumen and the traveling wave for bound Ca2+. For low-mobility buffers like calmodulin, the calculated profiles of free and bound Ca2+ are similar. Theoretical predictions are tested by imaging 1D profiles of Ca2+ bound to low-mobility fluo-4-dextran. The traveling waves of bound Ca2+ are observed that develop during the opening of single channels. The findings tempt to propose that Ca2+ signaling may not be solely related by the absolute free [Ca2+] at the sensor location, which is extremely localized, but determined by the time when a wave of bound Ca2+ reaches a threshold needed for sensor activation.

Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into eight fundamental clades with four of these clades (G, GH, GR, and GV) globally prevalent in 2020. To explain plausible epistatic effects of the signature co-occurring mutations of these circulating clades on viral replication and transmission fitness, we proposed a hypothetical model using in silico approach. Molecular docking and dynamics analyses showed the higher infectiousness of a spike mutant through more favorable binding of G614 with the elastase-2. RdRp mutation p.P323L significantly increased genome-wide mutations (p < 0.0001), allowing for more flexible RdRp (mutated)-NSP8 interaction that may accelerate replication. Superior RNA stability and structural variation at NSP3:C241T might impact protein, RNA interactions, or both. Another silent 5'-UTR:C241T mutation might affect translational efficiency and viral packaging. These four G-clade-featured co-occurring mutations might increase viral replication. Sentinel GH-clade ORF3a:p.Q57H variants constricted the ion-channel through intertransmembrane-domain interaction of cysteine(C81)-histidine(H57). The GR-clade N:p.RG203-204KR would stabilize RNA interaction by a more flexible and hypo-phosphorylated SR-rich region. GV-clade viruses seemingly gained the evolutionary advantage of the confounding factors; nevertheless, N:p.A220V might modulate RNA binding with no phenotypic effect. Our hypothetical model needs further retrospective and prospective studies to understand detailed molecular events and their relationship to the fitness of SARS-CoV-2.

Electroneutrality breakdown in nanopore arrays

The electrostatic screening of charge in one-dimensional confinement leads to long-range breakdown in electroneutrality within a nanopore. Through a series of continuum simulations, we demonstrate the principles of electroneutrality breakdown for electrolytes in one-dimensional confinement. We show how interacting pores in a membrane can counteract the phenomenon of electroneutrality breakdown, eventually returning to electroneutrality. Emphasis is placed on applying simplifying formulas to reduce the multidimensional partial differential equations into a single ordinary differential equation for the electrostatic potential. Dielectric mismatch between the electrolyte and membrane, pore aspect ratio, and confinement dimensionality are studied independently, outlining the relevance of electroneutrality breakdown in nanoporous membranes for selective ion transport and separations.

Structural Changes beyond the EF-Hand Contribute to Apparent Calcium Binding Affinities: Insights from Parvalbumins

Members of the parvalbumin (PV) family of calcium (Ca2+) binding proteins (CBPs) share a relatively high level of sequence similarity. However, their Ca2+ affinities and selectivities against competing ions like Mg2+ can widely vary. We conducted molecular dynamics simulations of several α-parvalbumin (αPV) constructs with micromolar to nanomolar Ca2+ affinities to identify structural and dynamic features that contribute to their binding of ions. Specifically, we examined a D94S/G98E construct with a lower Ca2+ affinity (≈-18 kcal/mol) relative to the wild type (WT) (≈-22 kcal/mol) and an S55D/E59D variant with enhanced affinity (≈-24 kcal/mol). Additionally, we also examined the binding of Mg2+ to these isoforms, which is much weaker than Ca2+. We used mean spherical approximation (MSA) theory to evaluate ion binding thermodynamics within the proteins' EF-hand domains to account for the impact of ions' finite sizes and the surrounding electrolyte composition. While the MSA scores differentiated Mg2+ from Ca2+, they did not indicate that Ca2+ binding affinities at the binding loop differed between the PV isoforms. Instead, molecular mechanics generalized Born surface area (MM/GBSA) approximation energies, which we used to quantify the thermodynamic cost of structural rearrangement of the proteins upon binding ions, indicated that S55D/E59D αPV favored Ca2+ binding by -20 kcal/mol relative to WT versus 30 kcal/mol for D94S/G98E αPV. Meanwhile, Mg2+ binding was favored for the S55D/E59D αPV and D94S/G98E αPV variants by -18.32 and -1.65 kcal/mol, respectively. These energies implicate significant contributions to ion binding beyond oxygen coordination at the binding loop, which stemmed from changes in α-helicity, β-sheet character, and hydrogen bonding. Hence, Ca2+ affinity and selectivity against Mg2+ are emergent properties stemming from both local effects within the proteins' ion binding sites as well as non-local contributions elsewhere. Our findings broaden our understanding of the molecular bases governing αPV ion binding that are likely shared by members of the broad family of CBPs.

Molecular Choreography and Structure of Ca2+ Release-Activated Ca2+ (CRAC) and KCa2+ Channels and Their Relevance in Disease with Special Focus on Cancer

Ca2+ ions play a variety of roles in the human body as well as within a single cell. Cellular Ca2+ signal transduction processes are governed by Ca2+ sensing and Ca2+ transporting proteins. In this review, we discuss the Ca2+ and the Ca2+-sensing ion channels with particular focus on the structure-function relationship of the Ca2+ release-activated Ca2+ (CRAC) ion channel, the Ca2+-activated K+ (KCa2+) ion channels, and their modulation via other cellular components. Moreover, we highlight their roles in healthy signaling processes as well as in disease with a special focus on cancer. As KCa2+ channels are activated via elevations of intracellular Ca2+ levels, we summarize the current knowledge on the action mechanisms of the interplay of CRAC and KCa2+ ion channels and their role in cancer cell development.

Modeling the Device Behavior of Biological and Synthetic Nanopores with Reduced Models

Biological ion channels and synthetic nanopores are responsible for passive transport of ions through a membrane between two compartments. Modeling these ionic currents is especially amenable to reduced models because the device functions of these pores, the relation of input parameters (e.g., applied voltage, bath concentrations) and output parameters (e.g., current, rectification, selectivity), are well defined. Reduced models focus on the physics that produces the device functions (i.e., the physics of how inputs become outputs) rather than the atomic/molecular-scale physics inside the pore. Here, we propose four rules of thumb for constructing good reduced models of ion channels and nanopores. They are about (1) the importance of the axial concentration profiles, (2) the importance of the pore charges, (3) choosing the right explicit degrees of freedom, and (4) creating the proper response functions. We provide examples for how each rule of thumb helps in creating a reduced model of device behavior.

Rectification of bipolar nanopores in multivalent electrolytes: effect of charge inversion and strong ionic correlations

Bipolar nanopores have powerful rectification properties due to the asymmetry in the charge pattern on the wall of the nanopore. In particular, bipolar nanopores have positive and negative surface charges along the pore axis. Rectification is strong if the radius of the nanopore is small compared to the screening length of the electrolyte so that both cations and anions have depletion zones in the respective regions. The depths of these depletion zones is sensitive to sign of the external voltage. In this work, we are interested in the effect of the presence of strong ionic correlations (both between ions and between ions and surface charge) due to the presence of multivalent ions and large surface charges. We show that strong ionic correlations cause leakage of the coions, a phenomenon that is absent in mean field theories. In this modeling study, we use both the mean-field Poisson-Nernst-Planck (PNP) theory and a particle simulation method, Local Equilibrium Monte Carlo (LEMC), to show that phenomena such as overcharging and charge inversion cannot be reproduced with PNP, while LEMC is able to produce nonmonotonic dependence of currents and rectification as a function of surface charge strength.

Critical parameters maintaining authentic CRAC channel hallmarks

Ca2+ ions represent versatile second messengers that regulate a huge diversity of processes throughout the cell's life. One prominent Ca2+ entry pathway into the cell is the Ca2+ release-activated Ca2+ (CRAC) ion channel. It is fully reconstituted by the two molecular key players: the stromal interaction molecule (STIM1) and Orai. STIM1 is a Ca2+ sensor located in the membrane of the endoplasmic reticulum, and Orai, a highly Ca2+ selective ion channel embedded in the plasma membrane. Ca2+ store-depletion leads initially to the activation of STIM1 which subsequently activates Orai channels via direct binding. Authentic CRAC channel hallmarks and biophysical characteristics include high Ca2+ selectivity with a reversal potential in the range of + 50 mV, small unitary conductance, fast Ca2+-dependent inactivation and enhancements in currents upon the switch from a Na+-containing divalent-free to a Ca2+-containing solution. This review provides an overview on the critical determinants and structures within the STIM1 and Orai proteins that establish these prominent CRAC channel characteristics.

Understanding Ion Binding Affinity and Selectivity in β-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory

Parvalbumin (PV) is a globular calcium (Ca(2+))-selective protein expressed in a variety of biological tissues. Our computational studies of the rat β-parvalbumin (β-PV) isoform seek to elucidate the molecular thermodynamics of Ca(2+) versus magnesium (Mg(2+)) binding at the protein's two EF-hand motifs. Specifically, we have utilized molecular dynamics (MD) simulations and a mean-field electrolyte model (mean spherical approximation (MSA) theory) to delineate how the EF-hand scaffold controls the "local" thermodynamics of Ca(2+) binding selectivity over Mg(2+). Our MD simulations provide the probability density of metal-chelating oxygens within the EF-hand scaffolds for both Ca(2+) and Mg(2+), as well the conformational strain induced by Mg(2+) relative to Ca(2+) binding. MSA theory utilizes the binding domain oxygen and charge distributions to predict the chemical potential of ion binding, as well as their corresponding concentrations within the binding domain. We find that the electrostatic and steric contributions toward ion binding were similar for Mg(2+) and Ca(2+), yet the latter was 5.5 kcal/mol lower in enthalpy when internal strain within the EF hand was considered. We therefore speculate that beyond differences in dehydration energies for the Ca(2+) versus Mg(2+), strain induced in the β-PV EF hand by cation binding significantly contributes to the nearly 10,000-fold difference in binding affinity reported in the literature. We further complemented our analyses of local factors governing cation binding selectivity with whole-protein (global) contributions, such as interhelical residue-residue contacts and solvent exposure of hydrophobic surface. These contributions were found to be comparable for both Ca(2+)- and Mg(2+)-bound β-PV, which may implicate local factors, EF-hand strain, and dehydration, in providing the primary means of selectivity. We anticipate these methods could be used to estimate metal binding thermodynamics across a broad range of PV sequence homologues and EF-hand-containing, Ca(2+) binding proteins.

Elucidating factors important for monovalent cation selectivity in enzymes: E. coli β-galactosidase as a model

Many enzymes require a specific monovalent cation (M(+)), that is either Na(+) or K(+), for optimal activity. While high selectivity M(+) sites in transport proteins have been extensively studied, enzyme M(+) binding sites generally have lower selectivity and are less characterized. Here we study the M(+) binding site of the model enzyme E. coli β-galactosidase, which is about 10 fold selective for Na(+) over K(+). Combining data from X-ray crystallography and computational models, we find the electrostatic environment predominates in defining the Na(+) selectivity. In this lower selectivity site rather subtle influences on the electrostatic environment become significant, including the induced polarization effects of the M(+) on the coordinating ligands and the effect of second coordination shell residues on the charge distribution of the primary ligands. This work expands the knowledge of ion selectivity in proteins to denote novel mechanisms important for the selectivity of M(+) sites in enzymes.

Ion selectivity strategies of sodium channel selectivity filters

CONSPECTUS: Sodium ion channels selectively transport Na(+) cations across the cell membrane. These integral parts of the cell machinery are implicated in regulating the cardiac, skeletal and smooth muscle contraction, nerve impulses, salt and water homeostasis, as well as pain and taste perception. Their malfunction often results in various channelopathies of the heart, brain, skeletal muscles, and lung; thus, sodium channels are key drug targets for various disorders including cardiac arrhythmias, heart attack, stroke, migraine, epilepsy, pain, cancer, and autoimmune disorders. The ability of sodium channels to discriminate the native Na(+) among other competing ions in the surrounding fluids is crucial for proper cellular functions. The selectivity filter (SF), the narrowest part of the channel's open pore, lined with amino acid residues that specifically interact with the permeating ion, plays a major role in determining Na(+) selectivity. Different sodium channels have different SFs, which vary in the symmetry, number, charge, arrangement, and chemical type of the metal-ligating groups and pore size: epithelial/degenerin/acid-sensing ion channels have generally trimeric SFs lined with three conserved neutral serines and/or backbone carbonyls; eukaryotic sodium channels have EKEE, EEKE, DKEA, and DEKA SFs with an invariant positively charged lysine from the second or third domain; and bacterial voltage-gated sodium (Nav) channels exhibit symmetrical EEEE SFs, reminiscent of eukaryotic voltage-gated calcium channels. How do these different sodium channel SFs achieve high selectivity for Na(+) over its key rivals, K(+) and Ca(2+)? What factors govern the metal competition in these SFs and which of these factors are exploited to achieve Na(+) selectivity in the different sodium channel SFs? The free energies for replacing K(+) or Ca(2+) bound inside different model SFs with Na(+), evaluated by a combination of density functional theory and continuum dielectric calculations, have shed light on these questions. The SFs of epithelial and eukaryotic Nav channels select Na(+) by providing an optimal number and ligating strength of metal ligands as well as a rigid pore whose size fits the cognate Na(+) ideally. On the other hand, the SFs of bacterial Nav channels select Na(+), as the protein matrix attenuates ion-protein interactions relative to ion-solvent interactions by enlarging the pore and allowing water to enter, so the ion interacts indirectly with the conserved glutamates via bridging water molecules. This shows how these various SFs have adapted to the specific physicochemical properties of the native ion, using different strategies to select Na(+) among its contenders.

Divergence of Ca(2+) selectivity and equilibrium Ca(2+) blockade in a Ca(2+) release-activated Ca(2+) channel

The Ca²⁺ selectivity of CRAC channels depends on the kinetics of ion entry and exit as well as the steady-state Ca²⁺ binding affinity.

Prevailing models postulate that high Ca²⁺ selectivity of Ca²⁺ release-activated Ca²⁺ (CRAC) channels arises from tight Ca²⁺ binding to a high affinity site within the pore, thereby blocking monovalent ion flux. Here, we examined the contribution of high affinity Ca²⁺ binding for Ca²⁺ selectivity in recombinant Orai3 channels, which function as highly Ca²⁺-selective channels when gated by the endoplasmic reticulum Ca²⁺ sensor STIM1 or as poorly Ca²⁺-selective channels when activated by the small molecule 2-aminoethoxydiphenyl borate (2-APB). Extracellular Ca²⁺ blocked Na⁺ currents in both gating modes with a similar inhibition constant (K_i; ∼25 µM). Thus, equilibrium binding as set by the K_i of Ca²⁺ blockade cannot explain the differing Ca²⁺ selectivity of the two gating modes. Unlike STIM1-gated channels, Ca²⁺ blockade in 2-APB–gated channels depended on the extracellular Na⁺ concentration and exhibited an anomalously steep voltage dependence, consistent with enhanced Na⁺ pore occupancy. Moreover, the second-order rate constants of Ca²⁺ blockade were eightfold faster in 2-APB–gated channels than in STIM1-gated channels. A four-barrier, three–binding site Eyring model indicated that lowering the entry and exit energy barriers for Ca²⁺ and Na⁺ to simulate the faster rate constants of 2-APB–gated channels qualitatively reproduces their low Ca²⁺ selectivity, suggesting that ion entry and exit rates strongly affect Ca²⁺ selectivity. Noise analysis indicated that the unitary Na⁺ conductance of 2-APB–gated channels is fourfold larger than that of STIM1-gated channels, but both modes of gating show a high open probability (P_o; ∼0.7). The increase in current noise during channel activation was consistent with stepwise recruitment of closed channels to a high P_o state in both cases, suggesting that the underlying gating mechanisms are operationally similar in the two gating modes. These results suggest that both high affinity Ca²⁺ binding and kinetic factors contribute to high Ca²⁺ selectivity in CRAC channels.

Competition among Ca2+, Mg2+, and Na+ for model ion channel selectivity filters: determinants of ion selectivity

Because voltage-gated ion channels play critical biological roles, understanding how they can discriminate the native metal ion from rival cations in the milieu is of great interest. Although Ca(2+), Mg(2+), and Na(+) are present in comparable concentrations outside the cell, the factors governing the competition among these cations for the selectivity filter of voltage-gated Ca(2+) ion channel remain unclear. Using density functional theory combined with continuum dielectric methods, we evaluate the effect of (1) the number, chemical type, and charge of the ligands lining the pore, (2) the pore's rigidity, size, symmetry, and solvent accessibility, and (3) the Ca(2+) hydration number outside the selectivity filter on the competition among Ca(2+), Mg(2+), and Na(+) in model selectivity filters. The calculations show how the outcome of this competition depends on the interplay between electronic and solvation effects. Selectivity for monovalent Na(+) over divalent Ca(2+)/Mg(2+) is achieved when solvation effects outweigh electrostatic effects; thus filters comprising a few weak charge-donating groups such as Ser/Thr side chains, where electrostatic effects are relatively weak and are easily overcome by solvation effects, are Na(+)-selective. In contrast, selectivity for divalent Ca(2+)/Mg(2+) over monovalent Na(+) is achieved when metal-ligand electrostatic effects outweigh solvation effects. The key differences in selectivity between Mg(2+) and Ca(2+) lie in the pore size, oligomericity, and solvent accessibility. The results, which are consistent with available experimental data, reveal how the structure and composition of the ion channel selectivity pore had adapted to the specific physicochemical properties of the native metal ion to enhance the competitiveness of the native metal toward rival cations.

Current and selectivity in a model sodium channel under physiological conditions: Dynamic Monte Carlo simulations

A reduced model of a sodium channel is analyzed using Dynamic Monte Carlo simulations. These include the first simulations of ionic current under approximately physiological ionic conditions through a model sodium channel and an analysis of how mutations of the sodium channel's DEKA selectivity filter motif transform the channel from being Na(+) selective to being Ca(2+) selective. Even though the model of the pore, amino acids, and permeant ions is simplified, the model reproduces the fundamental properties of a sodium channel (e.g., 10 to 1 Na(+) over K(+) selectivity, Ca(2+) exclusion, and Ca(2+) selectivity after several point mutations). In this model pore, ions move through the pore one at a time by simple diffusion and Na(+) versus K(+) selectivity is due to both the larger K(+) not fitting well into the selectivity filter that contains amino acid terminal groups and K(+) moving more slowly (compared to Na(+)) when it is in the selectivity filter.

Analyzing the components of the free-energy landscape in a calcium selective ion channel by Widom's particle insertion method

The selectivity filter of the L-type calcium channel works as a Ca(2+) binding site with a very large affinity for Ca(2+) versus Na(+). Ca(2+) replaces half of the Na(+) ions in the filter even when these ions are present in 1 μM and 30 mM concentrations in the bath, respectively. The energetics of this strong selectivity is analyzed in this paper. We use Widom's particle insertion method to compute the space-dependent profiles of excess chemical potential in our grand canonical Monte Carlo simulations. These profiles define the free-energy landscape for the various ions. Following Gillespie [Biophys. J. 94, 1169 (2008)], the difference of the excess chemical potentials for the two competing ions defines the advantage that one of the ions has over the other in the competition for space in the crowded selectivity filter. These advantages depend on ionic bath concentrations: the ion that is present in the bath in larger quantity (Na(+)) has the "number" advantage which is balanced by the free-energy advantage of the other ion (Ca(2+)). The excess chemical potentials are decomposed into hard sphere exclusion and electrostatic components. The electrostatic terms correspond to interactions with the mean electric field produced by ions and induced charges as well to ionic correlations beyond the mean field description. Dielectrics are needed to produce micromolar Ca(2+) versus Na(+) selectivity in the L-type channel. We study the behavior of these terms with changes in bath concentrations of ions, charges, and diameters of ions, as well as geometrical parameters such as radius of the pore and the dielectric constant of the protein. Ion selectivity in calcium binding proteins probably has a similar mechanism.

Selectivity sequences in a model calcium channel: role of electrostatic field strength

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 classic treatment (Biophys J 2(Suppl. 2):259, 1962) 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 classic relationship between field strength and selectivity sequences must be supplemented with additional information about selectivity filters such as the calcium channel that has amino acid side chains mixing with ions to make a crowded permeation pathway.

Simulations of calcium channel block by trivalent cations: Gd(3+) competes with permeant ions for the selectivity filter

Current through L-type calcium channels (Ca(V)1.2 or dihydropyridine receptor) can be blocked by micromolar concentrations of trivalent cations like the lanthanide gadolinium (Gd(3+)). It has been proposed that trivalent block is due to ions competing for a binding site in both the open and closed configuration, but possibly with different trivalent affinities. Here, we corroborate this general view of trivalent block by computing conductance of a model L-type calcium channel. The model qualitatively reproduces the Gd(3+) concentration dependence and the effect that substantially more Gd(3+) is required to produce similar block in the presence of Sr(2+) (compared to Ba(2+)) and even more in the presence of Ca(2+). Trivalent block is explained in this model by cations binding in the selectivity filter with the charge/space competition mechanism. This is the same mechanism that in the model channel governs other selectivity properties. Specifically, selectivity is determined by the combination of ions that most effectively screen the negative glutamates of the protein while finding space in the midst of the closely packed carboxylate groups of the glutamate residues.

Sieving experiments and pore diameter: it's not a simple relationship

The classic sieving experiment for estimating an ion channel's diameter with successively larger ions is re-examined. Using a very reduced model of a calcium channel, it is shown that sieving experiments measure a combination of three mechanisms: the cross-sectional area available to the sieving ions (the classic interpretation), the exclusion of the sieving ions from a pore crowded with amino acid side chains that protrude into the permeation pathway, and competitive selectivity of the sieving ions with other ions in the bath (even if those are present only at trace concentrations). The latter two can be called sieving-by-crowding because they stem from the excluded volume of the amino acids in the permeation pathway. The model shows that--to a first--order approximation-sieving experiments measure the available volume inside a selectivity filter, rather than the available cross-sectional area. The two are only the same if the narrow part of the pore does not have flexible amino acid side chains interacting directly with the permeant ions; this may be true of potassium channels, but not calcium, sodium, and other channels with "crowded" selectivity filters.