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Pharmacophore models for nicotinic agonists have been proposed for four decades. Central to these models is the presence of a cationic nitrogen and a hydrogen bond acceptor. It is now well-established that the cationic center makes an important cation-π interaction to a conserved tryptophan, but the donor to the proposed hydrogen bond acceptor has been more challenging to identify. A structure of nicotine bound to the acetylcholine binding protein predicted that the binding partner of the pharmacophore’s second component was a water molecule, which also hydrogen bonds to the backbone of the complementary subunit of the receptors. Here we use unnatural amino acid mutagenesis coupled with agonist analogs to examine whether such a hydrogen bond is functionally significant in the α4β2 neuronal nAChR, the receptor most associated with nicotine addiction. We find evidence for the hydrogen bond with the agonists nicotine, acetylcholine, carbamylcholine, and epibatidine. These data represent a completed nicotinic pharmacophore and offer insight into the design of new therapeutic agents that selectively target these receptors.

The similarity to crown ethers is apparent when the arrangement of the oxygen atoms of the carbonyl groups of the protein backbone in the structure of the potassium channel (see schematic drawing of a section of the structure) found in the bacterium Streptomyces lividans is considered. This particular part of the channel pore acts as the selectivity filter, with the permeability of the channel for K+ being as much as 10 000 times greater than for the Na+ ion. In fact, in this area of the structure two K+ ions are located, a feature that enables high flux through the channel.

The functions of two conserved residues, Phe(135) and Pro(136), located at the apex of the Cys loop of the nicotinic acetylcholine receptor are investigated. Both residues were substituted with natural and unnatural amino acids, focusing on the role of aromaticity at Phe(135), backbone conformation at Pro(136), side chain polarity and volume, and the specific interaction between the aromatic side chain and the proline. NMR spectroscopy studies of model peptides containing proline and unnatural proline analogues following a Phe show a consistent increase in the population of the cis conformer relative to peptides lacking the Phe. In the receptor, a strong interaction between the Phe and Pro residues is evident, as is a strong preference for aromaticity and hydrophobicity at the Phe site. A similar influence of hydrophobicity is observed at the proline site. In addition, across a simple homologous series of proline analogues, the results reveal a correlation between receptor function and cis bias at the proline backbone. This could suggest a significant role for the cis proline conformer at this site in receptor function.

Nicotinic acetylcholine receptors (nAChRs) are pentameric neurotransmitter-gated ion channels that mediate rapid synaptic transmission throughout the central and peripheral nervous systems. They are well-established targets for small molecule treatments for Alzheimer's disease, schizophrenia, Parkinson's disease, epilepsy, autism, and smoking cessation. To date, 17 human genes have been identified that code for nAChR subunits, termed α1-α10, β1-β4, γ, δ, and e. nAChRs are subdivided into two main categories: the prototypical muscle-type receptor with a precise stoichiometry of (α1)2βδγ (fetal form) and the “neuronal” nAChRs that are formed from various combinations of α2-α10 and β2-β4 subunits. Crystal structures of the acetylcholine binding protein have indicated that various ligands are positioned into a localized binding pocket formed from a cluster of conserved aromatic residues, termed the “aromatic box”. Previous work from our lab has indicated that a common component of the neurotransmitter-binding occurs through the cationic center of the ligand and the face of an aromatic amino acid, termed the cation-π interaction, as well as hydrogen bonding interactions. Together, these binding events cause a change in protein structure permitting ion flow through the channel pore. In the immediate vicinity of the agonist binding site, all nAChR subtypes show identical amino acid compositions, yet significant pharmacological variations are seen. Previous work identified a point mutation, G152K, located near but not directly contributing to the agonist binding site in the α7 nAChR that is critical to agonist potency. Interestingly, this residue is a glycine in the low affinity receptors, such as the muscle-type and α7 nAChRs, but a lysine in the high affinity α4β2 nAChR. Here, we investigate the importance of this residue (G or K) in influencing acetylcholine and nicotine binding interactions in the muscle-type, α7 and α4β2 nAChRs.

Cyclophane hosts 1 and 2 have been shown to be effective catalysts for both the alkylation of quinoline structures to produce quinolinium salts and the dealkylation of sulfonium salts to produce sulfides. Thus, reactions that develop positive charge in the transition state and reactions that destroy positive charge are accelerated. The former observation is not surprising, given the well-documented ability of these hosts to bind cations through the cation-π interaction. The catalysis of the dealkylation reactions, however, along with several other observations, suggests that some other factor is involved in the catalysis. It is proposed that the high polarizability of the transition states is well matched to the very polarizable hosts and that this contributes to the catalysis.

A strategy for photochemical cleavage of peptide and protein backbones is described, which is based on a selenide-mediated cleavage of a backbone ester moiety. Studies in model systems establish the viability of the chemistry and suggest the method could be a valuable tool for chemical biology studies of proteins.

Ion channel localization and trafficking is important for regulating excitability and synaptic transmission. Quantum dots (Qdots) coated with streptavidin were previously used to label membrane proteins that are recognized by biotinylated antibodies or by biotinylation of an acceptor peptide sequence. We report strategies, suitable for living cells, using strepatavidin-coated Qdots to count and locate extracellular domains of muscle and neuronal nicotinic acetylcholine receptors (nAChRs). Receptors were expressed in Xenopus oocytes. (1) The nonsense suppression methodology was used to incorporate the unnatural amino acid biocytin in the muscle nAChR α subunit, in the main immunogenic region, in place of the Asp70 residue. To accomplish this, the T. thermophila Gln amber suppressor (TQAS) was chemically aminoacylated with biocytin and co-injected with α70UAG:β:δ:γ mRNA. Functional expression was measured 24 - 48 hours post-injection. The muscle nAChR stoichiometry is (α)2(β)1(δ)1(γ/ɛ)1; in agreement, two colocalized Qdots were measured by blinking analysis with previously reported algorithms (Pantoja et al, Biophys J in press). (2) The muscle nicotinic receptor was labeled with α-bungarotoxin monoconjugated to biotin (α-Btx-Bio) and subsequently exposed to Qdots; some receptors exhibited the expected two Qdots. (3) The homopentameric α7 nAChR was labeled with α-Btx-Bio and subsequently labeled with Qdots. One to 3 Qdots per α7 receptor were detected, as expected from previous data. In all cases, the robust Qdot fluorescence enabled subunit localization with nanometer accuracy. Strategies (2) and (3) confirm that strategy (1), site-specific unnatural amino acid incorporation combined with Qdot labeling, provides a one-step, specific, efficient labeling approach to investigate composition and real-time trafficking of nicotinic receptors. Grants: NS11756, NS34407, HL79350. Fellowships: Ford and APA-DPN (RP), NSF (EAR).

Magnetism has fascinated and served humanity for almost 3000 years. Since the discovery of the lodestone (FeO-Fe_2O_3), many different magnetic materials have been developed, almost all based on transition metals and/or rare-earth elements. Technological application of magnetism also has a long history, from the compass to today's sophisticated magnetic memory systems. In contrast, the theory of magnetism has progressed more slowly, despite the efforts of great minds throughout history. The reason early theoretical models were not very valuable is now clear. Any viable theory of magnetism must be based on two inherently quantum mechanical concepts: electron spin and the Pauli exclusion principle. As such, only the 20th century has produced a competent model for magnetism, and that model continues to evolve. Studies over the last 20 years have revealed a bewildering array of new magnetic phenomena that continue to challenge our understanding of solid-state physics.

The acronym SePhaChARNS, for "selective pharmacological chaperoning of acetylcholine receptor number and stoichiometry," is introduced. We hypothesize that SePhaChARNS underlies classical observations that chronic exposure to nicotine causes "upregulation" of nicotinic receptors (nAChRs). If the hypothesis is proven, (1) SePhaChARNS is the molecular mechanism of the first step in neuroadaptation to chronic nicotine; and (2) nicotine addiction is partially a disease of excessive chaperoning. The chaperone is a pharmacological one, nicotine; and the chaperoned molecules are alpha4beta2* nAChRs. SePhaChARNS may also underlie two inadvertent therapeutic effects of tobacco use: (1) the inverse correlation between tobacco use and Parkinson's disease; and (2) the suppression of seizures by nicotine in autosomal dominant nocturnal frontal lobe epilepsy. SePhaChARNS arises from the thermodynamics of pharmacological chaperoning: ligand binding, especially at subunit interfaces, stabilizes AChRs during assembly and maturation, and this stabilization is most pronounced for the highest-affinity subunit compositions, stoichiometries, and functional states of receptors. Several chemical and pharmacokinetic characteristics render exogenous nicotine a more potent pharmacological chaperone than endogenous acetylcholine. SePhaChARNS is modified by desensitized states of nAChRs, by acid trapping of nicotine in organelles, and by other aspects of proteostasis. SePhaChARNS is selective at the cellular, and possibly subcellular, levels because of variations in the detailed nAChR subunit composition, as well as in expression of auxiliary proteins such as lynx. One important implication of the SePhaChARNS hypothesis is that therapeutically relevant nicotinic receptor drugs could be discovered by studying events in intracellular compartments rather than exclusively at the surface membrane.

The muscle nicotinic acetylcholine receptor is a large, allosteric, ligand-gated ion channel with the subunit composition alpha2betagammadelta. Although much is now known about the structure of the binding site, relatively little is understood about how the binding event is communicated to the channel gate, causing the pore to open. Here we identify a key hydrogen bond near the binding site that is involved in the gating pathway. Using mutant cycle analysis with the novel unnatural residue alpha-hydroxyserine, we find that the backbone N-H of alphaSer-191 in loop C makes a hydrogen bond to an anionic side chain of the complementary subunit upon agonist binding. However, the anionic partner is not the glutamate predicted by the crystal structures of the homologous acetylcholine-binding protein. Instead, the hydrogen-bonding partner is the extensively researched aspartate gammaAsp-174/deltaAsp-180, which had originally been identified as a key binding residue for cationic agonists.

Cys-loop receptor binding sites characteristically contain many aromatic amino acids. In nicotinic ACh and 5-HT3receptors, a Trp residue forms a cation-π interaction with the agonist, whereas in GABAAreceptors, a Tyr performs this role. The glycine receptor binding site, however, contains predominantly Phe residues. Homology models suggest that two of these Phe side chains, Phe159 and Phe207, and possibly a third, Phe63, are positioned such that they could contribute to a cation-π interaction with the primary amine of glycine. Here, we test this hypothesis by incorporation of a series of fluorinated Phe derivatives using unnatural amino acid mutagenesis. The data reveal a clear correlation between the glycine EC50value and the cation-π binding ability of the fluorinated Phe derivatives at position 159, but not at positions 207 or 63, indicating a single cation-π interaction between glycine and Phe159. The data thus provide an anchor point for locating glycine in its binding site, and demonstrate for the first time a cation-π interaction between Phe and a neurotransmitter.

Dennis A. Dougherty is the George Grant Hoag Professor of Chemistry at the California Institute of Technology. He received his B.S. and M.S. degrees from Bucknell University, and in 1978 he completed his Ph.D. with Kurt Mislow at Princeton University. After a year of postdoctoral studies with Jerome Berson at Yale University, he joined the faculty at Caltech. Professor Dougherty’s research employs the techniques of physical organic chemistry to probe biologically important systems, specifically in the field of neuroscience. He is known for the development of the cation−π interaction, a general noncovalent binding force of pervasive importance in biological systems. More recently, he has pursued chemical-scale studies of neuroreceptors and ion channels, such as the nicotinic acetylcholine receptor. Professor Dougherty’s research has been recognized with a number of awards, including the ACS James Flack Norris Award for Physical Organic Chemistry, the AstraZeneca Excellence in Chemistry Award, the Arthur C. Cope Scholar Award, and the Javits Neuroscience Investigator, NIH. He is a Fellow of the American Association for the Advancement of Science and a Fellow of the American Academy of Arts and Science. He is also the coauthor with Dr. Eric Anslyn of the influential textbook Modern Physical Organic Chemistry.

The challenges to obtaining chemical-scale information on the molecules of neuroscience are considerable. Most targets are complex integral membrane proteins that are not amenable to direct structural characterization. However, by combining the tools of organic synthesis, molecular biology, and electrophysiology, rational and systematic structure−function studies can be performed in what we have termed physical organic chemistry on the brain. Using these tools, we have probed hydrophobic effects, hydrogen bonding, cation−π interactions, and conformational changes associated with channel gating. The insights gained provide important guidance for drug discovery efforts targeting ion channels and neuroreceptors and mechanistic insights for the complex proteins of neuroscience.

The binding sites of Cys-loop receptors are formed from at least six loops (A-F). Here we have used mutagenesis, radioligand binding, voltage clamp electrophysiology, and homology modeling to probe the role of two residues in loop A of the 5-HT3 receptor: Asn128 and Glu129. The data show that substitution of Asn128, with a range of alternative natural and unnatural amino acids, changed the EC50 (from approximately 10-fold more potent to approximately 10-fold less potent than that of the wild type), increased the maximal peak current for mCPBG compared to 5-HT (R max) 2-19-fold, and decreased n H, indicating this residue is involved in receptor gating; we propose Asn128 faces away from the binding pocket and plays a role in facilitating transitions between conformational states. Substitutions of Glu129 resulted in functional receptors only when the residue could accept a hydrogen bond, but with both these and other substitutions, no [(3)H]granisetron binding could be detected, indicating a role in ligand binding. We propose that Glu129 faces into the binding pocket, where, through its ability to hydrogen bond, it plays a critical role in ligand binding. Thus, the data support a modified model of the 5-HT3 receptor binding site and show that loop A plays a critical role in both the ligand binding and function of this receptor.

A cation ― π-electron interaction is the essential factor responsible for the stabilization of the transition state during the methylation of quinoline (and related bases) with methyl iodide by a cage host compound. The stabilization results in a catalytic effect: In the presence of the host the reaction is accelerated by a factor of 100. The system provides a primitive model for enzymatic methylation

Variable-temperature binding studies are used to evaluate the thermodynamics of molecular recognition of a variety of guests by macrocyclic, cyclophane hosts. In both organic (CDCl_3) and aqueous media, significant heat capacity effects are evident. Curvature in the van't Hoff plots can be well-modeled by assuming a constant value for ΔC_p^0, and statistical analysis reveals a meaningful improvement in the correlation when ΔC_p^0 is included. Trends in the values for ΔH^0_(298) and ΔS^0_(298) reveal a predominantly enthalpic origin for the "cation-π" effect, which involves the stabilization of a positive charge by the electron-rich face of an aromatic ring.

The synthesis and preliminary doping studies of a new polymer designed to test the viability of polaronic ferromagnetism are described

Antiarrhythmics, anticonvulsants, and local anesthetics target voltage-gated sodium channels, decreasing excitability of nerve and muscle cells. Channel inhibition by members of this family of cationic, hydrophobic drugs relies on the presence of highly conserved aromatic residues in the pore-lining S6 segment of the fourth homologous domain of the channel. We tested whether channel inhibition was facilitated by an electrostatic attraction between lidocaine and π electrons of the aromatic rings of these residues, namely a cation-π interaction. To this end, we used the in vivo nonsense suppression method to incorporate a series of unnatural phenylalanine derivatives designed to systematically reduce the negative electrostatic potential on the face of the aromatic ring. In contrast to standard point mutations at the same sites, these subtly altered amino acids preserve the wild-type voltage dependence of channel activation and inactivation. Although these phenylalanine derivatives have no effect on low-affinity tonic inhibition by lidocaine or its permanently charged derivative QX-314 at any of the substituted sites, high-affinity use-dependent inhibition displays substantial cation-π energetics for 1 residue only: Phe1579 in rNa V 1.4. Replacement of the aromatic ring of Phe1579 by cyclohexane, for example, strongly reduces use-dependent inhibition and speeds recovery of lidocaine-engaged channels. Channel block by the neutral local anesthetic benzocaine is unaffected by the distribution of π electrons at Phe1579, indicating that our aromatic manipulations expose electrostatic contributions to channel inhibition. These results fine tune our understanding of local anesthetic inhibition of voltage-gated sodium channels and will help the design of safer and more salutary therapeutic agents.

The incorporation of unnatural amino acids into proteins is a valuable tool for addition of biophysical probes, bio-orthogonal functionalities, and photoreactive cross-linking agents, although these approaches often require quantities of protein that are difficult to access with chemically aminoacylated tRNAs. THG73 is an amber suppressor tRNA that has been used extensively, incorporating over 100 residues in 20 proteins. In vitro studies have shown that the Escherichia coli Asn amber suppressor (ENAS) suppresses better than THG73. However, we report here that ENAS suppresses with Xenopus oocytes. We then tested the newly developed Tetrahymena thermophila Gln amber suppressor (TQAS) tRNA library, which contains mutations in the second to fourth positions of the acceptor stem. The acceptor stem mutations have no adverse effect on suppression efficiency and, in fact, can increase the suppression efficiency. Combining mutations causes an averaging of suppression efficiency, and increased suppression efficiency does not correlate with increased ΔG of the acceptor stem. We created a T. thermophila opal suppressor, TQOpS′, which shows ∼50% suppression efficiency relative to THG73. The TQAS tRNA library, composed of functional suppressor tRNAs, has been created and will allow for screening in eukaryotic cells, where rapid analysis of large libraries is not feasible.

A novel synthetic route to 1-oxo-5-hydroxytryptamine, the benzofuran analogue of serotonin, has been developed. The new synthesis proceeds via the [3+2] cycloaddition of p-benzoquinone and 2,3-dihydrofuran, followed by a Lewis acid-catalyzed isomerization. This molecule proves to be a competent agonist (equipotent to serotonin) of the 5-HT_3 receptor, demonstrating that the indolic proton of serotonin is not essential to its activation of the receptor.

The cation-pi interaction is a general, strong, noncovalent binding force that is used throughout nature. The side chains of the aromatic amino acids [phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp)] provide a surface of negative electrostatic potential than can bind to a wide range of cations through a predominantly electrostatic interaction. In this brief overview, the fundamental nature of the cation-pi interaction will be described, relying on fundamental, gas phase studies of the effect. Then, several examples of cation-pi interactions involving aromatic amino acids will be described. These include contributions to protein secondary structure, in which Phe/Tyr/Trp...lysine (Lys)/arginine interactions are common. We will also describe several examples of protein-ligand interactions that make use of cation-pi interactions. We will place special emphasis on the binding of quaternary ammonium ions, such as trimethylated Lys and the neurotransmitter acetylcholine.

Voltage-gated sodium channels control the upstroke of the action potential in excitable cells of nerve and muscle tissue, making them ideal targets for exogenous toxins that aim to squelch electrical excitability. One such toxin, tetrodotoxin (TTX), blocks sodium channels with nanomolar affinity only when an aromatic Phe or Tyr residue is present at a specific location in the external vestibule of the ion-conducting pore. To test whether TTX is attracted to Tyr401 of NaV1.4 through a cation-pi interaction, this aromatic residue was replaced with fluorinated derivatives of Phe using in vivo nonsense suppression. Consistent with a cation-pi interaction, increased fluorination of Phe401, which reduces the negative electrostatic potential on the aromatic face, caused a monotonic increase in the inhibitory constant for block. Trifluorination of the aromatic ring decreased TTX affinity by approximately 50-fold, a reduction similar to that caused by replacement with the comparably hydrophobic residue Leu. Furthermore, we show that an energetically equivalent cation-pi interaction underlies both use-dependent and tonic block by TTX. Our results are supported by high level ab initio quantum mechanical calculations applied to a model of TTX binding to benzene. Our analysis suggests that the aromatic side chain faces the permeation pathway where it orients TTX optimally and interacts with permeant ions. These results are the first of their kind to show the incorporation of unnatural amino acids into a voltage-gated sodium channel and demonstrate that a cation-pi interaction is responsible for the obligate nature of an aromatic at this position in TTX-sensitive sodium channels.

The nicotinic acetylcholine receptor and related Cys-loop receptors are ligand-gated ion channels that mediate fast synaptic transmission throughout the central and peripheral nervous system. A highly conserved aspartate residue (D89) that is near the agonist binding site but does not directly contact the ligand plays a critical part in receptor function. Here we probe the role of D89 using unnatural amino acid mutagenesis coupled with electrophysiology. Homology modeling implicates several hydrogen bonds involving D89. We find that no single hydrogen bond is essential to proper receptor function. Apparently, the side chain of D89 establishes a redundant network of hydrogen bonds; these bonds preorganize the agonist binding site by positioning a critical tryptophan residue that directly contacts the ligand. Earlier studies of the D89N mutant led to the proposal that a negative charge at this position is essential for receptor function. However, we find that receptors with neutral side chains at position 89 can function well, if the side chain is less perturbing than the amide of asparagine (nitro or keto groups allow function) or if a compensating backbone mutation is introduced to relieve unfavorable electrostatics.

The similarity to crown ethers is apparent when the arrangement of the oxygen atoms of the carbonyl groups of the protein backbone in the structure of the potassium channel (see schematic drawing of a section of the structure) found in the bacterium Streptomyces lividans is considered. This particular part of the channel pore acts as the selectivity filter, with the permeability of the channel for K+ being as much as 10 000 times greater than for the Na+ ion. In fact, in this area of the structure two K+ ions are located, a feature that enables high flux through the channel.

Thus, most site-directed mutagenesis data render it untenable to consider that two or more roughly equivalent high affinity sites govern selectivity in multi-ion pores. The papers by Dang and McCleskey and Kiss et al. respond to this challenge by showing that a model with a single high affinity site, flanked by two binding sites of lower affinity close to the pore entrances, can generate much of the classical multi-ion behavior. The sites need not interact, and the two flanking sites could arise from one of several mechanisms: a featureless charged vestibule, a dehydration step, or a specific weak binding site. The multi-ion pore remains a cornerstone of permeation theory, but the new theory features only a single high affinity site and no mutual repulsion. The high flux rate occurs because ions pause at the flanking sites and reequilibrate thermally, gaining enough energy to move over the next barrier.

Open-channel blockers such as tetraethylammonium (TEA) have a long history as probes of the permeation pathway of ion channels. High affinity blockade by extracellular TEA requires the presence of an aromatic amino acid at a position that sits at the external entrance of the permeation pathway (residue 449 in the eukaryotic voltage-gated potassium channel Shaker). We investigated whether a cation–π interaction between TEA and such an aromatic residue contributes to TEA block using the in vivo nonsense suppression method to incorporate a series of increasingly fluorinated Phe side chains at position 449. Fluorination, which is known to decrease the cation–π binding ability of an aromatic ring, progressively increased the inhibitory constant Ki for the TEA block of Shaker. A larger increase in Ki was observed when the benzene ring of Phe449 was substituted by nonaromatic cyclohexane. These results support a strong cation–π component to the TEA block. The data provide an empirical basis for choosing between Shaker models that are based on two classes of reported crystal structures for the bacterial channel KcsA, showing residue Tyr82 in orientations either compatible or incompatible with a cation–π mechanism. We propose that the aromatic residue at this position in Shaker is favorably oriented for a cation–π interaction with the permeation pathway. This choice is supported by high level ab initio calculations of the predicted effects of Phe modifications on TEA binding energy.

A silicon wafer with eight individually addressable microfabricated orifices was used for ion channel reconstitution and single-channel recording. A spin-on fluoropolymer created an insulating, hydrophobic interface that was more stable than silane. Total capacitance of the membranes was10 pF, making it easy to evaluate bilayer formation by capacitance change. Orifices of 50-250 microm diameter were tested for ease and stability of bilayer formation; only those100 microm resulted in ion channel function. Bilayers were formed over an agarose supporting layer by application of lipid in decane with a paintbrush; a second layer of agarose could then be added to stabilize the structure and prevent evaporation. Microfluidic wells were constructed on glass plates for ease of assembly and visualization of fluid flow, as well as high-resolution microscopy for studies using fluorescent lipids and channels. The microfluidics consisted of reversibly bonded silicone rubber (PDMS), so that the entire device could be washed and reused. Total electrical noise in the device was low enough to permit single-channel resolution. Successful channel insertions were observed with a self-assembling ionophore (alamethicin) as well as a complex, vesicle-associated mammalian channel (human glycine receptor, GlyR). A "hands-free" approach to bilayer formation was also tested, where lipid in solvent was applied to the wafer by spin-coating, dried, and then "sandwiched" between layers of agarose above and below the nitride. Electrical properties consistent with bilayers were observed and alamethicin recordings were obtained, however this method is not compatible with the fusion of vesicles containing mammalian channels.

A detailed picture of water and ion properties in small pores is important for understanding the behavior of biological ion channels. Several recent modeling studies have shown that small, hydrophobic pores exclude water and ions even if they are physically large enough to accommodate them, a mechanism called hydrophobic gating. This mechanism has been implicated in the gating of several channels, including the mechanosensitive channel of small conductance (MscS). Although the pore in the crystal structure of MscS is wide and was initially hypothesized to be open, it is lined by hydrophobic residues and may represent a nonconducting state. Molecular dynamics simulations were performed on MscS to determine whether or not the structure can conduct ions. Unlike previous simulations of hydrophobic nanopores, electric fields were applied to this system to model the transmembrane potential, which proved to be important. Although simulations without a potential resulted in a dehydrated, occluded pore, the application of a potential increased the hydration of the pore and resulted in current flow through the channel. The calculated channel conductance was in good agreement with experiment. Therefore, it is likely that the MscS crystal structure is closer to a conducting than a nonconducting state.

5-Hydroxytryptamine type 3 (5-HT_3) receptors are members of the Cys-loop receptor superfamily. Neurotransmitter binding in these proteins triggers the opening (gating) of an ion channel by means of an as-yet-uncharacterized conformational change. Here we show that a specific proline (Pro 8*), located at the apex of the loop between the second and third transmembrane helices (M2–M3), can link binding to gating through a cis–trans isomerization of the protein backbone. Using unnatural amino acid mutagenesis, a series of proline analogues with varying preference for the cis conformer was incorporated at the 8* position. Proline analogues that strongly favour the trans conformer produced non-functional channels. Among the functional mutants there was a strong correlation between the intrinsic cis–trans energy gap of the proline analogue and the activation of the channel, suggesting that cis–trans isomerization of this single proline provides the switch that interconverts the open and closed states of the channel. Consistent with this proposal, nuclear magnetic resonance studies on an M2–M3 loop peptide reveal two distinct, structured forms. Our results thus confirm the structure of the M2–M3 loop and the critical role of Pro 8* in the 5-HT_3 receptor. In addition, they suggest that a molecular rearrangement at Pro 8* is the structural mechanism that opens the receptor pore.

In the Cys loop superfamily of ligand-gated ion channels, a global conformational change, initiated by agonist binding, results in channel opening and the passage of ions across the cell membrane. The detailed mechanism of channel gating is a subject that has lent itself to both structural and electrophysiological studies. Here we defined a gating interface that incorporates elements from the ligand binding domain and transmembrane domain previously reported as integral to proper channel gating. An overall analysis of charged residues within the gating interface across the entire superfamily showed a conserved charging pattern, although no specific interacting ion pairs were conserved. We utilized a combination of conventional mutagenesis and the high precision methodology of unnatural amino acid incorporation to study extensively the gating interface of the mouse muscle nicotinic acetylcholine receptor. We found that charge reversal, charge neutralization, and charge introduction at the gating interface are often well tolerated. Furthermore, based on our data and a reexamination of previously reported data on {gamma}-aminobutyric acid, type A, and glycine receptors, we concluded that the overall charging pattern of the gating interface, and not any specific pairwise electrostatic interactions, controls the gating process in the Cys loop superfamily.

GABA(C) (rho) receptors are members of the Cys-loop superfamily of neurotransmitter receptors, which includes nicotinic acetylcholine (nACh), 5-HT(3), and glycine receptors. As in other members of this family, the agonist binding site of GABA(C) receptors is rich in aromatic amino acids, but while other receptors bind agonist through a cation-pi interaction to a tryptophan, the GABA(C) binding site has tyrosine at the aligning positions. Incorporating a series of tyrosine derivatives at position 198 using unnatural amino acid mutagenesis reveals a clear correlation between the cation-pi binding ability of the side chain and EC(50) for receptor activation, thus demonstrating a cation-pi interaction between a tyrosine side chain and a neurotransmitter. Comparisons among four homologous receptors show variations in cation-pi binding energies that reflect the nature of the cationic center of the agonist.

New hypotheses and predictions have arisen from recent work revealing atomic-scale or near-atomic-scale structures of receptors in the 'Cys-loop' superfamily. How general is the cation-pi interaction between the natural ligand and a tryptophan residue in the aromatic box, and does this interaction extend to other ligands? What is the pathway from the binding site to gating, and what are the conformational changes during gating and desensitization? Is current flow through intracellular 'portals' in the wall of the channel a general feature? This article discusses these and related questions, emphasizing nicotinic ACh receptors and also discussing data from other members of this superfamily.

Total chemical protein synthesis was used to generate multimilligram quantities of the mechanosensitive channel of large conductance from Escherichia coli (Ec-MscL) and Mycobacterium tuberculosis (Tb-MscL). Cysteine residues introduced to allow chemical ligation were masked with cysteine-reactive molecules, resulting in side chain functional groups similar to those of the wild-type protein. Synthetic channel proteins were transferred to 2,2,2-trifluoroethanol and reconstituted into vesicle membranes. Fluorescent imaging of vesicles showed that channel proteins were membrane-localized. Single-channel recordings showed that reconstituted synthetic Ec-MscL has conductance, pressure dependence, and substate distribution similar to those of the recombinant channel. Reconstituted synthetic Tb-MscL also displayed conductance and pressure dependence similar to that of the recombinant protein. Possibilities for the incorporation of unnatural amino acids and biophysical probes, and applications of such synthetic ion channel analogs, are discussed.

We characterized the differential accessibility of the nicotinic acetylcholine receptor alpha1 subunit in the open, closed, and desensitized states by using electrophysiology-coordinated photolabeling by several lipophilic probes followed by mass spectrometric analysis. Voltage-clamped oocytes expressing receptors were preincubated with one of the lipophilic probes and were continually exposed to acetylcholine; UV irradiation was applied during 500-ms pulses to + 40 or to -140 mV (which produced closed or approximately 50% open receptors, respectively). In the open state, there was specific probe incorporation within the N-terminal domain at residues that align with the beta8-beta9 loop of the acetylcholine-binding protein. In the closed state, probe incorporation was identified at several sites of the N-terminal domain within the conserved cysteine loop (residues 128-142), the cytoplasmic loop (M3-M4), and M4. The labeling pattern in the M4 region is consistent with previous results, further defining the lipid-exposed face of this transmembrane alpha-helix. These results show regions within the N-terminal domain that are involved in gating-dependent conformational shifts, confirm that the cysteine loop resides at or near the protein-membrane interface, and show that segments of the M3-M4 loop are near to the lipid bilayer.

Using unnatural amino acid mutagenesis, the binding site for serotonin at the novel Caenorhabditis elegans receptor MOD-1 has been probed. As with the closely related serotonin receptor 5-HT_3, MOD-1 makes use of a strong cation−π interaction between the ammonium of serotonin and the indole side chain of a tryptophan. However, the specific Trp used by MOD-1 is different from that used for 5-HT_3 (and the nAChR), aligning with a residue more than 40 amino acids distant in sequence space and on a different “loop” of the agonist binding site. This suggests a significant rearrangement of the ligand on binding these two closely related receptors. It is suggested that, unlike enzymes, receptors and other signaling molecules may need only to deliver an agonist to a general binding region, rather than establishing precise drug−receptor interactions.

Random mutagenesis of the mechanosensitive channel of large conductance (MscL) from Escherichia coli coupled with a high-throughput functional screen has provided new insights into channel structure and function. Complementary interactions of conserved residues proposed in a computational model for gating have been evaluated, and important functional regions of the channel have been identified. Mutational analysis shows that the proposed S1 helix, despite having several highly conserved residues, can be heavily mutated without significantly altering channel function. The pattern of mutations that make MscL more difficult to gate suggests that MscL senses tension with residues located near the lipid headgroups of the bilayer. The range of phenotypical changes seen has implications for a proposed model for the evolutionary origin of mechanosensitive channels.

The caging of specific residues of proteins is a powerful tool. This discussion attempts to alert the reader to the considerations that must be made in preparing and analyzing a caged protein through nonsense suppression. Although the suppression methodology is conceptually straightforward, it not possible to provide a failsafe "cook book" method for using caged unnaturals. We have emphasized the preparation of caged receptors expressed in Xenopus oocytes, but these approaches can clearly be adapted to many other systems.

The caging of specific residues of proteins is a powerful tool. This discussion attempts to alert the reader to the considerations that must be made in preparing and analyzing a caged protein through nonsense suppression. Although the suppression methodology is conceptually straightforward, it not possible to provide a failsafe “cook book” method for using caged unnaturals. We have emphasized the preparation of caged receptors expressed in Xenopus oocytes, but these approaches can clearly be adapted to many other systems.

A series of tryptophan analogues has been introduced into the binding site regions of two ion channels, the ligand-gated nicotinic acetylcholine and serotonin 5-HT(3A) receptors, using unnatural amino acid mutagenesis and heterologous expression in Xenopus oocytes. A cation-pi interaction between serotonin and Trp183 of the serotonin channel 5-HT(3A)R is identified for the first time, precisely locating the ligand-binding site of this receptor. The energetic contribution of the observed cation-pi interaction between a tryptophan and the primary ammonium ion of serotonin is estimated to be approximately 4 kcal/mol, while the comparable interaction with the quaternary ammonium of acetylcholine is approximately 2 kcal/mol. The binding mode of nicotine to the nicotinic receptor of mouse muscle is examined by the same technique and found to differ significantly from that of the natural agonist, acetylcholine.

A combination of computational methods has been used to evaluate the interaction between the pi face of a benzene molecule and the monovalent cations of lithium, sodium, potassium, and rubidium. In the gas phase, the ions are strongly bound, and the affinity for benzene follows the expected electrostatic trend (lithium, largest; rubidium, smallest). However, in an aqueous environment, a reordering occurs such that the potassium ion is preferred over all the other ions for 2:1 benzene:ion complexes. The selectivity sequence parallels that seen in voltage-gated potassium channels. Given that several conserved aromatic residues are present in the pore region of such channels, these results suggest that the cation-pi interaction may be responsible for the ion selectivity in potassium channels.

A novel fluorescence-based screen for bacterial mechanosensitive ion-channel activity has been developed. This assay is capable of clearly distinguishing the previously observed gain of function and loss of function phenotypes for the Escherichia coli mechanosensitive channel of large conductance (Ec-MscL). The method modifies Molecular Probes’ Live/Dead® BacLight™ bacterial viability assay to monitor MscL channel activity as a function of bacterial survival from osmotic downshock.

The nonsense codon suppression technique was used to incorporate o-nitrobenzyl cysteine or o-nitrobenzyl tyrosine (caged Cys or Tyr) into the 9' position of the M2 transmembrane segment of the gamma-subunit of the muscle nicotinic ACh receptor expressed in Xenopus oocytes. The caged amino acids replaced an endogenous Leu residue that has been implicated in channel gating. ACh-induced current increased substantially after ultraviolet (UV) irradiation to remove the caging group. This represents the first successful incorporation of caged Cys into a protein in vivo and the first incorporation of caged amino acids within a transmembrane segment of a membrane protein. The bulky nitrobenzyl group does not prevent the synthesis, assembly, or trafficking of the ACh receptor. When side chains were decaged using 1-ms UV light flashes, the channels with caged Cys or caged Tyr responded with strikingly different kinetics. The increase in current upon photolysis of caged Cys was too rapid for resolution by the voltage-clamp circuit [time constant (tau)10 ms], whereas the increase in current upon photolysis of caged Tyr was dominated by a phase with tau approximately 500 ms. Apparently, the presence of a bulky o-nitrobenzyl Tyr residue distorts the receptor into an abnormal conformation. Upon release of the caging group, the receptor relaxes, with tau approximately 500 ms, into a conformation that allows the channel to open. Tyr at the 9' position of the gamma-subunit greatly increases the ability of ACh to block the channel by binding within the channel pore. This is manifested in two ways. 1) A "rebound," or increase in current, occurs upon removal of ACh from the bathing medium; and 2) at ACh concentrations400 microM, inward currents are decreased through the mutated channel. The ability to incorporate caged amino acids into proteins should have widespread utility.

The integral membrane proteins of neurons and other excitable cells are generally resistant to high-resolution structural tools. In this thesis we present our efforts to probe the structure of the agonist-binding site of the nicotinic acetylcholine receptor (nAChR) using the tethered agonist approach, which combines chemical synthesis, the nonsense suppression methodology for unnatural amino acid incorporation and electrophysiology. In Chapter 2, we present the results of incorporating a series of tethered quaternary ammonium derivatives of tyrosine into the nAChR using the in vivo nonsense suppression methodology for incorporating unnatural amino acids site-specifically. At three sites, a constitutively active receptor results, but the pattern of activation as a function of chain length is different. At position alpha149, there is a clear preference for a three-carbon tether, while at position alpha93 tethers of 2-5 carbons are comparably effective. At position gamma55/delta57, all tethers except the shortest one can activate the receptor. Based on these and other data, a model for the binding site of the receptor can be developed by analogy to the acetylcholine esterase crystal structure. In Chapter 3, we report evidence that the N-terminal extracellular domain of nAChR is closely related to acetylcholine binding protein (AChBP), whose crystal structure was solved in May 2001. Based on the model obtained from docking acetylcholine into the structure of AChBP, we designed and incorporated a new tethered agonist, lysyl-carbamylcholine. Incorporation of this tethered agonist at several positions produced constitutively active receptors, with significant activity seen at alpha192, alpha193, and gamma119/delta121. These results demonstrated that the loop E residue gamma119/delta121 on the complementary subunit is very near the agonist-binding site. We also investigated the role of an intersubunit hydrogen bond, which was seen in the crystal structure of AChBP. Incorporation of tryptophan analogs that abolish the hydrogen bonding abilities slowed the desensitization of the receptor, which implied that this hydrogen bond might play a key role in the allosteric transitions of desensitization. In Chapter 4, we describe our efforts to prepare a short tethered agonist and the results of incorporating it into nAChR at alpha198 by chemical modification of cysteine mutants introduced by nonsense suppression methodology. Methanethiosulphonate ethyltrimethylammonium (MTSET) modification resulted in constitutive activity, which suggested the closeness of alpha198 to the agonist-binding site. In Chapter 5, methods in molecular biology, electrophysiology and molecular docking, and the synthesis of amino acids and dinucleotide dCA-amino acids are summarized.