Modeling of the outer vestibule and selectivity filter of the L-type Ca2+ channel

Non-ionotropic voltage-gated calcium channel signaling

Voltage-gated calcium channels (VGCCs) are the major conduits for calcium ions (Ca2+) within excitable cells. Recent studies have highlighted the non-ionotropic functionality of VGCCs, revealing their capacity to activate intracellular pathways independently of ion flow. This non-ionotropic signaling mode plays a pivotal role in excitation-coupling processes, including gene transcription through excitation-transcription (ET), synaptic transmission via excitation-secretion (ES), and cardiac contraction through excitation-contraction (EC). However, it is noteworthy that these excitation-coupling processes require extracellular calcium (Ca2+) and Ca2+ occupancy of the channel ion pore. Analogous to the "non-canonical" characterization of the non-ionotropic signaling exhibited by the N-methyl-D-aspartate receptor (NMDA), which requires extracellular Ca2+ without the influx of ions, VGCC activation requires depolarization-triggered conformational change(s) concomitant with Ca2+ binding to the open channel. Here, we discuss the contributions of VGCCs to ES, ET, and EC coupling as Ca2+ binding macromolecules that transduces external stimuli to intracellular input prior to elevating intracellular Ca2+. We emphasize the recognition of calcium ion occupancy within the open ion-pore and its contribution to the excitation coupling processes that precede the influx of calcium. The non-ionotropic activation of VGCCs, triggered by the upstroke of an action potential, provides a conceptual framework to elucidate the mechanistic aspects underlying the microseconds nature of synaptic transmission, cardiac contractility, and the rapid induction of first-wave genes.

Probing ion binding in the selectivity filter of the Cav1.1 channel with molecular dynamics

Cav1.1 is the voltage-gated calcium channel essential for the contraction of skeletal muscles upon membrane potential changes. Structural determination of the Cav1.1 channel opens the avenue toward understanding of the structure-function relationship of voltage-gated calcium channels. Here, we show that there exist two Ca2+-binding sites, termed S1 and S2, within the selectivity filter of Cav1.1 through extensive molecular dynamics simulations on various initial ion arrangement configurations. The formation of both binding sites is associated with the four Glu residues (Glu292/614/1014/1323) that constitute the so-called EEEE locus. At the S1 site near the extracellular side, the Ca2+ ion is coordinated with the negatively charged carboxylic groups of these Glu residues and of the Asp615 residue either in a direct way or via an intermediate water molecule. At the S2 site, Ca2+ binding shows two distinct states: an upper state involving two out of the four Glu residues in the EEEE locus and a lower state involving only one Glu residue. In addition, there exist two recruitment sites for Ca2+ above the entrance of the filter. These findings promote the understanding of mechanism for ion permeation and selectivity in calcium channels.

Molecular Mean-Field Theory of Ionic Solutions: A Poisson-Nernst-Planck-Bikerman Model

We have developed a molecular mean-field theory—fourth-order Poisson–Nernst–Planck–Bikerman theory—for modeling ionic and water flows in biological ion channels by treating ions and water molecules of any volume and shape with interstitial voids, polarization of water, and ion-ion and ion-water correlations. The theory can also be used to study thermodynamic and electrokinetic properties of electrolyte solutions in batteries, fuel cells, nanopores, porous media including cement, geothermal brines, the oceanic system, etc. The theory can compute electric and steric energies from all atoms in a protein and all ions and water molecules in a channel pore while keeping electrolyte solutions in the extra- and intracellular baths as a continuum dielectric medium with complex properties that mimic experimental data. The theory has been verified with experiments and molecular dynamics data from the gramicidin A channel, L-type calcium channel, potassium channel, and sodium/calcium exchanger with real structures from the Protein Data Bank. It was also verified with the experimental or Monte Carlo data of electric double-layer differential capacitance and ion activities in aqueous electrolyte solutions. We give an in-depth review of the literature about the most novel properties of the theory, namely Fermi distributions of water and ions as classical particles with excluded volumes and dynamic correlations that depend on salt concentration, composition, temperature, pressure, far-field boundary conditions etc. in a complex and complicated way as reported in a wide range of experiments. The dynamic correlations are self-consistent output functions from a fourth-order differential operator that describes ion-ion and ion-water correlations, the dielectric response (permittivity) of ionic solutions, and the polarization of water molecules with a single correlation length parameter.

MDIMP, a novel cardiac Ca(2+) channel blocker with atrial selectivity

In cardiac muscle cells both T-and L-type Ca(2+) channels (TTCCs and LTCCs, respectively) are expressed, and the latter are relevant to a process known as excitation-contraction coupling (ECC). Evidence obtained from docking studies suggests that isoindolines derived from α-amino acids bind to the LTCC CaV1.2. In the present study, we investigated whether methyl (S)-2-(1,3-dihydroisoindol-2-yl)-4-methylpentanoate (MDIMP), which is derived from L-leucine, modulates both Ca(2+) channels and ECC. To this end, mechanical properties, as well as Ca(2+) transients and currents, were all investigated in isolated cardiac myocytes. The effects of MDIMP on CaV1.2 (transiently expressed in 293T/17 cells) were also studied. In this system, evidence was found for an inhibitory action that develops and recovers in min, with an IC50 of 450µM. With respect to myocytes: atrial-TTCCs, atrial-LTCCs, and ventricular-LTCCs were also inhibited, in that order of potency. Accordingly, Ca(2+) transients, contractions, and window currents of LTCCs were all reduced more strongly in atrial cells. Interestingly, while the modulation of LTCCs was state-independent in these cells, it was state-dependent, and dual, on the ventricular ones. Furthermore, practically all of the ventricular LTCCs were closed at resting membrane potentials. This could explain their resistance to MDIMP, as they were affected in only open or inactivated states. All these features in turn explain the preferential down-regulation of the atrial ECC. Thus, our results support the view that isoindolines bind to Ca(2+) channels, improve our knowledge of the corresponding structure-function relationship, and may be relevant for conditions where decreased atrial activity is desired.

Numerical methods for a Poisson-Nernst-Planck-Fermi model of biological ion channels

Numerical methods are proposed for an advanced Poisson-Nernst-Planck-Fermi (PNPF) model for studying ion transport through biological ion channels. PNPF contains many more correlations than most models and simulations of channels, because it includes water and calculates dielectric properties consistently as outputs. This model accounts for the steric effect of ions and water molecules with different sizes and interstitial voids, the correlation effect of crowded ions with different valences, and the screening effect of polarized water molecules in an inhomogeneous aqueous electrolyte. The steric energy is shown to be comparable to the electrical energy under physiological conditions, demonstrating the crucial role of the excluded volume of particles and the voids in the natural function of channel proteins. Water is shown to play a critical role in both correlation and steric effects in the model. We extend the classical Scharfetter-Gummel (SG) method for semiconductor devices to include the steric potential for ion channels, which is a fundamental physical property not present in semiconductors. Together with a simplified matched interface and boundary (SMIB) method for treating molecular surfaces and singular charges of channel proteins, the extended SG method is shown to exhibit important features in flow simulations such as optimal convergence, efficient nonlinear iterations, and physical conservation. The generalized SG stability condition shows why the standard discretization (without SG exponential fitting) of NP equations may fail and that divalent Ca(2+) may cause more unstable discrete Ca(2+) fluxes than that of monovalent Na(+). Two different methods-called the SMIB and multiscale methods-are proposed for two different types of channels, namely, the gramicidin A channel and an L-type calcium channel, depending on whether water is allowed to pass through the channel. Numerical methods are first validated with constructed models whose exact solutions are known. The experimental data of both channels are then used to verify and explain novel features of PNPF as compared with previous PNP models. The PNPF currents are in accord with the experimental I-V (V for applied voltages) data of the gramicidin A channel and I-C (C for bath concentrations) data of the calcium channel with 10(-8)-fold bath concentrations that pose severe challenges in theoretical simulations.

Voltage-gated calcium channels: Determinants of channel function and modulation by inorganic cations

Voltage-gated calcium channels (VGCCs) represent a key link between electrical signals and non-electrical processes, such as contraction, secretion and transcription. Evolved to achieve high rates of Ca(2+)-selective flux, they possess an elaborate mechanism for selection of Ca(2+) over foreign ions. It has been convincingly linked to competitive binding in the pore, but the fundamental question of how this is reconcilable with high rates of Ca(2+) transfer remains unanswered. By virtue of their similarity to Ca(2+), polyvalent cations can interfere with the function of VGCCs and have proven instrumental in probing the mechanisms underlying selective permeation. Recent emergence of crystallographic data on a set of Ca(2+)-selective model channels provides a structural framework for permeation in VGCCs, and warrants a reconsideration of their diverse modulation by polyvalent cations, which can be roughly separated into three general mechanisms: (I) long-range interactions with charged regions on the surface, affecting the local potential sensed by the channel or influencing voltage-sensor movement by repulsive forces (electrostatic effects), (II) short-range interactions with sites in the ion-conducting pathway, leading to physical obstruction of the channel (pore block), and in some cases (III) short-range interactions with extracellular binding sites, leading to non-electrostatic modifications of channel gating (allosteric effects). These effects, together with the underlying molecular modifications, provide valuable insights into the function of VGCCs, and have important physiological and pathophysiological implications. Allosteric suppression of some of the pore-forming Cavα1-subunits (Cav2.3, Cav3.2) by Zn(2+) and Cu(2+) may play a major role for the regulation of excitability by endogenous transition metal ions. The fact that these ions can often traverse VGCCs can contribute to the detrimental intracellular accumulation of metal ions following excessive release of endogenous Cu(2+) and Zn(2+) or exposure to non-physiological toxic metal ions.

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.

A molecular model of the inner pore of the Ca channel in its open state

Structure of the Ca channel open pore is unlikely to be the same as that of the K channel because Ca channels do not contain the hinge residues Gly or Pro. The Ca channel does not have a wide entry into the inner pore, as is found in K channels. First we sought to simulate the open state of the Ca channel by modeling forced opening of the KcsA channel using a procedure of restrained minimization with distance constraints at the level of the α-helical bundle, corresponding to segments Thr-107-Val-115. This produced an intermediate open state, which was populated by amino acid residues of Ca channels and then successively optimized until the opening of the pore reached a diameter of about 10 Å, large enough to allow verapamil to enter and block the Ca channel from inside. Although this approach produced a sterically plausible structure, it was in significant disagreement with the MTSET accessibility data for single cysteine mutations of S6 segments of the P/Q channel(1) that do not fit with an α-helical pattern. Last we explored the idea that the four S6 segments of Ca channels may contain intra-molecular deformations that lead to reorientation of its side chains. After introduction of π-bulges, the model agreed with the MTSET accessibility data. MTSET modification of a cysteine at the C-end of only one S6 could produce physical occlusion and block of the inner pore of the open Ca channel, as observed experimentally, and as expected if the pore opening is narrower than that of K channels.

Timothy mutation disrupts the link between activation and inactivation in Ca(V)1.2 protein

The Timothy syndrome mutations G402S and G406R abolish inactivation of Ca_V1.2 and cause multiorgan dysfunction and lethal arrhythmias. To gain insights into the consequences of the G402S mutation on structure and function of the channel, we systematically mutated the corresponding Gly-432 of the rabbit channel and applied homology modeling. All mutations of Gly-432 (G432A/M/N/V/W) diminished channel inactivation. Homology modeling revealed that Gly-432 forms part of a highly conserved structure motif (G/A/G/A) of small residues in homologous positions of all four domains (Gly-432 (IS6), Ala-780 (IIS6), Gly-1193 (IIIS6), Ala-1503 (IVS6)). Corresponding mutations in domains II, III, and IV induced, in contrast, parallel shifts of activation and inactivation curves indicating a preserved coupling between both processes. Disruption between coupling of activation and inactivation was specific for mutations of Gly-432 in domain I. Mutations of Gly-432 removed inactivation irrespective of the changes in activation. In all four domains residues G/A/G/A are in close contact with larger bulky amino acids from neighboring S6 helices. These interactions apparently provide adhesion points, thereby tightly sealing the activation gate of Ca_V1.2 in the closed state. Such a structural hypothesis is supported by changes in activation gating induced by mutations of the G/A/G/A residues. The structural implications for Ca_V1.2 activation and inactivation gating are discussed.

Verapamil block of T-type calcium channels

Verapamil is a prototypical phenylalkylamine (PAA), and it was the first calcium channel blocker to be used clinically. It tonically blocks L-type channels in the inner pore with micromolar affinity, and its affinity increases at depolarized membrane potentials. In T-type calcium channels, verapamil blocks with micromolar affinity and has modestly increased affinity at depolarized potentials. We found that a related PAA, 4-desmethoxyverapamil (D888), is comparable with verapamil both in affinity and in state-dependence. Permanently charged verapamil was more effective intracellularly than neutral verapamil. Charged PAAs were able to access their binding site from both inside and outside the cell. Furthermore, membrane-impermeant [2-(trimethylammonium)ethyl]methanethiosulfonate was able to access the inner pore from outside of the cell. We examined a homology model of the T-type calcium channel to look for possible routes of drug entry. Mutation of L1825W produced a channel that was blocked significantly more slowly by charged verapamil from the outside, with an increase in apparent affinity when the drug was applied from the inside. Data suggest that T-type channels have a back pathway through which charged drugs can access the inner pore of the channel without passing through the plasma membrane.

Molecular modeling study of isoindolines as L-type Ca(2+) channel blockers by docking calculations

Two series of isoindolines 1(a-g) and 2(a-g) were found by docking calculations to be possible L-type Ca(2+) channel (LCC) blockers. The theoretical 3-D model of the outer vestibule and the selective filter of the LCC was provided by Professor Lipkind; this model consists of transmembrane segments S5 and S6 and P-loops contributed by each of four repeats (I, II, III, and IV) of Ca(v) 1.2. Therefore, two well-known LCC blockers, nifedipine 3 and (R)-ethosuccinimide 4 were also evaluated, and their binding sites on the LCC were identified and compared with those obtained for 1(a-g) and 2(a-g). Analysis of the results shows that the target compounds tested probably could be LCC blockers, since they interact with or near the glutamic acid residues Glu393, Glu736, Glu1145 and Glu1446 (the EEEE locus), which belong to the LCC selectivity region. The G values for all of the Ca(2+) channel ligands are between-10.78 and -3.67 (kcal mol(-1)), showing that LCC-1b, -1e and -1f complexes are more stable than the other compounds tested. Therefore, theoretically calculated dissociation constants K(d) (microM) were obtained for all compounds. Comparing these values reveals that compounds 1b (0.0244 microM), 1e (0.0176 microM) and 1f (0.0125 microM) exhibit more affinity for the LCC than the other compounds. This screening shows that the two series of isoindolines probably could act as LCC blockers.

The tetrodotoxin binding site is within the outer vestibule of the sodium channel

Tetrodotoxin and saxitoxin are small, compact asymmetrical marine toxins that block voltage-gated Na channels with high affinity and specificity. They enter the channel pore’s outer vestibule and bind to multiple residues that control permeation. Radiolabeled toxins were key contributors to channel protein purification and subsequent cloning. They also helped identify critical structural elements called P loops. Spacial organization of their mutation-identified interaction sites in molecular models has generated a molecular image of the TTX binding site in the outer vestibule and the critical permeation and selectivity features of this region. One site in the channel’s domain I P loop determines affinity differences in mammalian isoforms.

Structural modeling of calcium binding in the selectivity filter of the L-type calcium channel

Calcium channels play crucial physiological roles. In the absence of high-resolution structures of the channels, the mechanism of ion permeation is unknown. Here we used a method proposed in an accompanying paper (Cheng and Zhorov in Eur Biophys J, 2009) to predict possible chelation patterns of calcium ions in a structural model of the L-type calcium channel. We compared three models in which two or three calcium ions interact with the four selectivity filter glutamates and a conserved aspartate adjacent to the glutamate in repeat II. Monte Carlo energy minimizations yielded many complexes with calcium ions bound to at least two selectivity filter carboxylates. In these complexes calcium-carboxylate attractions are counterbalanced by calcium-calcium and carboxylate-carboxylate repulsions. Superposition of the complexes suggests a high degree of mobility of calcium ions and carboxylate groups of the glutamates. We used the predicted complexes to propose a permeation mechanism that involves single-file movement of calcium ions. The key feature of this mechanism is the presence of bridging glutamates that coordinate two calcium ions and enable their transitions between different chelating patterns involving four to six oxygen atoms from the channel protein. The conserved aspartate is proposed to coordinate a calcium ion incoming to the selectivity filter from the extracellular side. Glutamates in repeats III and IV, which are most distant from the repeat II aspartate, are proposed to coordinate the calcium ion that leaves the selectivity filter to the inner pore. Published experimental data and earlier proposed permeation models are discussed in view of our model.

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

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+) versus 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.

Structural model for phenylalkylamine binding to L-type calcium channels

Phenylalkylamines (PAAs), a major class of L-type calcium channel (LTCC) blockers, have two aromatic rings connected by a flexible chain with a nitrile substituent. Structural aspects of ligand-channel interactions remain unclear. We have built a KvAP-based model of LTCC and used Monte Carlo energy minimizations to dock devapamil, verapamil, gallopamil, and other PAAs. The PAA-LTCC models have the following common features: (i) the meta-methoxy group in ring A, which is proximal to the nitrile group, accepts an H-bond from a PAA-sensing Tyr_IIIS6; (ii) the meta-methoxy group in ring B accepts an H-bond from a PAA-sensing Tyr_IVS6; (iii) the ammonium group is stabilized at the focus of P-helices; and (iv) the nitrile group binds to a Ca(2+) ion coordinated by the selectivity filter glutamates in repeats III and IV. The latter feature can explain Ca(2+) potentiation of PAA action and the presence of an electronegative atom at a similar position of potent PAA analogs. Tyr substitution of a Thr in IIIS5 is known to enhance action of devapamil and verapamil. Our models predict that the para-methoxy group in ring A of devapamil and verapamil accepts an H-bond from this engineered Tyr. The model explains structure-activity relationships of PAAs, effects of LTCC mutations on PAA potency, data on PAA access to LTCC, and Ca(2+) potentiation of PAA action. Common and class-specific aspects of action of PAAs, dihydropyridines, and benzothiazepines are discussed in view of the repeat interface concept.

Roles of transmembrane segment M1 of Na+,K+-ATPase and Ca2-ATPase, the gatekeeper and the pivot

In this review we summarize mutagenesis work on the structure-function relationship of transmembrane segment M1 in the Na+,K+-ATPase and the sarco(endo)plasmic reticulum Ca2+-ATPase. The original hypothesis that charged residues in the N-terminal part of M1 interact with the transported cations can be rejected. On the other hand hydrophobic residues in the middle part of M1 turned out to play crucial roles in Ca2+ interaction/occlusion in Ca2+-ATPase and K+ interaction/occlusion in Na+,K+-ATPase. Leu65 of the Ca2+-ATPase and Leu99 of the Na+,K+-ATPase, located at homologous positions in M1, function as gate-locking residues that restrict the mobility of the side chain of the cation binding/gating residue of transmembrane segment M4, Glu309/Glu329. A pivot formed between a pair of a glycine and a bulky residue in M1 and M3 seems critical to the opening of the extracytoplasmic gate in both the Ca2+-ATPase and the Na+,K+-ATPase.

Molecular modeling of benzothiazepine binding in the L-type calcium channel

Benz(othi)azepine (BTZ) derivatives constitute one of three major classes of L-type Ca(2+) channel ligands. Despite intensive experimental studies, no three-dimensional model of BTZ binding is available. Here we have built KvAP- and KcsA-based models of the Ca(v)1.2 pore domain in the open and closed states and used multiple Monte Carlo minimizations to dock representative ligands. In our open channel model, key functional groups of BTZs interact with BTZ-sensing residues, which were identified in previous mutational experiments. The bulky tricyclic moiety occupies interface between domains III and IV, while the ammonium group protrudes into the inner pore, where it is stabilized by nucleophilic C-ends of the pore helices. In the closed channel model, contacts with several ligand-sensing residues in the inner helices are lost, which weakens ligand-channel interactions. An important feature of the ligand-binding mode in both open and closed channels is an interaction between the BTZ carbonyl group and a Ca(2+) ion chelated by the selectivity filter glutamates in domains III and IV. In the absence of Ca(2+), the tricyclic BTZ moiety remains in the domain interface, while the ammonium group directly interacts with a glutamate residue in the selectivity filter. Our model suggests that the Ca(2+) potentiation involves a direct electrostatic interaction between aCa(2+) ion and the ligand rather than an allosteric mechanism. Energy profiles indicate that BTZs can reach the binding site from the domain interface, whereas access through the open activation gate is unlikely, because reorientation of the bulky molecule in the pore is hindered.

Molecular determinant for specific Ca/Ba selectivity profiles of low and high threshold Ca2+ channels

Voltage-gated Ca²⁺ channels (VGCC) play a key role in many physiological functions by their high selectivity for Ca²⁺ over other divalent and monovalent cations in physiological situations. Divalent/monovalent selection is shared by all VGCC and is satisfactorily explained by the existence, within the pore, of a set of four conserved glutamate/aspartate residues (EEEE locus) coordinating Ca²⁺ ions. This locus however does not explain either the choice of Ca²⁺ among other divalent cations or the specific conductances encountered in the different VGCC. Our systematic analysis of high- and low-threshold VGCC currents in the presence of Ca²⁺ and Ba²⁺ reveals highly specific selectivity profiles. Sequence analysis, molecular modeling, and mutational studies identify a set of nonconserved charged residues responsible for these profiles. In HVA (high voltage activated) channels, mutations of this set modify divalent cation selectivity and channel conductance without change in divalent/monovalent selection, activation, inactivation, and kinetics properties. The Ca_V2.1 selectivity profile is transferred to Ca_V2.3 when exchanging their residues at this location. Numerical simulations suggest modification in an external Ca²⁺ binding site in the channel pore directly involved in the choice of Ca²⁺, among other divalent physiological cations, as the main permeant cation for VGCC. In LVA (low voltage activated) channels, this locus (called DCS for divalent cation selectivity) also influences divalent cation selection, but our results suggest the existence of additional determinants to fully recapitulate all the differences encountered among LVA channels. These data therefore attribute to the DCS a unique role in the specific shaping of the Ca²⁺ influx between the different HVA channels.

Importance of Leu99 in Transmembrane Segment M1 of the Na+,K+-ATPase in the Binding and Occlusion of K+

Twenty-six point mutations were introduced into the N-terminal and middle parts of transmembrane segment M1 of the Na+, K+ -ATPase and its cytosolic extension. None of the alterations to charged and polar residues in the N-terminal part of M1 and its cytosolic extension had any major effect on the cation binding properties, thus rejecting the hypothesis that these residues are involved in cation selectivity. By contrast, specific residues in the middle part of M1, particularly Leu(99), were found critical to K+ interaction of the enzyme. Hence, mutation L99A reduced the affinity for K+ activation of E2P dephosphorylation 17-fold, and L99F reduced the equilibrium level of the K+-occluded intermediate [K2]E2 and increased the rate of K+ deocclusion 39-fold, i.e. more than seen for mutation E329Q of the cation-binding glutamate in M4. L99Q affected K+ interaction in yet another way, the equilibrium level of [K2]E2 being slightly increased despite an increased rate of K+ deocclusion, suggesting that the K+ ions leave and enter the occlusion pocket more frequently than in the wild type. L99Q furthermore affected the ability to discriminate between Na+ and K+ on the extracellular side. Our findings can be explained by a structural model in which Leu(99) and Glu(329) interact and cooperate in K+ binding and gating of the K+ sites. The disturbance of K+ interaction in mutants with alteration to Leu(91), Phe(95), Ser(96), or Leu(98) could be a consequence of the roles of these residues in positioning the M1 helix optimally for the interaction between Leu(99) and Glu(329). Phe(95) may serve to stabilize the pivot for movement of M1 through interaction with Ile(287) in M3.

Ion channels of glutamate receptors: structural modeling

Ionotropic glutamate receptors belong to the superfamily of P-loop channels as well as K(+), Na(+), and Ca(2+) channels. However, the structural similarity between ion channels of the glutamate receptors and K(+) channels is a matter of discussion. The aim of this study was to analyze differences between the structures of K(+) channels and glutamate receptor channels. For this purpose, homology models of NMDA and AMPA receptor channels (M2 and M3 segments) were built using X-ray structures of K(+) channels as templates. The models were optimized and used to reproduce specific data on the structure of glutamate receptor channels. Particular attention was paid to the data of the binding of channel blockers and to the results of scanning mutagenesis. The modeling demonstrates that properties of glutamate receptor channel can be reproduced assuming only local structural deformations of the K(+) channel templates. The most valuable differences were found in the selectivity-filter region, whereas helical parts of M2 and M3 segments could have similar spatial organization with homologous segments in K(+) channels. It is concluded that the current experimental data on glutamate receptor channels does not reveal global structural differences with K(+) channels.

Calcicludine binding to the outer pore of L-type calcium channels is allosterically coupled to dihydropyridine binding

How dihydropyridines modulate L-type voltage-gated Ca2+ channels is not known. Dihydropyridines bind cooperatively with Ca2+ binding to the selectivity filter, suggesting that they alter channel activity by promoting structural rearrangements in the pore. We used radioligand binding and patch-clamp electrophysiology to demonstrate that calcicludine, a toxin from the venom of the green mamba snake, binds in the outer vestibule of the pore and, like Ca2+, is a positive modulator of dihydropyridine binding. Data were fit using an allosteric scheme where dissociation constants for dihydropyridine and calcicludine binding, KDHP and KCaC, are linked via the coupling factor, alpha. Nine acidic amino acids located within the S5-Pore-helix segment of repeat III were sequentially changed to alanine in groups of three, resulting in the mutant channels, Mut-A, Mut-B, and Mut-C. Mut-A, whose substitutions are proximal to IIIS5, exhibits a 4.5-fold reduction in dihydropyridine binding and is insensitive to calcicludine binding. Block of Mut-A currents by calcicludine is indistinguishable from wild-type, indicating that KCaC is unchanged and that the coupling between dihydropyridine and calcicludine binding (i.e., alpha) is disrupted. Mut-B and Mut-C possess KDHP values that resemble that of the wild type. Mut-C, the most C-terminal of the mutant channels, is insensitive to calcicludine binding and block. KCaC values for the Mut-C single mutants, E1122A, D1127A, and D1129A, increase from 0.3 (wild type) to 1.14, 2.00, and 20.5 microM, respectively. Together, these findings suggest that dihydropyridine antagonist and calcicludine binding to L-type Ca2+ channels promote similar structural changes in the pore that stabilize the channel in a nonconducting, blocked state.

Characterizing the 1,4-dihydropyridines binding interactions in the L-type Ca2+ channel: model construction and docking calculations

L-type Ca2+ channels (LCC) are membrane heteromultimeric proteins that allow the selective entrance of Ca2+ ions into excitable cells upon membrane depolarization. Despite the large amount of compounds (1,4-dihydropyridines, phenylalkylamines, and benzothiazepines) that impede the passage of Ca2+ ions through the channel, it is still not clear how these molecules bind to LCC at an atomic level. In this study, a 3D model of the central pore of LCC was constructed using the X-ray structure of the KcsA K+ channel as template. The resulting LCC model was then used to dock nine different DHPs to shed light on their binding mode. The accordance between the developed model and several experimental data gives us the confidence to propose our model as a valuable platform for future studies aimed at the identification of new potent and LCC-selective ligands.

Allosteric interactions required for high-affinity binding of dihydropyridine antagonists to Ca(V)1.1 Channels are modulated by calcium in the pore

Dihydropyridines (DHPs) are an important class of drugs, used extensively in the treatment of angina pectoris, hypertension, and arrhythmia. The molecular mechanism by which DHPs modulate Ca(2+) channel function is not known in detail. We have found that DHP binding is allosterically coupled to Ca(2+) binding to the selectivity filter of the skeletal muscle Ca(2+) channel Ca(V)1.1, which initiates excitation-contraction coupling and conducts L-type Ca(2+) currents. Increasing Ca(2+) concentrations from approximately 10 nM to 1 mM causes the DHP receptor site to shift from a low-affinity state to a high-affinity state with an EC(50) for Ca(2+) of 300 nM. Substituting each of the four negatively charged glutamate residues that form the ion selectivity filter with neutral glutamine or positively charged lysine residues results in mutant channels whose DHP binding affinities are decreased up to 10-fold and are up to 150-fold less sensitive to Ca(2+) than wild-type channels. Analysis of mutations of amino acid residues adjacent to the selectivity filter led to identification of Phe-1013 and Tyr-1021, whose mutation causes substantial changes in DHP binding. Thermo-dynamic mutant cycle analysis of these mutants demonstrates that Phe-1013 and Tyr-1021 are energetically coupled when a single Ca(2+) ion is bound to the channel pore. We propose that DHP binding stabilizes a nonconducting state containing a single Ca(2+) ion in the pore through which Phe-1013 and Tyr-1021 are energetically coupled. The selectivity filter in this energetically coupled high-affinity state is blocked by bound Ca(2+), which is responsible for the high-affinity inhibition of Ca(2+) channels by DHP antagonists.

Permeation and selectivity of TRP channels

Ion channels are pore-forming transmembrane proteins that allow ions to permeate biological membranes. Pore structure plays a crucial role in determining the ion permeation and selectivity properties of particular channels. In the past few decades, efforts have been undertaken to identify key elements of the pore regions of different classes of ion channels. In this review, we summarize current knowledge about permeation and selectivity of channel proteins from the transient receptor potential (TRP) superfamily. Whereas all TRP channels are permeable for cations, only two TRP channels are impermeable for Ca2+ (TRPM4, TRPM5), and two others are highly Ca2+ permeable (TRPV5, TRPV6). Despite the great advances in the TRP channel field during the past decade, only a limited number of reports have dealt with functional characterization of pore properties, biophysical aspects of cation permeation, or description of pore structures of TRP channels. This review gives an overview of available experimental and theoretical data and discusses the functional impact of pore-structure modifications on TRP channel properties.

Understanding ion channel selectivity and gating and their role in cellular signalling

Ion channels play an essential role in the communication between and within cells. Here some of the different ion channel proteins and the roles they perform are introduced, before a discussion of the mechanisms by which they discriminate between different ion types and open and close to allow the passage of ions at the appropriate times.

Amino acid substitutions in the pore of the Ca(V)1.2 calcium channel reduce barium currents without affecting calcium currents

Ba(2+) currents through Ca(V)1.2 Ca(2+) channels are typically twice as large as Ca(2+) currents. Replacing Phe-1144 in the pore-loop of domain III with glycine and lysine, and Tyr-1152 with lysine, reduces whole-cell G(Ba)/G(Ca) from 2.2 (wild-type) to 0.95, 1.21, and 0.90, respectively. Whole-cell and single-channel measurements indicate that reductions in G(Ba)/G(Ca) result specifically from a decrease in Ba(2+) conductance and not changes in V(h) or P(O). Half-maximal block of I(Li) is increased by 3.2-, 3.8-, and 1.6-fold in Ca(2+), and 3.8-, 4.2-, and 1.8-fold in Ba(2+) for F1144G, Y1152K, and F1144K, respectively. High affinity interactions of individual divalent cations to the pore are not important for determining G(Ba)/G(Ca), because the fold increases in IC(50) values for Ba(2+) and Ca(2+) are similar. On the contrary, conductance-concentration curves indicate that G(Ba)/G(Ca) is reduced because the interactions of multiple Ba(2+) ions in the mutant pores are altered. The complexity of these interactions is exemplified by the anomalous mole fraction effect, which is flattened for F1144G and FY/GK but accentuated for F1144K. In summary, the physicochemical properties of the amino acid residues at positions 1144 and 1152 are crucial to the pore's ability to distinguish between multiple Ba(2+) ions and Ca(2+) ions.

A CACNA1F mutation identified in an X-linked retinal disorder shifts the voltage dependence of Cav1.4 channel activation

Light stimuli produce graded hyperpolarizations of the photoreceptor plasma membrane and an associated decrease in a voltagegated calcium channel conductance that mediates release of glutamate neurotransmitter. The Ca(v)1.4 channel is thought to be involved in this process. The CACNA1F gene encodes the poreforming subunit of the Ca(v)1.4 channel and various mutations in CACNA1F cause X-linked incomplete congenital stationary night blindness (CSNB2). The molecular mechanism of the pathology underlying the CSNB2 phenotype remains to be established. Recent clinical investigations of a New Zealand family found a severe visual disorder that has some clinical similarities to, but is clearly distinct from, CSNB2. Here, we report investigations into the molecular mechanism of the pathology of this condition. Molecular genetic analyses identified a previously undescribed nucleotide substitution in CACNA1F that is predicted to encode an isoleucine to threonine substitution at CACNA1F residue 745. The I745T CACNA1F allele produced a remarkable approximately -30-mV shift in the voltage dependence of Ca(v)1.4 channel activation and significantly slower inactivation kinetics in an expression system. These findings imply that substitution of this wild-type residue in transmembrane segment IIS6 may have decreased the energy required to open the channel. Collectively, these findings suggest that a gain-of-function mechanism involving increased Ca(v)1.4 channel activity is likely to cause the unusual phenotype.

KvAP-based model of the pore region of shaker potassium channel is consistent with cadmium- and ligand-binding experiments

Potassium channels play fundamental roles in excitable cells. X-ray structures of bacterial potassium channels show that the pore-lining inner helices obstruct the cytoplasmic entrance to the closed channel KcsA, but diverge in widely open channels MthK and KvAP, suggesting a gating-hinge role for a conserved Gly in the inner helix. A different location of the gating hinge and a narrower open pore were proposed for voltage-gated Shaker potassium channels that have the Pro-473-Val-Pro motif. Two major observations back the proposal: cadmium ions lock mutant Val-476-Cys in the open state by bridging Cys-476 and His-486 in adjacent helices, and cadmium blocks the locked-open double mutant Val-474-Cys/Val-476-Cys by binding to Cys-474 residues. Here we used molecular modeling to show that the open Shaker should be as wide as KvAP to accommodate an open-channel blocker, correolide. We further built KvAP-, MthK-, and KcsA-based models of the Shaker mutants and Monte-Carlo-minimized them with constraints Cys-476-Cd(2+)-His-486. The latter were consistent with the KvAP-based model, causing a small-bend N-terminal to the Pro-473-Val-Pro motif. The constraints significantly distorted the MthK-based structure, making it similar to KvAP. The KcsA structure resisted the constraints. Two Cd(2+) ions easily block the locked-open KvAP-based model at Cys-474 residues, whereas constraining a single cadmium ion to four Cys-474 caused large conformational changes and electrostatic imbalance. Although mutual disposition of the voltage-sensor and pore domains in the KvAP x-ray structure is currently disputed, our results suggest that the pore-region domain retains a nativelike conformation in the crystal.

Ca2+ currents in cardiac myocytes: Old story, new insights

Calcium is a ubiquitous second messenger which plays key roles in numerous physiological functions. In cardiac myocytes, Ca2+ crosses the plasma membrane via specialized voltage-gated Ca2+ channels which have two main functions: (i) carrying depolarizing current by allowing positively charged Ca2+ ions to move into the cell; (ii) triggering Ca2+ release from the sarcoplasmic reticulum. Recently, it has been suggested than Ca2+ channels also participate in excitation-transcription coupling. The purpose of this review is to discuss the physiological roles of Ca2+ currents in cardiac myocytes. Next, we describe local regulation of Ca2+ channels by cyclic nucleotides. We also provide an overview of recent studies investigating the structure-function relationship of Ca2+ channels in cardiac myocytes using heterologous system expression and transgenic mice, with descriptions of the recently discovered Ca2+ channels alpha(1D) and alpha(1E). We finally discuss the potential involvement of Ca2+ currents in cardiac pathologies, such as diseases with autoimmune components, and cardiac remodeling.

Modeling P-loops domain of sodium channel: homology with potassium channels and interaction with ligands

A large body of experimental data on Na+ channels is available, but the interpretation of these data in structural terms is difficult in the absence of a high-resolution structure. Essentially different electrophysiological and pharmacological properties of Na+ and K+ channels and poor identity of their sequences obstruct homology modeling of Na+ channels. In this work, we built the P-loops model of the Na+ channel, in which the pore helices are arranged exactly as in the MthK bacterial K+ channel. The conformation of the selectivity-filter region, which includes residues in positions -2 through +4 from the DEKA locus, was shaped around rigid molecules of saxitoxin and tetrodotoxin that are known to form multiple contacts with this region. Intensive Monte Carlo minimization that started from the MthK-like conformation produced practically identical saxitoxin- and tetrodotoxin-based models. The latter was tested to explain a wide range of experimental data that were not used at the model building stage. The docking of tetrodotoxin analogs unambiguously predicted their optimal orientation and the interaction energy that correlates with the experimental activity. The docking of mu-conotoxin produced a binding model consistent with experimentally known toxin-channel contacts. Monte Carlo-minimized energy profiles of tetramethylammonium pulled through the selectivity-filter region explain the paradoxical experimental data that this organic cation permeates via the DEAA but not the AAAA mutant of the DEKA locus. The model is also consistent with earlier proposed concepts on the Na+ channel selectivity as well as Ca2+ selectivity of the EEEE mutant of the DEKA locus. Thus, the model integrates available experimental data on the Na+ channel P-loops domain, and suggests that it is more similar to K+ channels than was believed before.

Applied field nonequilibrium molecular dynamics simulations of ion exit from a β-barrel model of the L-type calcium channel

We present results of applied field nonequilibrium molecular dynamics simulations (AF NEMD) of a minimal beta-barrel model channel intended to represent an L-type calcium channel that suggests a possible relationship between glutamate side chain conformational changes and ion flux in calcium channels. The beta-barrel is used to provide a scaffolding for glutamate side chains and a confinement for electrolyte of dimensions similar to the expected channel structure. It was preloaded with ions to explore relative rates of ion exit for different occupancy configurations. Our simulations with an asymmetrical flexible selectivity filter represented by four glutamate side chains (EEEE), one of which differs in initial dihedrals from the other three, indicate a plausible mechanism for the observed anomalous mole fraction effect seen in calcium channels. Apparent rates of electric field-induced exit from channels preloaded with three Na+ ions are much higher than for channels with one Ca2+ followed by two Na+ ions, consistent with the common notion that Ca2+ block of Na+ current is due to competition between the Ca2+ and Na+ ions for the negatively charged (EEEE) locus. In our model, the Ca2+ ion ligates simultaneously to the four negatively charged glutamate side chains and sterically blocks the permeation pathway. Ca2+-relief of Ca2+-block is suggested by a much higher rate of exit for channels preloaded with three Ca2+ ions than for channels with two Ca2+ ions.

Importance of Transmembrane Segment M1 of the Sarcoplasmic Reticulum Ca2+-ATPase in Ca2+ Occlusion and Phosphoenzyme Processing

The functional consequences of a series of point mutations in transmembrane segment M1 of sarcoplasmic reticulum Ca2+-ATPase were analyzed in steady-state and transient kinetic experiments examining the partial reaction steps involved in Ca2+ interaction and phosphoenzyme turnover. Arginine or leucine substitution of Glu51, Glu55, or Glu58, located in the N-terminal third of M1, did not affect these functions. Arginine or leucine substitution of Asp59, located right at the bend of M1 seen in the crystal structure of the thapsigargin-bound form, caused a 10-fold increase of the rate of Ca2+ dissociation toward the cytoplasmic side. Mutation of Leu60 to alanine or proline and of Val62 to alanine also enhanced Ca2+ dissociation, whereas an 11-fold reduction of the rate of Ca2+ dissociation was observed upon alanine substitution of Leu65, thus providing evidence for a relation of the middle part of M1 to a gating mechanism controlling the dissociation of occluded Ca2+ from its membranous binding sites. Moreover, phosphoenzyme processing was affected by some of the latter mutations, in particular leucine substitution of Asp59, and alanine substitution of Leu65 accelerated the transition to ADP-insensitive phosphoenzyme and blocked its dephosphorylation, thus demonstrating that this part of M1, besides being important in Ca2+ interaction, furthermore, is a critical element in the long range signaling between the transmembrane domain and the cytoplasmic catalytic site.

Potassium, sodium, calcium and glutamate-gated channels: pore architecture and ligand action

In the last decade, the idea of common organization of certain ion channel families exhibiting diverse physiological and pharmacological properties has received strong experimental support. Transmembrane topologies and patterns of the pore-facing residues are conserved in P-loop channels that include high-selective cation channels and certain ligand-gated channels. X-ray structures of bacterial K+ channels, KcsA, MthK and KvAP, help to understand structure-function relationships of other P-loop channels. Data on binding sites and mechanisms of action of ligands of K+, Na+, Ca2+ and glutamate gated ion channels are considered in view of their possible structural similarity to the bacterial K+ channels. Emphasized are structural determinants of ligand-receptor interactions within the channels and mechanisms of state-dependent action of the ligands.

[Molecular and pharmacological bases for the gating regulation of L-type voltage-dependent Ca2+ channels]

The voltage-dependent L-type Ca(2+) channel plays a key role in the spacial and temporal regulation of Ca(2+). In cardiac excitation-contraction coupling, Ca(2+)-induced Ca(2+) release (CICR) from ryanodine receptors (RyRs), triggered by Ca(2+) entry through the nearby L-type Ca(2+) channel, induces the Ca(2+)-dependent inactivation (CDI) of the Ca(2+) channel. We demonstrated that the CICR-dependent CDI of L-type Ca(2+) channels, under control of the privileged cross-signaling between L-type Ca(2+) channels and RyRs, plays important roles for monitoring and tuning the SR Ca(2+) content via changes of AP waveform and the amount of Ca(2+)-influx during AP in ventricular myocytes. L-type Ca(2+) channels are modulated by the binding of Ca(2+) channel antagonists and agonists to the pore-forming alpha(1C) subunit. We identified Phe(1112) and Ser(1115) in the pore-forming IIIS5-S6 linker region of the alpha(1C) subunit as critical determinants of the binding of dihydropyridines (DHP). Interestingly, double mutant Ca(2+) channel (F1112A/S1115A) failed to discriminate between a DHP Ca(2+) channel agonist and antagonist stereoisomers. We proposed that Phe(1112) and Ser(1115) in the pore-forming IIIS5-S6 linker region is required for the stabilization of the Ca(2+) channel in the open state by Ca(2+) channel agonists and further proposed a novel model for the DHP-binding pocket of the alpha(1C) subunit. These integrative studies on the gating regulation of cardiac L-type Ca(2+) channels will provide the molecular basis for the pharmacology of Ca(2+) channel modulators.

A model of graded calcium release and L-type Ca2+ channel inactivation in cardiac muscle

We have developed a model of Ca(2+) handling in ferret ventricular myocytes. This model includes a novel L-type Ca(2+) channel, detailed intracellular Ca(2+) movements, and graded Ca(2+)-induced Ca(2+) release (CICR). The model successfully reproduces data from voltage-clamp experiments, including voltage- and time-dependent changes in intracellular Ca(2+) concentration ([Ca(2+)](i)), L-type Ca(2+) channel current (I(CaL)) inactivation and recovery kinetics, and Ca(2+) sparks. The development of graded CICR is critically dependent on spatial heterogeneity and the physical arrangement of calcium channels in opposition to ryanodine-sensitive release channels. The model contains spatially distinct subsystems representing the subsarcolemmal regions where the junctional sarcoplasmic reticulum (SR) abuts the T-tubular membrane and where the L-type Ca(2+) channels and SR ryanodine receptors (RyRs) are localized. There are eight different types of subsystems in our model, with between one and eight L-type Ca(2+) channels distributed binomially. This model exhibits graded CICR and provides a quantitative description of Ca(2+) dynamics not requiring Monte-Carlo simulations. Activation of RyRs and release of Ca(2+) from the SR depend critically on Ca(2+) entry through L-type Ca(2+) channels. In turn, Ca(2+) channel inactivation is critically dependent on the release of stored intracellular Ca(2+). Inactivation of I(CaL) depends on both transmembrane voltage and local [Ca(2+)](i) near the channel, which results in distinctive inactivation properties. The molecular mechanisms underlying many I(CaL) gating properties are unclear, but [Ca(2+)](i) dynamics clearly play a fundamental role.

Visualization of the domain structure of an L-type Ca2+ channel using electron cryo-microscopy

The three-dimensional structure of the skeletal muscle voltage-gated L-type calcium channel (Ca(v)1.1; dihydropyridine receptor, DHPR) was determined using electron cryo-microscopy and single-particle averaging. The structure shows a single channel complex with an approximate total molecular mass of 550 kDa, corresponding to the five known subunits of the DHPR, and bound detergent and lipid. Features visible in our structure together with antibody labeling of the beta and alpha(2) subunits allowed us to assign locations for four of the five subunits within the structure. The most striking feature of the structure is the extra-cellular alpha(2) subunit that protrudes from the membrane domain in close proximity to the alpha(1) subunit. The cytosolic beta subunit is located close to the membrane and adjacent to subunits alpha(1), gamma and delta. Our structure correlates well with the functional and biochemical data available for this channel and suggests a three-dimensional model for the excitation-contraction coupling complex consisting of DHPR tetrads and the calcium release channel.

Key roles of Phe1112 and Ser1115 in the pore-forming IIIS5-S6 linker of L-type Ca2+ channel alpha1C subunit (CaV 1.2) in binding of dihydropyridines and action of Ca2+ channel agonists

Voltage-dependent L-type Ca2+ channels are modulated by the binding of Ca2+ channel antagonists and agonists to the pore-forming alpha1c subunit (CaV 1.2). We recently identified Ser1115 in IIIS5-S6 linker of alpha1C subunit as a critical determinant of the action of 1,4-dihydropyridine agonists. In this study, we applied alanine-scanning mutational analysis in IIIS5-S6 linker of rat brain alpha1C subunit (rbCII) to illustrate the role of pore-forming IIIS5-S6 linker in the action of Ca2+ channel modulators. Ca2+ channel currents through wild-type (rbCII) or mutated alpha1C subunits, transiently expressed in BHK6 cells with beta1a and alpha2/delta subunits, were analyzed. The replacement of Phe1112 by Ala (F1112A) significantly impaired the sensitivity to Ca2+ channel agonists (S)-(-)-Bay k 8644 and FPL-64176, and modestly to 1,4-dihydropyridine (DHP) antagonists. The low sensitivity of F1112A and S1115A to DHP antagonists was consistent with the reduced binding affinity for [3H](+)PN200-110. The replacement of Phe1112 by Tyr, but not by Ala, restored the long openings produced by FPL-64176, thus indicating the critical role of aromatic ring of Phe1112 in the Ca2+ channel agonist action. Interestingly, double-mutant Ca2+ channel (F1112A/S1115A) failed to discriminate between Ca2+ channel agonist (S)-(-)-1,4-dihydro-2,6-dimethyl-5-nitro-4-(2-[trifluoromethyl] phenyl)-3-pyridine carboxylic acid methyl ester (Bay k 8644) and antagonist (R)-(+)-Bay k 8644 and was blocked by the two enantiomers in an identical manner. These results indicate that both Phe1112 and Ser1115 in linker IIIS5-S6 are required for the action of Ca2+ channel agonists. A model of the DHP receptor is proposed to visualize possible interactions of Phe1112, Ser1115, and other DHP-sensing residues with a typical DHP ligand nifedipine.

Permeation and selectivity in calcium channels

Recent advances-both experimental and theoretical-provide a tentative image of the structures in Ca channels that make them exceptionally selective. The image is very different from K channels, which obtain high selectivity with a rigid pore that tightly fits K(+) ions and is lined by carbonyl oxygens of the polypeptide backbone. Ca channels rely on four glutamate residues (the EEEE locus), whose carboxyl side chains likely reach into the pore lumen to interact with passing Ca(2+) ions. The structure is thought to be flexible, tightly binding a single Ca(2+) ion in order to block Na(+) flux but rearranging to interact with multiple Ca(2+) ions to allow Ca(2+) flux. The four glutamates are not equivalent, a fact that seems important for Ca(2+) permeation. This review describes the experimental evidence that leads to these conclusions and the attempts by theorists to explain the combination of high selectivity and high flux that characterizes Ca channels.

Molecular modeling of interactions of dihydropyridines and phenylalkylamines with the inner pore of the L-type Ca2+ channel

Domains IIIS5, IIIS6, and IVS6 transmembrane segments of L-type Ca(2+) channels participate in dihydropyridine (DHP) and phenylalkylamine (PAA) binding. The inner pore structure of the Ca(v)1.2 channel was reconstructed from coordinates of the transmembrane alpha-helices of the KcsA channel. S6s were aligned with M2 by comparative analysis of the pore-facing M2 side chains and those required for drug binding. Two neighboring tilted S6 helices of domains III and IV below the selectivity filter formed an interdomain crevice. Docking of DHPs inside this crevice located the DHP ring between Phe-1159 of IIIS6 and Ala-1467 of IVS6, parallel to the pore axis, whereas the 4-aryl ring participated in aromatic and polar interactions with the side chains of Tyr-1152 and Tyr-1463. Nonpolar interactions of the port side ester group with hydrophobic side chains of Ile-1156, Ile-1163, and Ile-1471 on the bottom of the binding cavity, formed by the crossover of IIIS6 and IVS6, could stabilize the channel's closed/inactivated state. Similar arrangements were found for DHP agonist drugs, except for the absence of hydrophobic interactions with the helical crossing. In this arrangement, DHPs do not physically block the pore. Locating the central amine group of desmethoxyverapamil near the selectivity filter domain III glutamic acid allows one aromatic ring through its CH(2)CH(2) linker to interact with the side chain of Tyr-1463 inside the DHP binding site, whereas the opposite aromatic ring is in contact with the side chain of Ile-1470 of IVS6, blocking the pore.

Potential of mean force calculations on an L-type calcium channel model

To understand the mechanisms of Na(+)/Li(+) permeation at submicromolar Ca(2+) concentrations, Na(+)/Li(+) blocking at higher Ca(2+) concentrations (10(-6)-10(-4) M) and Ca(2+) permeation at millimolar Ca(2+) concentrations, we used our recently described L-type calcium channel model. For this purpose, we obtained potential of mean force (pmf) curves for the position change of one Na(+) and one Ca(2+) ion inside the channel and for the position change of a second Ca(2+) ion when the EEEE locus is coordinated to Ca(2+). The pmf curves suggest that (i) at submicromolar Ca(2+) concentrations, because of the low velocity of Ca(2+) entry in the channel, monovalent ion flux occurs; (ii) at Ca(2+) concentrations between 10(-6) and 10(-4) M, thermodynamic equilibrium between the channel and Ca(2+) is achieved; as the coordination of Ca(2+) with the locus is more favorable than the coordination of Na(+), the monovalent ion flux is blocked; and (iii) to put a second Ca(2+) ion inside the channel at an appropriate rate, the Ca(2+) concentration should reach millimolar levels. Nevertheless, the entry of a second Ca(2+) is thermodynamically unfavorable, indicating that the competition of two Ca(2+) ions for the locus leads to Ca(2+) permeation.

A molecular dynamics study of an L-type calcium channel model

In this work, we propose a molecular model of the L-type calcium channel pore from the human cardiac alpha1 subunit. Four glutamic acid residues, the EEEE locus, located at highly conserved P loops (also called SS1-SS2 segments) of the alpha1 subunit, molecularly express the calcium channel selectivity. The proposed alpha-helix structure for the SS1 segment, analyzed through molecular dynamics simulations in aqueous-phase, was validated by the plotting of Ramachandran diagrams for the averaged structures and by the analysis of i and i + 4 helical hydrogen bonding between the amino acid residues. The results of the simulation of the calcium channel model with one and two Ca2+ ions at the binding site are in accordance with mutation studies which suggest that the EEEE locus in the L-type calcium channel must form a single high-affinity binding site. These results suggest that the Ca2+ permeation through the channel would be derived from competition between two ions for the only high-affinity binding site. Furthermore, the experimentally observed blocking of the Na+ flux at micromolar Ca2+ concentrations, probably due to the occupancy of the single high-affinity binding site for one Ca2+, was also reproduced by our model.