Molecular modelling of specific and non-specific anaesthetic interactions

Hydrocarbon molar water solubility predicts NMDA vs. GABAA receptor modulation

Background

Many anesthetics modulate 3-transmembrane (such as NMDA) and 4-transmembrane (such as GABA_A) receptors. Clinical and experimental anesthetics exhibiting receptor family specificity often have low water solubility. We hypothesized that the molar water solubility of a hydrocarbon could be used to predict receptor modulation in vitro.

Methods

GABA_A (α₁β₂γ_2s) or NMDA (NR1/NR2A) receptors were expressed in oocytes and studied using standard two-electrode voltage clamp techniques. Hydrocarbons from 14 different organic functional groups were studied at saturated concentrations, and compounds within each group differed only by the carbon number at the ω-position or within a saturated ring. An effect on GABA_A or NMDA receptors was defined as a 10% or greater reversible current change from baseline that was statistically different from zero.

Results

Hydrocarbon moieties potentiated GABA_A and inhibited NMDA receptor currents with at least some members from each functional group modulating both receptor types. A water solubility cut-off for NMDA receptors occurred at 1.1 mM with a 95% CI = 0.45 to 2.8 mM. NMDA receptor cut-off effects were not well correlated with hydrocarbon chain length or molecular volume. No cut-off was observed for GABA_A receptors within the solubility range of hydrocarbons studied.

Conclusions

Hydrocarbon modulation of NMDA receptor function exhibits a molar water solubility cut-off. Differences between unrelated receptor cut-off values suggest that the number, affinity, or efficacy of protein-hydrocarbon interactions at these sites likely differ.

Scattering studies of hydrophobic monomers in liposomal bilayers: an expanding shell model of monomer distribution

Hydrophobic monomers partially phase separate from saturated lipids when loaded into lipid bilayers in amounts exceeding a 1:1 monomer/lipid molar ratio. This conclusion is based on the agreement between two independent methods of examining the structure of monomer-loaded bilayers. Complete phase separation of monomers from lipids would result in an increase in bilayer thickness and a slight increase in the diameter of liposomes. A homogeneous distribution of monomers within the bilayer would not change the bilayer thickness and would lead to an increase in the liposome diameter. The increase in bilayer thickness, measured by the combination of small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS), was approximately half of what was predicted for complete phase separation. The increase in liposome diameter, measured by dynamic light scattering (DLS), was intermediate between values predicted for a homogeneous distribution and complete phase separation. Combined SANS, SAXS, and DLS data suggest that at a 1.2 monomer/lipid ratio approximately half of the monomers are located in an interstitial layer sandwiched between lipid sheets. These results expand our understanding of using self-assembled bilayers as scaffolds for the directed covalent assembly of organic nanomaterials. In particular, the partial phase separation of monomers from lipids corroborates the successful creation of nanothin polymer materials with uniform imprinted nanopores. Pore-forming templates do not need to span the lipid bilayer to create a pore in the bilayer-templated films.

A hybrid approach to advancing quantitative prediction of tissue distribution of basic drugs in human

A general toxicity of basic drugs is related to phospholipidosis in tissues. Therefore, it is essential to predict the tissue distribution of basic drugs to facilitate an initial estimate of that toxicity. The objective of the present study was to further assess the original prediction method that consisted of using the binding to red blood cells measured in vitro for the unbound drug (RBCu) as a surrogate for tissue distribution, by correlating it to unbound tissue:plasma partition coefficients (Kpu) of several tissues, and finally to predict volume of distribution at steady-state (V(ss)) in humans under in vivo conditions. This correlation method demonstrated inaccurate predictions of V(ss) for particular basic drugs that did not follow the original correlation principle. Therefore, the novelty of this study is to provide clarity on the actual hypotheses to identify i) the impact of pharmacological mode of action on the generic correlation of RBCu-Kpu, ii) additional mechanisms of tissue distribution for the outlier drugs, iii) molecular features and properties that differentiate compounds as outliers in the original correlation analysis in order to facilitate its applicability domain alongside the properties already used so far, and finally iv) to present a novel and refined correlation method that is superior to what has been previously published for the prediction of human V(ss) of basic drugs. Applying a refined correlation method after identifying outliers would facilitate the prediction of more accurate distribution parameters as key inputs used in physiologically based pharmacokinetic (PBPK) and phospholipidosis models.

Normal mode gating motions of a ligand-gated ion channel persist in a fully hydrated lipid bilayer model

We have previously used molecular modeling and normal-mode analyses combined with experimental data to visualize a plausible model of a transmembrane ligand-gated ion channel. We also postulated how the gating motion of the channel may be affected by the presence of various ligands, especially anesthetics. As is typical for normal-mode analyses, those studies were performed in vacuo to reduce the computational complexity of the problem. While such calculations constitute an efficient way to model the large scale structural flexibility of transmembrane proteins, they can be criticized for neglecting the effects of an explicit phospholipid bilayer or hydrated environment. Here, we show the successful calculation of normal-mode motions for our model of a glycine α-1 receptor, now suspended in a fully hydrated lipid bilayer. Despite the almost uniform atomic density, the introduction of water and lipid does not grossly distort the overall gating motion. Normal-mode analysis revealed that even a fully immersed glycine α-1 receptor continues to demonstrate an iris-like channel gating motion as a low-frequency, high-amplitude natural harmonic vibration consistent with channel gating. Furthermore, the introduction of periodic boundary conditions allows the examination of simultaneous harmonic vibrations of lipid in synchrony with the protein gating motions that are compatible with reasonable lipid bilayer perturbations. While these perturbations tend to influence the overall protein motion, this work provides continued support for the iris-like motion model that characterizes gating within the family of ligand-gated ion channels.

The Molecular Mechanisms of Anesthetic Action: Updates and Cutting Edge Developments from the Field of Molecular Modeling

For over 160 years, general anesthetics have been given for the relief of pain and suffering. While many theories of anesthetic action have been purported, it has become increasingly apparent that a significant molecular focus of anesthetic action lies within the family of ligand-gated ion channels (LGIC’s). These protein channels have a transmembrane region that is composed of a pentamer of four helix bundles, symmetrically arranged around a central pore for ion passage. While initial and some current models suggest a possible cavity for binding within this four helix bundle, newer calculations postulate that the actual cavity for anesthetic binding may exist between four helix bundles. In either scenario, these cavities have a transmembrane mode of access and may be partially bordered by lipid moieties. Their physicochemical nature is amphiphilic. Anesthetic binding may alter the overall motion of a ligand-gated ion channel by a “foot-in-door” motif, resulting in the higher likelihood of and greater time spent in a specific channel state. The overall gating motion of these channels is consistent with that shown in normal mode analyses carried out both in vacuo as well as in explicitly hydrated lipid bilayer models. Molecular docking and large scale molecular dynamics calculations may now begin to show a more exact mode by which anesthetic molecules actually localize themselves and bind to specific protein sites within LGIC’s, making the design of future improvements to anesthetic ligands a more realizable possibility.

Thiopental inhibits function of different inward rectifying potassium channel isoforms by a similar mechanism

Thiopental is a well-known intravenous barbiturate anesthetic with important cardiac side effects. The actions of thiopental on the transmembrane ionic currents that determine the resting potential and action potential duration in cardiomyocytes have been studied widely. We aimed at elucidating the characteristics and mechanism of inhibition by thiopental on members of the subfamily of inward rectifying Kir2.x (Kir2.1, 2.2 and 2.3), Kir1.1 and Kir6.2/SUR2A channels. These inward rectifier potassium channels were transfected in HEK-293 cells and macroscopic currents were recorded in the whole-cell and inside-out configurations of the patch-clamp technique. Thiopental inhibited Kir2.1, Kir2.2, Kir2.3, Kir1.1 and Kir6.2/SUR2A currents with similar potency; in whole-cell experiments 30 microM thiopental decreased Kir2.1, Kir2.2, Kir2.3 and Kir1.1 currents to 55+/-6, 39+/-8, 42+/-5 and 49+/-5% at -120 mV, respectively. Point mutations on Kir2.3 (I213L) or Kir2.1 (L222I) did not modify the potency of block. Thiopental inhibited all Kir channels in a concentration-dependent and voltage-independent manner. Also, the time course of thiopental inhibition was slow (T(1/2) approximately 4 min) and independent of external or internal drug application. However, in the presence of PIP(2), inhibition by thiopental on Kir2.1 was significantly decreased. Thiopental at clinically relevant concentrations significantly inhibited all Kir channels evaluated in this work. The reduction of thiopental effects during PIP(2) treatment suggests that thiopental inhibition on Kir2.1 channels is related to channel-PIP(2) interaction.

An atomistic model for simulations of the general anesthetic isoflurane

An atomistic model of isoflurane is constructed and calibrated to describe its conformational preferences and intermolecular interactions. The model, which is compatible with the CHARMM force field for biomolecules, is based on target quantities including bulk liquid properties, molecular conformations, and local interactions with isolated water molecules. Reference data is obtained from tabulated thermodynamic properties and high-resolution structural information from gas-phase electron diffraction, as well as DFT calculations at the B3LYP level. The model is tested against experimentally known solvation properties in water and oil, and shows quantitative agreement. In particular, isoflurane is faithfully described as lipophilic, yet nonhydrophobic, a combination of properties critical to its pharmacological activity. Intermolecular interactions of the model are further probed through simulations of the binding of isoflurane to a binding site in horse spleen apoferritin (HSAF). The observed binding mode compares well with crystallographic data, and the calculated binding affinities are compatible with experimental results, although both computational and experimental measurements are challenging and provide results with limited precision. The model is expected to be useful for detailed simulations of the elementary molecular processes associated with anesthesia. Full parameters are provided as Supporting Information.

Computational studies on the interactions of inhalational anesthetics with proteins

Despite the widespread clinical use of anesthetics since the 19th century, a clear understanding of the mechanism of anesthetic action has yet to emerge. On the basis of early experiments by Meyer, Overton, and subsequent researchers, the cell's lipid membrane was generally concluded to be the primary site of action of anesthetics. However, later experiments with lipid-free globular proteins, such as luciferase and apoferritin, shifted the focus of anesthetic action to proteins. Recent experimental studies, such as photoaffinity labeling and mutagenesis on membrane proteins, have suggested specific binding sites for anesthetic molecules, further strengthening the proteocentric view of anesthetic mechanism. With the increased availability of high-resolution crystal structures of ion channels and other integral membrane proteins, as well as the availability of powerful computers, the structure-function relationship of anesthetic-protein interactions can now be investigated in atomic detail. In this Account, we review recent experiments and related computer simulation studies involving interactions of inhalational anesthetics and proteins, with a particular focus on membrane proteins. Globular proteins have long been used as models for understanding the role of protein-anesthetic interactions and are accordingly examined in this Account. Using selected examples of membrane proteins, such as nicotinic acetyl choline receptor (nAChR) and potassium channels, we address the issues of anesthetic binding pockets in proteins, the role of conformation in anesthetic effects, and the modulation of local as well as global dynamics of proteins by inhaled anesthetics. In the case of nicotinic receptors, inhalational anesthetic halothane binds to the hydrophobic cavity close to the M2-M3 loop. This binding modulates the dynamics of the M2-M3 loop, which is implicated in allosterically transmitting the effects to the channel gate, thus altering the function of the protein. In potassium channels, anesthetic molecules preferentially potentiate the open conformation by quenching the motion of the aromatic residues implicated in the gating of the channel. These simulations suggest that low-affinity drugs (such as inhalational anesthetics) modulate the protein function by influencing local as well as global dynamics of proteins. Because of intrinsic experimental limitations, computational approaches represent an important avenue for exploring the mode of action of anesthetics. Molecular dynamics simulations-a computational technique frequently used in the general study of proteins-offer particular insight in the study of the interaction of inhalational anesthetics with membrane proteins.

Mitochondria are involved in stress response of A549 alveolar cells to halothane toxicity

During inhalation anaesthesia lung epithelial cells are directly exposed to halogenated hydrocarbons such as halothane. Information about the effects of volatile anaesthetics on lung cells is rather limited although their noxious effect on the A549 alveolar cells has been shown recently. The present study indicated that halothane decreases cell viability, impairs DNA integrity and provokes stress-induced apoptosis in A549 cells when applied at clinically relevant concentrations. Data obtained clearly demonstrated intensive expression of anti-apoptotic Bcl-2 protein during treatment with all tested concentrations. In post-treatment periods the increased DNA injury was accompanied by reduction of Bcl-2 expression. We concluded that the in vitro effect of halothane on lung cells involved alteration in the expression of proteins of the mitochondrial apoptotic pathway.

Normal-mode analysis of the glycine alpha1 receptor by three separate methods

Predicting collective dynamics and structural changes in biological macromolecules is pivotal toward a better understanding of many biological processes. Limitations due to large system sizes and inaccessible time scales have prompted the development of alternative techniques for the calculation of such motions. In this work, we present the results of a normal-mode analysis technique based on molecular mechanics that enables the calculation of accurate force-field based vibrations of extremely large molecules and compare it with two elastic network approximate models. When applied to the glycine alpha1 receptor, all three normal-mode analysis algorithms demonstrate an "iris-like" gating motion. Such gating motions have implications for understanding the effects of anesthetic and other ligand binding sites and for the means of transducing agonist binding into ion channel opening. Unlike the more approximate methods, molecular mechanics based analyses can also reveal approximate vibrational frequencies. Such analyses may someday allow the use of protein dynamics elucidated via normal-mode calculations as additional endpoints for future drug design.

Involvement of NMDA Receptors in Thiopental-Induced Loss of Righting Reflex, Antinociception and Anticonvulsion Effects in Mice

Potentiation of GABA(A) receptor-mediated inhibitory neurotransmission contributes to the anesthetic action of thiopental. However, the inhibiting action of general anesthetic on excitatory neurotransmission also purportedly underlies its effects. The aim of the study was to elucidate the role of glutamate receptors (NMDA and AMPA receptors) in thiopental-induced anesthesia. Intracerebroventricular (i.c.v.) NMDA (50 ng) significantly increased the induction time of loss of righting reflex and decreased sleep time induced by intraperitoneal injection (i.p.) of thiopental (50 mg/kg). Furthermore, NMDA at 50 ng i.c.v. increased the 50% effective dose values for thiopental to produce loss of righting reflex and immobility in response to noxious tail clamp by 25% and 21% (p < 0.05), respectively. However, intrathecal (IT) administration of NMDA or both of i.c.v. or IT administration of AMPA did not show such antagonizing effects on thiopental action at subconvulsive dose. Finally, thiopental (25 mg/kg i.p.) inhibited convulsions induced by NMDA (0.4 microg i.c.v.) or bicuculline (0.6 microg i.c.v.). However, i.p. muscimol (1 mg/kg) blocked the convulsions induced by bicuculline, but not those induced by NMDA at 3 mg/kg. Similarly, i.p. MK-801 (0.1 mg/kg) antagonized NMDA-induced convulsions, but not bicuculline-induced convulsions at 0.3 mg/kg. Therefore, we suggest that the effects of the selective GABA(A) and NMDA receptors on convulsive behavior are special to their sites of action, and that the inhibitory action of thiopental on NMDA receptors is possibly not mediated by secondary effects of its GABA(A) receptors agonism. These results above indicate the involvement of NMDA receptors in thiopental-induced anesthesia in mice.

Morphological Transitions in Model Membrane Systems by the Addition of Anesthetics

The mechanism of anesthetic action on membranes is still an open question, regardless of their extensive use in medical practice. It has been proposed that anesthetics may have the effect of promoting pore formation across membranes or at least switching transmembrane channels. In both cases this may be the result of changes in the interfacial curvature of the membrane due to the presence of anesthetic molecules. Aqueous solutions of surfactants display phases that mimic, in a simplified manner, real biological membranes. Therefore, in this study, two nonionic surfactant systems C16E6/H2O in concentrated solution and C10E3/H2O in dilute solution have been used as model membranes for the investigation of the effects of six common anesthetics (halothane, sodium thiopental, lidocaine base form and hydrochloride, prilocaine hydrochloride, and ketamine hydrochloride). Both binary surfactant-water systems exhibit phase transitions from the lamellar phase, Lalpha, that has zero spontaneous curvature and zero monolayer curvature to phases with more local interfacial curvature. These are the random mesh phase, Mh1(0), which consists of lamellae pierced by water-filled pores with local areas of positive interfacial curvature and the sponge phase, L3, that consists of the lamellar phase with interlamellae attachments, often referred to as a "melted" cubic phase, possessing negative monolayer curvature. Small-angle X-ray scattering and 2H NMR experiments upon the C16E6/2H2O system and optical observations of the C10E3/H2O system showed that all anesthetics employed in this study cause a shift in the Mh1(0) to Lalpha phase transition temperature and in the Lalpha to L3 transition temperature, respectively. All of the anesthetics studied bind to the interfacial region of the surfactant systems. Two types of behavior were observed on anesthetic addition: type I anesthetics, which decreased interfacial curvature, and type II, which increased it. However, at physiological pH both types of anesthetics decreased interfacial curvature.

Molecular surface electrostatic potentials and anesthetic activity

General anesthetics apparently act through weak, noncovalent and reversible interactions with certain sites in appropriate brain proteins. As a means of gaining insight into the factors underlying anesthetic potency, we have analyzed the computed electrostatic potentials V (S)(r) on the surfaces of 20 molecules with activities that vary between zero and high. Our results are fully consistent with, and help to interpret, what has been observed experimentally. We find that an intermediate level of internal charge separation is required; this is measured by Pi, the average absolute deviation of V (S)(r), and the approximate window is 7 < Pi < 13 kcal mol(-1). This fits in well with the fact that anesthetics need to be lipid soluble, but also to have some degree of hydrophilicity. We further show that polyhalogenated alkanes and ethers, which include the most powerful known anesthetics, have strong positive potentials, V (S,max), associated with their hydrogens, chlorines and bromines (but not fluorines). These positive sites may impede the functioning of key brain proteins, for example by disrupting their normal hydrogen-bond patterns. It has indeed been recognized for some time that the most active polyhalogenated alkanes and ethers contain hydrogens usually in combination with chlorines and/or bromines.

Modulating inhibitory ligand-gated ion channels

The glycine and gamma-aminobutyric acid receptors (GlyR and GABA(A)R, respectively) are the major inhibitory neurotransmitter-gated receptors in the central nervous system of animals. Given the important role of these receptors in neuronal inhibition, they are prime targets of many therapeutic agents and are the object of intense studies aimed at correlating their structure and function. In this review, the structure and dynamics of these and other homologous members of the nicotinicoid superfamily are described. The modulatory actions of the major biological macromolecules that bind and allosterically affect these receptors are also discussed.

State-dependent cross-linking of the M2 and M3 segments: functional basis for the alignment of GABAA and acetylcholine receptor M3 segments

Construction of a GABAA receptor homology model based on the acetylcholine (ACh) receptor structure is complicated by the low sequence similarity between GABAA and ACh M3 transmembrane segments that creates significant uncertainty in their alignment. We determined the orientation of the GABAA M2 and M3 transmembrane segments using disulfide cross-linking. The M2 residues alpha1M266 (11') and alpha1T267 (12') were mutated to cysteine in either wild type or single M3 cysteine mutant (alpha1V297C, alpha1A300C to alpha1A305C) backgrounds. We assayed spontaneous and induced disulfide bond formation. Reduction with DTT significantly potentiated GABA-induced currents in alpha1T267C-L301C and alpha1T267C-F304C. Copper phenanthroline-induced oxidation inhibited GABA-induced currents in these mutants and in alpha1T267C-A305C. Intrasubunit disulfide bonds formed between these Cys pairs, implying that the alpha-carbon separation was at most 5.6 A. The reactive alpha1M3 residues (L301, F304, A305) lie on the same face of an alpha-helix. The unresponsive ones (A300, I302, E303) lie on the opposite face. In the resting state, the reactive side of alpha1M3 faces M2-alpha1T267. In conjunction with the ACh structure, our data indicate that alignment of GABAA and ACh M3 requires a single gap in the GABAA M2-M3 loop. In the presence of GABA, oxidation of alpha1T267C-L301C and alpha1T267C-F304C had no effect, but oxidation of alpha1T267C-A305C caused a significant increase in spontaneous channel opening. We infer that, as the channel opens, the distance and/or orientation between M2-alpha1T267 and M3-alpha1A305 changes such that the disulfide bond stabilizes the open state. This begins to define the conformational motion that M2 undergoes during channel opening.

Interactions of anesthetics with their targets: non-specific, specific or both?

What makes a general anesthetic a general anesthetic? We shall review first what general anesthesia is all about and which drugs are being used as anesthetics. There is neither a unique definition of general anesthesia nor any consensus on how to measure it. Diverse drugs and combinations of drugs generate general anesthetic states of sometimes very different clinical quality. Yet the principal drugs are still considered to belong to the same class of 'general anesthetics'. Effective concentrations of inhalation anesthetics are in the high micromolar range and above, and even for intravenous anesthetics they do not go below the micromolar range. At these concentrations, many molecular and higher level targets are affected by inhalation anesthetics, fewer probably by intravenous anesthetics. The only physicochemical characteristic shared by anesthetics is the correlation of their anesthetic potencies with hydrophobicity. These correlations depend on the group of general anesthetics considered. In this review, anesthetic potencies for many different targets are plotted against octanol/water partition coefficients as measure of hydrophobicity. Qualitatively, similar correlations result, suggesting several but weak interactions with proteins as being characteristic of anesthetic actions. The polar interactions involved are weak, being roughly equal in magnitude to hydrophobic interactions. Generally, intravenous anesthetics are noticeably more potent than inhalation anesthetics. They differ considerably more between each other in their interactions with various targets than inhalation anesthetics do, making it difficult to come to a decision which of these should be used in future studies as representative 'prototypical general anesthetics'.

Cardiovascular changes and catecholamine release following anaesthesia in Chinook salmon (Oncorhynchus tshawytscha) and snapper (Pagrus auratus)

We investigated recovery from anaesthesia in Chinook salmon (Oncorhynchus tshawytscha) with and without surgery. Fish either underwent light sedation on exposure to 60 ppm AQUI-S or surgical depth anaesthesia with 120 ppm AQUI-S. Surgical depth anaesthesia experiments were replicated using New Zealand snapper (Pagrus auratus). During light sedation, there was no evidence of catecholamine release in salmon despite changes in heart rate and blood pressure. Following surgical anaesthesia both salmon and snapper released high concentrations of catecholamines into the circulation. Plasma half-life of adrenaline in salmon was 9.3+/-0.7 min (n = 7) and in snapper was 4.4+/-3.3 min (n = 7). There was no further release of catecholamines, despite attempts by both species to escape their enclosures. Though clearance of the catecholamines was rapid, the cardiovascular effects of anaesthesia were prolonged. Dorsal aortic blood pressure (P(DA)) and heart rate (HR) were high following anaesthesia, falling by 60 min in the 60 ppm exposed salmon but remaining high in the 120 ppm group. Following anaesthesia ventral aorta blood pressure (P(VA)) in snapper was positively correlated with HR, as was P(DA) and haematocrit in salmon. Recovery of cardiovascular control processes is prolonged in recovery from anaesthesia if the fish become hypoxic.

The Site of Action of General Anesthetics - A Chemical Approach

Recently Urban (Br. J. Anaesth. 2002, 89, 167) and Trudell (Br. J. Anaesth. 2002, 89, 32) assessed the present state of the art in anesthesiological research. This article is an attempt to add to the discussion some ideas from the chemist's point of view. General anesthesia is a matter of molecular associations. Among the intermolecular interactions that can be involved, weak hydrogen bonding and van der Waals forces are believed to be most important. A pluralistic view is proposed, thereby different anesthetics can choose different interactions in conformity with their chemical structure. This can involve proteins, lipids, and sugars. Special attention is given to glycoproteins and glycosphingolipids. A review with 90 references.

Homology Modeling of a Human Glycine Alpha 1 Receptor Reveals a Plausible Anesthetic Binding Site

The superfamily of ligand-gated ion channels (LGICs) has been implicated in anesthetic and alcohol responses. Mutations within glycine and GABA receptors have demonstrated that possible sites of anesthetic action exist within the transmembrane subunits of these receptors. The exact molecular arrangement of this transmembrane region remains at intermediate resolution with current experimental techniques. Homology modeling methods were therefore combined with experimental data to produce a more exact model of this region. A consensus from multiple bioinformatics techniques predicted the topology within the transmembrane domain of a glycine alpha one receptor (GlyRa1) to be alpha helical. This fold information was combined with sequence information using the SeqFold algorithm to search for modeling templates. Independently, the FoldMiner algorithm was used to search for templates that had structural folds similar to published coordinates of the homologous nAChR (1OED). Both SeqFold and Foldminer identified the same modeling template. The GlyRa1 sequence was aligned with this template using multiple scoring criteria. Refinement of the alignment closed gaps to produce agreement with labeling studies carried out on the homologous receptors of the superfamily. Structural assignment and refinement was achieved using Modeler. The final structure demonstrated a cavity within the core of a four-helix bundle. Residues known to be involved in modulating anesthetic potency converge on and line this cavity. This suggests that the binding sites for volatile anesthetics in the LGICs are the cavities formed within the core of transmembrane four-helix bundles.

Comparative modeling of a GABAA alpha1 receptor using three crystal structures as templates

We built a model of a GABAA alpha1 receptor (GABAAR) that combines the ligand binding (LBD) and the transmembrane domains (TMD). We used six steps: (1) a four-alpha helical bundle in the crystal structure of bovine cytochrome c oxidase (2OCC) was identified as a template for the TMD of a single subunit. (2) The five pore-forming alpha helices of a bacterial mechanosensitive channel (1MSL) served as a template for the pentameric ion channel. (3) Five copies of the tetrameric template from 2OCC were superimposed on 1MSL to produce a homopentamer containing 20 alpha helices arranged around a funnel-shaped central pore. (4) Five copies of the GABAAR sequence were threaded onto the alpha-helical segments of this template and inter-helical loops were generated to produce the TMD model. (5) A model of the LBD was built by threading the aligned sequence of GABAAR onto the crystal structure of the acetylcholine binding protein (1I9B). (6) The models of the LBD and the TMD were aligned along a common five-fold axis, moved together along that axis until in vdW contact, merged, and then optimized with restrained molecular dynamics. Our model corresponds closely with recently published coordinates of the acetylcholine receptor (1OED) but also explains additional features. Our model reveals structures of loops that were not visible in the cryoelectron micrograph and satisfies most labeling and mutagenesis data. It also suggests mechanisms for ligand binding transduction, ion selectivity, and anesthetic binding.

Alanine-Scanning Mutagenesis in the Signature Disulfide Loop of the Glycine Receptor α1 Subunit: Critical Residues for Activation and Modulation

The glycine receptor enables the generation of inhibitory postsynaptic currents at synapses via neurotransmitter-dependent activation. These receptors belong to the ligand-gated ion channel gene superfamily, in which all members are comprised of five subunits, each of which possesses a signature 13-residue disulfide loop (Cys loop) in the extracellular domain. In this study, we used alanine-scanning mutagenesis of the residues between C138 and C152 of the Cys loop of the glycine receptor alpha1 subunit to identify residues critical for receptor activation and allosteric modulation. Mutation of L142, F145, or P146 to alanine produced decreases in the potency, maximal amplitude, and Hill coefficient for currents elicited by glycine and impaired receptor activation by the agonist taurine. These residues, along with D148, are positionally conserved in the family of LGIC subunits. Mutation at several other positions had little or no effect. The inhaled anesthetics halothane and isoflurane potentiate submaximal agonist responses at wild-type receptors, via an allosteric site. The mutations L142A, F145A, P146A, and D148A abolished positive modulation by these anesthetics, in some cases revealing a small inhibitory effect. A molecular model of the glycine receptor alpha1 subunit suggests that the Cys loop is positioned in a region of the receptor at the interface between the extracellular and transmembrane domains and that the critical functional residues identified here lie along the face of a predominantly hydrophobic surface. The present data implicate the Cys loop as an important functional moiety in the process of glycine receptor activation and allosteric regulation by anesthetics.

A Novel Hyperekplexia-causing Mutation in the Pre-transmembrane Segment 1 of the Human Glycine Receptor α1 Subunit Reduces Membrane Expression and Impairs Gating by Agonists

In this study, we have compared the functional consequences of three mutations (R218Q, V260M, and Q266H) in the alpha(1) subunit of the glycine receptor (GlyRA1) causing hyperekplexia, an inherited neurological channelopathy. In HEK-293 cells, the agonist EC(50s) for glycine-activated Cl(-) currents were increased from 26 microm in wtGlyRA1, to 5747, 135, and 129 microm in R218Q, V260M, and Q266H GlyRA1 channels, respectively. Cl(-) currents elicited by beta-alanine and taurine, which behave as agonists at wtGlyRA1, were decreased in V260M and Q266H mutant receptors and virtually abolished in GlyRA1 R218Q receptors. Gly-gated Cl(-) currents were similarly antagonized by low concentrations of strychnine in both wild-type (wt) and R218Q GlyRA1 channels, suggesting that the Arg-218 residue plays a crucial role in GlyRA1 channel gating, with only minor effects on the agonist/antagonist binding site, a hypothesis supported by our molecular model of the GlyRA1 subunit. The R218Q mutation, but not the V260M or the Q266H mutation, caused a marked decrease of receptor subunit expression both in total cell lysates and in isolated plasma membrane proteins. This decreased expression does not seem to explain the reduced agonist sensitivity of GlyRA1 R218Q channels since no difference in the apparent sensitivity to glycine or taurine was observed when wtGlyRA1 receptors were expressed at levels comparable with those of R218Q mutant receptors. In conclusion, multiple mechanisms may explain the dramatic decrease in GlyR function caused by the R218Q mutation, possibly providing the molecular basis for its association with a more severe clinical phenotype.

Mechanisms of channel gating of the ligand-gated ion channel superfamily inferred from protein structure

The nicotinic-like ligand-gated ion channel superfamily consists of a group of structurally related receptors that activate an ion channel after the binding of extracellular ligand. The recent publications of the crystal structure of an acetylcholine binding protein and a refined electron micrograph structure of the membrane-bound segment of an acetylcholine receptor have led to insights into the molecular determinants of receptor function. Although the structures confirmed much biochemical and electrophysiological data obtained about the receptors, they also provide opportunities to study further the mechanisms that allow channel activation stimulated by ligand-binding. Here we review the mechanisms of channel gating that have been elucidated by information gained from the structures of the acetylcholine binding protein and membrane-bound segment of the acetylcholine receptor.

Sevoflurane Inhibition of the Slowly Activating Delayed Rectifier K+ Current in Guinea Pig Ventricular Cells

Single ventricular cells were enzymatically isolated from guinea pig hearts and the effects of sevoflurane on the delayed rectifier K(+) current were investigated by the patch clamp method. The rapidly (I(Kr)) and slowly activating delayed rectifier K(+) current (I(Ks)) were isolated using chromanol 293B, a selective blocker for I(Ks) or E4031 (N-[4-[[1-[2-(6-methyl-2-pyridinyl)ethyl]-4-piperidinyl]carbonyl]phenyl]methanesulfonamide dihydrochloride), a blocker for I(Kr). Sevoflurane and halothane decreased I(Ks) in a concentration-dependent manner with an IC(50) value of 0.38 mM for sevoflurane and 1.05 mM for halothane. I(Ks) inhibition was characterized by suppression of maximum conductance with little effect on activation kinetics. Inhibition occurred immediately after anesthetic application and recovered upon wash-out. In contrast to the marked inhibition of I(Ks), I(Kr) was hardly affected by sevoflurane. Under the current clamp, sevoflurane prolonged the action potential duration in a reversible manner and this effect was more marked when I(Kr) was inhibited by E4031. The results suggest that sevoflurane inhibits I(Ks), and not I(Kr), in a concentration-dependent manner at clinically relevant concentrations. The resulting prolongation of ventricular repolarization may partly account for the clinical observation of excessive QT prolongation by these anesthetics.

Glycine receptor knock-in mice and hyperekplexia-like phenotypes: comparisons with the null mutant

Strychnine-sensitive glycine receptors (GlyRs) inhibit neurotransmission in the spinal cord and brainstem. To better define the function of this receptor in vivo, we constructed a point mutation that impairs receptor function in the alpha1-subunit and compared these knock-in mice to oscillator (spdot) mice lacking functional GlyR alpha1-subunits. Mutation of the serine residue at amino acid 267 to glutamine (alpha1S267Q) results in a GlyR with normal glycine potency but decreased maximal currents, as shown by electrophysiological recordings using Xenopus oocytes. In addition, single-channel recordings using human embryonic kidney 293 cells indicated profoundly altered properties of the mutated GlyR. We produced knock-in mice bearing the GlyR alpha1 S267Q mutation to assess the in vivo consequences of selectively decreasing GlyR efficacy. Chloride uptake into brain synaptoneurosomes from knock-in mice revealed decreased responses to maximally effective glycine concentrations, although wild-type levels of GlyR expression were observed using 3H-strychnine binding and immunoblotting. A profound increase in the acoustic startle response was observed in knock-in mice as well as a "limb clenching" phenotype. In contrast, no changes in coordination or pain perception were observed using the rotarod or hot-plate tests, and there was no change in GABA(A)-receptor-mediated chloride uptake. Homozygous S267Q knock-in mice, like homozygous spdot mice, exhibited seizures and died within 3 weeks of birth. In heterozygous spdot mice, both decreased 3H-strychnine binding and chloride flux were observed; however, neither enhanced acoustic startle responses nor limb clenching were seen. These data demonstrate that a dominant-negative point mutation in GlyR disrupting normal function can produce a more dramatic phenotype than the corresponding recessive null mutation, and provides a new animal model to evaluate GlyR function in vivo.

Molecular features of an alcohol binding site in a neuronal potassium channel

Aliphatic alcohols (1-alkanols) selectively inhibit the neuronal Shaw2 K(+) channel at an internal binding site. This inhibition is conferred by a sequence of 13 residues that constitutes the S4-S5 loop in the pore-forming subunit. Here, we combined functional and structural approaches to gain insights into the molecular basis of this interaction. To infer the forces that are involved, we employed a fast concentration-clamp method (10-90% exchange time = 800 micros) to examine the kinetics of the interaction of three members of the homologous series of 1-alkanols (ethanol, 1-butanol, and 1-hexanol) with Shaw2 K(+) channels in Xenopus oocyte inside-out patches. As expected for a second-order mechanism involving a receptor site, only the observed association rate constants were linearly dependent on the 1-alkanol concentration. While the alkyl chain length modestly influenced the dissociation rate constants (decreasing only approximately 2-fold between ethanol and 1-hexanol), the second-order association rate constants increased e-fold per carbon atom. Thus, hydrophobic interactions govern the probability of productive collisions at the 1-alkanol binding site, and short-range polar interactions help to stabilize the complex. We also examined the relationship between the energetics of 1-alkanol binding and the structural properties of the S4-S5 loop. Circular dichroism spectroscopy applied to peptides corresponding to the S4-S5 loop of various K(+) channels revealed a correlation between the apparent binding affinity of the 1-alkanol binding site and the alpha-helical propensity of the S4-S5 loop. The data suggest that amphiphilic interactions at the Shaw2 1-alkanol binding site depend on specific structural constraints in the pore-forming subunit of the channel.

Inhaled anesthetics and immobility: mechanisms, mysteries, and minimum alveolar anesthetic concentration

Studies using molecular modeling, genetic engineering, neurophysiology/pharmacology, and whole animals have advanced our understanding of where and how inhaled anesthetics act to produce immobility (minimum alveolar anesthetic concentration; MAC) by actions on the spinal cord. Numerous ligand- and voltage-gated channels might plausibly mediate MAC, and specific amino acid sites in certain receptors present likely candidates for mediation. However, in vivo studies to date suggest that several channels or receptors may not be mediators (e.g., gamma-aminobutyric acid A, acetylcholine, potassium, 5-hydroxytryptamine-3, opioids, and alpha(2)-adrenergic), whereas other receptors/channels (e.g., glycine, N-methyl-D-aspartate, and sodium) remain credible candidates.

Coupling of agonist binding to channel gating in the GABA(A) receptor

Neurotransmitters such as acetylcholine and GABA (gamma-aminobutyric acid) mediate rapid synaptic transmission by activating receptors belonging to the gene superfamily of ligand-gated ion channels (LGICs). These channels are pentameric proteins that function as signal transducers, converting chemical messages into electrical signals. Neurotransmitters activate LGICs by interacting with a ligand-binding site, triggering a conformational change in the protein that results in the opening of an ion channel. This process, which is known as 'gating', occurs rapidly and reversibly, but the molecular rearrangements involved are not well understood. Here we show that optimal gating in the GABA(A) receptor, a member of the LGIC superfamily, is dependent on electrostatic interactions between the negatively charged Asp 57 and Asp 149 residues in extracellular loops 2 and 7, and the positively charged Lys 279 residue in the transmembrane 2-3 linker region of the alpha1-subunit. During gating, Asp 149 and Lys 279 seem to move closer to one another, providing a potential mechanism for the coupling of ligand binding to opening of the ion channel.

The nature of sites of general anaesthetic action

The molecular nature of the site of general anaesthesia has long been sought through the process of comparing the in vivo potencies of general anaesthetics with their physical properties, particularly their ability to dissolve in solvents of various polarities. This approach has led to the conclusion that the site of general anaesthesia is largely apolar but contains a strong polar component. However, there is growing evidence that several physiological targets underlie general anaesthesia, and that different agents may act selectively on subsets of these targets. Consequently research now focuses on the details of general-anaesthetic-protein interactions. There are large amounts of structural data that identify cavities where anaesthetics bind on soluble proteins that are readily crystallizable. These proteins serve as models, having no role in anaesthesia. Two problems make studies of the more likely targets--excitable membrane proteins--difficult. One is that they rarely crystallize and the other is that the sites have their highest affinity for general anaesthetics when the channels are in the open state. Such states rarely exist for more than tens of milliseconds. Crystallographers are making progress with the first problem, whilst anaesthesia researchers have developed a number of strategies for addressing the second. Some of these (kinetic analysis, site-directed mutagenesis) provide indirect evidence for sites and their nature, whilst others seek direct identification of sites by employing newly developed general anaesthetics that are photoaffinity labels. Such studies on acetylcholine, glycine and GABA receptors point to the existence of sites located within the plane of the membrane either within the ion channel lumen (acetylcholine receptor), or on the outer side of the alpha-helix lining that lumen (GABAA and glycine receptors). Bound anaesthetics generally exert their actions on ion channels by binding to allosteric sites whose topology varies from one conformation to another, but definitive proof for this mechanism remains elusive.

The effects of general anaesthetics on ligand-gated ion channels

The experimental effort that has been expended in investigating the effects of general anaesthetics on LGICs has been enormous over the past decade. Members of all three LGIC superfamilies have been examined using electrophysiological techniques. Anaesthetics that have been examined include volatile anaesthetics, gaseous anaesthetics, alcohols, i.v. anaesthetics and non-immobilizers. Obsolete anaesthetics (ether, cyclopropane, butane) have been used in order to increase the variability of the structure and polarity of experimental compounds. The tools of molecular biology have been used to make chimeric receptors and to make single-site mutations. Interestingly, this work has been taking place in parallel with efforts to understand the structure of these proteins. Anaesthetic research often stimulates structural research as well as vice versa. There are some common themes in the interactions between anaesthetics and the three superfamilies of LGICs. In many cases, anaesthetics have both inhibitory and potentiating effects on the channels. It is likely that the number of examples of this will increase when experiments are designed to look specifically for one or the other type of effect. So we must conclude that there are multiple binding sites for anaesthetics on LGICs. The degree of inhibition or potentiation is not easily predictable. In retrospect, this is not surprising when we consider that the sensitivity of a channel to anaesthetics can be altered by a single amino-acid mutation. The large structural differences between the cys-loop, glutamate-activated and P2X superfamilies do not lead to large differences in anaesthetic sensitivity. It is the smaller, almost insignificant, changes that do this. This observation that small changes may lead to large effects reinforces the idea that at least some of the interactions between anaesthetics and LGICs are direct drug-protein interactions that are not mediated by the lipids. This review has not addressed the question of whether the effects of anaesthetics seen on LGICs are relevant to anaesthesia. This question cannot really be answered at present. Although potent effects can be observed on the channels themselves, we have only begun to try to understand whether these effects are important for a synapse, a neuronal circuit or the function of an animal's nervous system. We have studied the trees; now we must go on to study the forest and the ecosystem.