Biomedical subjects

Sarah C R Lummis

Publications and source records attributed to Sarah C R Lummis.

At least 19 recordsLinked to original sources

PubMed2006

Exploring the binding of serotonin to the 5-HT3 receptor by density functional theory.

The 5-HT3 receptor is a typical ligand-gated ion channel of the Cys-loop superfamily, which is activated by binding of serotonin (5-HT). Models of the binding site of this protein reveal potential interactions between 5-HT and Tyr143, Tyr153, and Tyr234. Here we describe a series of ab initio calculations, based on density functional theory, to assess the effects of mutating these tyrosine residues on the binding of 5-HT. A series of mutations to these tyrosines, previously studied experimentally, were tested, and the binding energies compared with the available experimental data. Our results show that Tyr153 could form a hydrogen bond with the tertiary amine of 5-HT, and that mutation in this location revealed binding energies broadly in line with experimentally determined EC50s. Tyr143 could also form a hydrogen bond, but as EC50s do not relate to binding energies, it is unlikely that such a bond is formed here. Tyr234 is quite distinct in that it may interact with 5-HT via a mixed hydrogen bond/cation-pi interaction.

Amino Acid Substitution↗

PubMed2006

Locating the carboxylate group of GABA in the homomeric rho GABA(A) receptor ligand-binding pocket.

gamma-Aminobutyric acid, type A (GABA(A)) receptors, of which the GABA(C) receptor family is a subgroup, are members of the Cys loop family of neurotransmitter receptors. Homology modeling of the extracellular domain of these proteins has revealed many molecular details, but it is not yet clear how GABA is orientated in the binding pocket. Here we have examined the role of arginine residues that the homology model locates in or close to the binding site of the GABA(C) receptor (Arg-104, Arg-170, Arg-158, and Arg-249) using mutagenesis and functional studies. The data suggest that Arg-158 is critical for GABA binding and/or function; substitution with Lys, Ala, or Glu resulted in nonfunctional receptors, and modeling placed the carboxylate of GABA within 3A of this residue. Substitution of Arg-104 with Ala or Glu resulted in >10,000-fold increases in EC(50) values compared with wild type receptors, and modeling indicated a role of this residue both in binding GABA and in the structure of the binding pocket. Substitution of Arg-170 with Asp or Ala yielded nonfunctional receptors, whereas Lys caused an approximately 10-fold increase in EC(50). Arg-249 was substituted with Ala, Glu, or Asp with relatively small ( approximately 4-30-fold) changes in EC(50). These and data from other residues that the model suggested could interact with GABA (His-105, Ser-168, and Ser-243) support a location for GABA in the binding site with its carboxylate pincered between Arg-158 and Arg-104, with Arg-104, Arg-170, and Arg-249 contributing to the structure of the binding pocket through salt bridges and/or hydrogen bonds.

Amino Acid Sequence↗

PubMed2006

Mutagenesis and molecular modeling reveal the importance of the 5-HT3 receptor F-loop.

The 5-HT(3) receptor is a member of the Cys-loop family of ligand-gated ion channels. The extracellular domains of these proteins contain six amino acid loops (A-F) that converge to form the ligand binding site. In this study we have mutated 21 residues in or close to the 5-HT(3) receptor F-loop (Ile(192) to Gly(212)) to Ala or to a residue with similar chemical properties. Mutant receptors were expressed in HEK293 cells, and binding affinity was measured using [(3)H]granisetron. Two regions displayed decreases in binding affinity when mutated to Ala (Ile(192)-Arg(196) and Asp(204)-Ser(206)), but only one region was sensitive when mutated to chemically similar residues (Ile(192)-Val(201)). Homology modeling using acetylcholine-binding protein crystal structures with a variety of different bound ligands suggests there may be distinct movements of Trp(195) and Asp(204) upon ligand binding, indicating that these residues and their immediate neighbors have the ability to interact differently with different ligands. The models suggest predominantly lateral movement around Asp(204) and rotational movement around Trp(195), indicating the former is in a more flexible region. Overall our results are consistent with a flexible 5-HT(3) receptor F-loop with two regions that have specific but distinct roles in ligand binding.

Alanine↗

PubMed2006

Detection of human and rodent 5-HT3B receptor subunits by anti-peptide polyclonal antibodies.

BACKGROUND: The 5-HT3 receptor is a member of a neurotransmitter-gated ion channel family which includes nicotinic acetylcholine, GABAA, and glycine receptors. While antibodies specific for the 5-HT3A receptor subunit are plentiful, and have revealed a wealth of structural and functional information, few antisera exist for the detection of 5-HT3B receptor subunits. Here we describe the generation and characterisation of a rabbit polyclonal antiserum that specifically recognises 5-HT3B receptor subunits RESULTS: Immunization of a rabbit with a 20-mer peptide, corresponding to the N-terminus of the human 5-HT3B receptor subunit, generated serum with polyclonal antibodies from which an IgG fraction was purified, yielding pAb77. The antibodies were shown to label 5-HT3B receptor subunits in transfected human embryonic kidney cells and rodent tissues using Western blots. Immunocytochemistry using pAb77 on these cells showed that 5-HT3B receptor subunits do not reach the plasma membrane in the absence of 5-HT3A receptor subunits. Immunohistochemical analysis of rat brain sections showed pAb77 immunoreactivity in distinct populations of cells in the hippocampus. CONCLUSION: We have demonstrated that pAb77 antibodies specifically label native and recombinant 5-HT3B receptor subunits with high affinity and specificity. The antibody was shown to be useful for the determination of both receptor trafficking and also mapping 5-HT3B receptor subunit expression in the CNS.

Animals↗

PubMed2005

Cis-trans isomerization at a proline opens the pore of a neurotransmitter-gated ion channel.

5-hydroxytryptamine type 3 (5-HT3) 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-HT3 receptor. In addition, they suggest that a molecular rearrangement at Pro 8* is the structural mechanism that opens the receptor pore.

Animals↗

PubMed2005

Molecular modeling of the GABA(C) receptor ligand-binding domain.

We have constructed a molecular model of the ligand-binding domain of the GABA(C) receptor, which is a member of the Cys-loop ligand-gated ion channel family. The extracellular domains of these receptors share similar sequence homology (20%) with Limnaea acetylcholine-binding protein for which an X-ray crystal structure is available. We used this structure as a template for homology modeling of the GABA(C) receptor extracellular domain using FUGUE and MODELLER software. FlexX was then used to dock GABA into the receptor ligand-binding site, resulting in three alternative energetically favorable orientations. Residues located no more than 5 A from the docked GABA were identified for each model; of these, three were found to be common to all models with 14 others present only in certain models. Using data from experimental studies, we propose that the most likely orientation of GABA is with its amine close to Y198, and its carboxylate close to R104. These studies have therefore provided a model of the ligand-binding domain, which will be useful for both GABA(C) and GABA(A) receptor studies, and have also yielded an experimentally testable hypothesis of the location of GABA in the binding pocket. [Figure: see text].

Amino Acid Sequence↗

PubMed2005

FlexStation examination of 5-HT3 receptor function using Ca2+ - and membrane potential-sensitive dyes: advantages and potential problems.

The FlexStation is a 96 or 384 fluorescent plate reader with the capability of adding solutions during readings; it therefore has the potential to provide high throughput analyses of the functional characteristics of neurotransmitter-gated ion channels that can be examined using changes in fluorescence. The 5-HT3 receptor is one such protein, as its activation results in a change in membrane potential due to the opening of a Ca2+ -permeant, cation-selective channel; it can therefore be studied using both Ca2+ - and membrane potential-sensitive fluorescent dyes. Here we have used the FlexStation to examine the function of recombinant 5-HT3 receptors expressed in HEK293 cells using both these classes of dye. The results show that the pharmacological characteristics of the receptor obtained using the FlexStation is similar to those reported using other functional methods, although caution must be applied when using the membrane potential dye as large changes in membrane potential can yield inaccurate EC50s. Modifying the constituents of the buffer, however, so that the change in membrane potential was reduced, yielded EC50 values that were similar to previously reported data. We conclude that the FlexStation is a useful tool for high throughput studies when examining the function of neurotransmitter receptors that result in either a change in Ca2+ concentration or membrane potential.

Calcium↗

PubMed2005

Locating an antagonist in the 5-HT3 receptor binding site using modeling and radioligand binding.

We have used a homology model of the extracellular domain of the 5-HT(3) receptor to dock granisetron, a 5-HT(3) receptor antagonist, into the binding site using AUTODOCK. This yielded 13 alternative energetically favorable models. The models fell into 3 groups. In model type A the aromatic rings of granisetron were between Trp-90 and Phe-226 and its azabicyclic ring was between Trp-183 and Tyr-234, in model type B this orientation was reversed, and in model type C the aromatic rings were between Asp-229 and Ser-200 and the azabicyclic ring was between Phe-226 and Asn-128. Residues located no more than 5 A from the docked granisetron were identified for each model; of 26 residues identified, 8 were found to be common to all models, with 18 others being represented in only a subset of the models. To identify which of the docking models best represents the ligand-receptor complex, we substituted each of these 26 residues with alanine and a residue with similar chemical properties. The mutant receptors were expressed in human embryonic kidney (HEK)293 cells and the affinity of granisetron determined using radioligand binding. Mutation of 2 residues (Trp-183 and Glu-129) ablated binding, whereas mutation of 14 other residues caused changes in the [(3)H]granisetron binding affinity in one or both mutant receptors. The data showed that residues both in and close to the binding pocket can affect antagonist binding and overall were found to best support model B.

Amino Acid Sequence↗

PubMed2005

Rapid functional assays of recombinant IP3 receptors.

Functional assays of inositol 1,4,5-trisphosphate receptors (IP3R) currently use 45Ca2+ release methods, fluorescent Ca2+ indicators within either the ER or cytosol, or electrophysiological analyses of IP3R in the nuclear envelope or artificial bilayers. None of the methods is presently amenable to the rapid, high-throughput quantitative analyses of IP3R function needed to address the structural determinants of IP3R behavior. We use a low-affinity Ca2+ indicator (Mag-fluo-4) to measure free [Ca2+] within the ER of permeabilized DT40 cells expressing only rat type 1 IP(3)R, and establish that the indicator is capable of reliably reporting the Ca(2+) release evoked by IP3. A 96-well fluorescence plate reader equipped for automated fluid additions (FlexStation, Molecular Devices) is used to monitor IP3-evoked Ca2+ release. The method allows quick and economical functional assays of recombinant IP3R in small volumes (< or = 100 microl).

Animals↗

PubMed2005

A cation-pi binding interaction with a tyrosine in the binding site of the GABAC receptor.

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.

Amino Acid Substitution↗

PubMed2004

Tyrosine residues that control binding and gating in the 5-hydroxytryptamine3 receptor revealed by unnatural amino acid mutagenesis.

The mechanism by which agonist binding triggers pore opening in ligand-gated ion channels is poorly understood. Here, we used unnatural amino acid mutagenesis to introduce subtle changes to the side chains of tyrosine residues (Tyr141, Tyr143, Tyr153, and Tyr234), which dominate the 5-HT3 receptor binding site. Heterologous expression in oocytes, combined with radioligand binding data and a model of 5-HT (serotonin) computationally docked into the binding site, has allowed us to determine which of these residues are responsible for binding and/or gating. We have shown that Tyr 143 forms a hydrogen bond that is essential for receptor gating but does not affect binding, whereas a hydrogen bond formed by Tyr153 is involved in both binding and gating of the receptor. The aromatic group of Tyr234 is essential for binding and gating, whereas its hydroxyl does not affect binding but plays a steric role in receptor gating. Tyr141 is not involved in agonist binding or receptor gating but is important for antagonist interactions. These data, combined with a new model of the nonliganded 5-HT3 receptor, lead to a mechanistic explanation of the interactions that initiate the conformational change leading to channel opening. Thus, we suggest that agonist entry into the binding pocket may displace Tyr143 and Tyr153 and results in their forming new hydrogen bonds. These bonds may form part of the network of bond rearrangements that trigger the conformational change leading to channel opening. Similar rearrangements may initiate gating in all Cys-loop receptors.

Amino Acids↗

PubMed2004

The role of tyrosine residues in the extracellular domain of the 5-hydroxytryptamine3 receptor.

Aromatic residues play an important role in the ligand-binding domain of Cys loop receptors. Here we examine the role of the 11 tyrosines in this domain of the 5-HT3 receptor in ligand binding and receptor function by substituting them for alanine, for serine, and, for some residues, also for phenylalanine. The mutant receptors were expressed in HEK293 cells and Xenopus oocytes and examined using radioligand binding, Ca2+ imaging, electrophysiology, and immunochemistry. The data suggest that Tyr50 and Tyr91 are critical for receptor assembly and/or structure, Tyr141 is important for antagonist binding and/or the structure of the binding pocket, Tyr143 plays a critical role in receptor gating and/or agonist binding, and Tyr153 and Tyr234 are involved in ligand binding and/or receptor gating. Tyr73, Tyr88, Tyr94, Tyr167, and Tyr240 do not appear to play major roles either in the structure of the extracellular domain or in ligand binding. The data support the location of these residues on a model of 5-HT docked into the ligand-binding domain and also provide evidence for the structural similarity of the extracellular domain to AChBP and the homologous regions of other Cys loop ligand-gated ion channels.

Amino Acid Sequence↗

PubMed2004

Biolistic and diolistic transfection: using the gene gun to deliver DNA and lipophilic dyes into mammalian cells.

Delivery of genes by firing them into mammalian cells is becoming increasingly popular for cells such as neurones, that have proved difficult to transfect by conventional means. In addition it is becoming apparent that this technique also provides a suitable method of introducing cell-specific dyes into mammalian tissues. Here we describe improved protocols for the rapid and efficient delivery of both DNA and lipophilic dyes into mammalian cells in both monolayers and in brain slices. The results show that transfection of genes, such as that for enhanced yellow fluorescent protein, using a modified microcarrier preparation technique combined with either a conventional or novel accelerator channel, yields rapid and efficient production of protein, which can be visualised in 24-48 h. Following similar delivery of lipophilic dyes neurones can be visualised in minutes. These techniques therefore provide an excellent means not only to examine the structure and function of neurones and neuronal genes, but also those of other cell types.

Bacterial Proteins↗

PubMed2003

A single ring of charged amino acids at one end of the pore can control ion selectivity in the 5-HT3 receptor.

1. To determine the mechanisms by which cation- or anion-specific channels select between these ions, we have examined the role of electrostatic factors in a typical ligand-gated ion channel, the 5-hydroxytryptamine3 (5-HT3) receptor, by removal and/or insertion of rings of conserved charged residues at either end of the pore. 2. Neutralization of the negatively charged ring at the intracellular end of the channel (E-1'A) results in a nonselective channel (PNa/PCl=0.89). 3. Insertion of positively charged residues at the extracellular end of the pore either results in a nonfunctional receptor (A24'K) or one that remains cation-selective (PNa/PCl=110; S19'R). 4. Combining the removal of a negatively charged ring (E-1'A) with the insertion of a positively charged ring (S19'R), however, results in a channel that is predominantly anion-selective (PNa/PCl=0.37). 5. The data suggest that for the cation-selective 5-HT3 receptor, the control of selectivity exerted by charged rings at either end of the pore is dominated by the ring of negatively charged residues at the intracellular side of the channel. As changing the charge at this position has also been shown to change ionic selectivity in anion-selective receptors, these data suggest that electrostatic factors can control selectivity in the whole Cys-loop family.

Amino Acid Sequence↗

PubMed2003

Prediction of 5-HT3 receptor agonist-binding residues using homology modeling.

5-HT(3) receptors demonstrate significant structural and functional homology to other members of the Cys-loop ligand-gated ion channel superfamily. The extracellular domains of these receptors share similar sequence homology (approximately 20%) with Limnaea acetylcholine binding protein, for which an x-ray crystal structure is available. We used this structure as a template for computer-based homology modeling of the 5-HT(3) receptor extracellular domain. AutoDock software was used to dock 5-HT into the putative 5-HT(3) receptor ligand-binding site, resulting in seven alternative energetically favorable models. Residues located no more than 5 A from the docked 5-HT were identified for each model; of these, 12 were found to be common to all seven models with five others present in only certain models. Some docking models reflected the cation-pi interaction previously demonstrated for W183, and data from these and other studies were used to define our preferred models.

Amino Acid Sequence↗

PubMed2002

Mutation of the GABAA receptor M1 transmembrane proline increases GABA affinity and reduces barbiturate enhancement.

All GABA(A) receptor (GABAR) subunits include an invariant proline in a consensus motif in the first transmembrane segment (M1). In receptors containing bovine alpha1, beta1 and gamma2 subunits, we analyzed the effect of mutating this M1 proline to alanine in the alpha1 or beta1 subunit using 3 different expression systems. The beta1 subunit mutant, beta1(P228A), reduced the EC(50) for GABA about 10-fold in whole cell recordings in HEK293 cells and L929 fibroblasts. The corresponding alpha1 subunit mutant (alpha1(P233A)) also reduced the GABA EC(50) when expressed in Xenopus oocytes; alpha1(P233A)beta1gamma2S receptors failed to assemble in HEK293 cells. Binding of [(3)H]flumazenil and [(3)H]muscimol to transfected HEK293 cell membranes showed similar levels of receptor expression with GABARs containing beta1 or beta1(P228A) subunits and no change in the affinity for [(3)H]flumazenil; however, the affinity for [(3)H]muscimol was increased 6-fold in GABARs containing beta1(P228A) subunits. In L929 cells, presence of the beta1(P228A) subunit reduced enhancement by barbiturates without affecting enhancement by diazepam or alfaxalone. Single channel recordings from alpha1beta1gamma2S and alpha1beta1(P228A)gamma2L GABARs showed similar channel kinetics, but beta-mutant containing receptors opened at lower GABA concentrations. We conclude that the beta1 subunit M1 segment proline affects the linkage between GABA binding and channel gating and is critical for barbiturate enhancement. Mutation of the M1 proline in the alpha1 subunit also inhibited receptor assembly.

Animals↗

PubMed2002

Identification of a new site in the S1 ligand binding region of the NMDA receptor NR2A subunit involved in receptor activation by glutamate.

Activation of N-methyl-d-aspartate (NMDA) receptors requires the binding of both glutamate and glycine to independent sites on the receptor. These ligands bind to NR2 and NR1 subunits respectively. Ligand binding residues are located in two non-contiguous domains, S1 and S2, which have been implicated in glutamate binding in other ionotropic glutamate receptor subunits. To further define the amino acids through which glutamate activates the receptor, we generated single-site mutations to the NR2A subunit, and expressed them with wild type NR1 in HEK 293 cells. Using calcium imaging and whole cell patch clamp we determined glutamate and glycine potencies. Of the eight residues mutated we identified five (E413, K484, A508, G685 and G688), whose mutation leads to a large reduction (from 4- to 1000-fold) in glutamate potency, consistent with a role for these residues in receptor activation by glutamate. The potency of glycine was largely unchanged by these mutations. Thus our results extend the knowledge base of residues involved in NMDA receptor function and identifies a new site in S1, in the region of A508, that has a role in receptor activation by glutamate.

Amino Acid Sequence↗

PubMed2002

An improved method of preparing microcarriers for biolistic transfection.

The hand-held gene gun uses a pulse of helium to fire small gold particles coated with desiccated DNA (microcarriers) at target cells. This method of biolistic transfection is becoming increasingly popular as an effective means of rapid gene delivery into mammalian tissue. Current methods of microcarrier preparation, however, are slow (up to 2 days) and can result in variations in transfection efficiency due to a number of problems including shearing of DNA, agglomeration and adhesion of gold particles. Here we describe an improved, more rapid method of microcarrier preparation. To evaluate the new procedure we have used DNA encoding yellow fluorescent protein (EYFP), a modified version of the green fluorescent protein, which we have transfected into HEK293 cells. The data show that transfection by the new method results in high levels of transfection efficiency and low variability compared to an alternative method.

Bacterial Proteins↗