Biology subjects

Gouaux, E.

Publications and source records attributed to Gouaux, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Programmable gold nanoparticle conjugates enable precise AMPA receptor localization at brain synapses by cryo-ET

Cryo-electron tomography (cryo-ET) is a powerful approach to image cells, organelles, viruses and molecular assemblies. However, resolving smaller complexes and molecules is challenging and presents a roadblock to the broad application of cryo-ET. Gold nanoparticles (AuNPs) have been used to localize otherwise unidentifiable molecules and complexes in tomograms but are typically tethered to the target of interest via a flexible linker. As a result, the position of the AuNP does not directly define the location of the target. Here we attach AuNPs to Fab antibody fragments via cysteine residues on defined elements of secondary structure and show that the AuNPs are rigidly bound to the Fab. We use these Fab-AuNP conjugates to locate AMPA receptors and probe their conformation upon desensitization with sub nanometer resolution in tomograms derived from brain slice lamella. By harnessing small, homogeneous AuNPs with precise conjugation to a Fab, we have developed reagents that enable direct investigation of conformational states of previously unidentifiable biomolecules and complexes in tomograms.

biochemistry↗

bioRxiv2026

AMPAR immunization induces progressive autoimmune encephalitis with autoreactive B cells in the brain

AMPA and NMDA receptors are central to synaptic plasticity and cognitive function. In anti-NMDA receptor and anti-AMPA receptor (AMPAR) encephalitis, autoantibodies targeting these receptors disrupt synaptic signaling, leading to severe neuropsychiatric symptoms. However, the cellular autoimmune responses and source of pathogenic autoantibodies during onset and progression of central nervous system (CNS) pathology remain poorly understood. By immunizing mice with intact AMPARs in proteoliposomes, we developed a mouse model of anti-AMPAR encephalitis. Mice developed rapidly progressing neuropsychiatric deficits, autoantibodies targeting the AMPAR amino-terminal domain (ATD) and IgG deposition in the brain, accompanied by reduced AMPAR detection. Throughout disease onset and progression, AMPAR-ATD-specific non-proliferating plasma cells and plasmablasts accumulated in the brain and were predominantly localized in AMPAR-expressing brain parenchyma. In contrast, differentiated AMPAR-ATD specific B cells were far less enriched in peripheral lymphoid tissues. Our results suggest that humoral autoimmune responses directly in the CNS drives disease progression in anti-AMPAR encephalitis.

neuroscience↗

bioRxiv2026

Native architecture, allosteric modulation and gating mechanism of glycine-dependent NMDA receptors

N-methyl-D-aspartate receptors (NMDARs) mediate excitatory signaling essential for synaptic plasticity and memory. Unlike GluN2-containing NMDARs, GluN3-containing receptors are activated solely by glycine, exhibit profound desensitization and paradoxical potentiation by GluN1-selective antagonists, including CGP-78608 (CGP). Although GluN3 NMDARs regulate synapse pruning, excitotoxicity, and are associated with schizophrenia, autism and stroke, their native stoichiometry and gating mechanism poorly defined. Using single-molecule pulldown analysis, we show that native GluN3A receptors are diheteromeric assemblies. Cryo-EM analysis of GluN1/GluN3A receptors in antagonist-bound, pre-active, active, and desensitized states, augmented by electrophysiology and pharmacology experiments, show how glycine activates the receptor solely via GluN3A-dependent conformational changes, opening the gate with [~]2-fold symmetry, and induces a [~]4-fold symmetric desensitized state. CGP-bound GluN1 restricts GluN3A rotation, promoting glycine-induced activation by blocking desensitization. These findings illuminate how CGP potentiates GluN3A receptor activity, place the receptor gating mechanism on a solid structural foundation, and define the molecular basis for pharmacological modulation.

neuroscience↗

bioRxiv2025

The bile acid-sensitive ion channel is gated by Ca2+-dependent conformational changes in the transmembrane domain

The bile acid-sensitive ion channel (BASIC) is the least understood member of the mammalian epithelial Na+ channel/degenerin (ENaC/DEG) superfamily of ion channels, which are involved in a variety of physiological processes. While some members of this superfamily, including BASIC, are inhibited by extracellular Ca2+ (Ca2+), the molecular mechanism underlying Ca2+ modulation remains unclear. Here, by determining the structure of human BASIC in the presence and absence of Ca2+ using single particle cryo-electron microscopy (cryo-EM), we reveal Ca2+-dependent conformational changes in the transmembrane domain and {beta}-linkers. Electrophysiological experiments further show that a glutamate residue in the extracellular vestibule of the pore underpins the Ca2+-binding site, whose occupancy determines the conformation of the pore and therefore ion flow through the channel. These results reveal the molecular principles governing gating of BASIC and its regulation by Ca2+ ions, demonstrating that Ca2+ ions modulate BASIC function via changes in protein conformation rather than solely from pore-block, as proposed for other members of this superfamily.

biochemistry↗

bioRxiv2024

Cryo-electron tomographic investigation of native hippocampal glutamatergic synapses

Chemical synapses are the major sites of communication between neurons in the nervous system and mediate either excitatory or inhibitory signaling [1]. At excitatory synapses, glutamate is the primary neurotransmitter and upon release from presynaptic vesicles, is detected by postsynaptic glutamate receptors, which include ionotropic AMPA and NMDA receptors [2, 3]. Here we have developed methods to identify glutamatergic synapses in brain tissue slices, label AMPA receptors with small gold nanoparticles (AuNPs), and prepare lamella for cryo-electron tomography studies. The targeted imaging of glutamatergic synapses in the lamella is facilitated by fluorescent pre- and postsynaptic signatures, and the subsequent tomograms allow for identification of key features of chemical synapses, including synaptic vesicles, the synaptic cleft and AuNP-labeled AMPA receptors. These methods pave the way for imaging brain regions at high resolution, using unstained, unfixed samples preserved under near-native conditions.

biochemistry↗

bioRxiv2023

Single molecule studies of the native hair cell mechanosensory transduction complex

Hearing and balance rely on the conversion of a mechanical stimulus into an electrical signal, a process known as mechanosensory transduction (MT). In vertebrates, this process is accomplished by an MT complex that is located in hair cells of the inner ear. While the past three decades of research have identified many subunits that are important for MT and revealed interactions between these subunits, the composition and organization of a functional complex remains unknown. The major challenge associated with studying the MT complex is its extremely low abundance in hair cells; current estimates of MT complex quantity range from 3-60 attomoles per cochlea or utricle, well below the detection limit of most biochemical assays that are used to characterize macromolecular complexes. Here we describe the optimization of two single molecule assays, single molecule pull-down (SiMPull) and single molecule array (SiMoA), to study the composition and quantity of native mouse MT complexes. We demonstrate that these assays are capable of detecting and quantifying low attomoles of the native MT subunits protocadherin-15 (PCDH15) and lipoma HMGIC fusion partner-like protein 5 (LHFPL5). Our results illuminate the stoichiometry of PCDH15- and LHFPL5-containing complexes and establish SiMPull and SiMoA as productive methods for probing the abundance, composition, and arrangement of subunits in the native MT complex. Impact StatementIn the present work, the authors develop and employ single molecule methods to detect, characterize, and quantitate attomole quantities of the hair cell mechanosensory transduction complex.

biochemistry↗

bioRxiv2023

Structure of C. elegans TMC-2 complex suggests roles of lipid-mediated subunit contacts in mechanosensory transduction

Mechanotransduction is the process by which a mechanical force, such as touch, is converted into an electrical signal. Transmembrane channel-like (TMC) proteins are an evolutionarily-conserved family of ion channels whose function has been linked to a variety of mechanosensory processes, including hearing and balance sensation in vertebrates and locomotion in Drosophila. The molecular features that tune homologous TMC ion channel complexes to diverse mechanical stimuli are unknown. Caenorhabditis elegans express two TMC homologs, TMC-1 and TMC-2, both of which are the likely pore-forming subunits of mechanosensitive ion channels but differ in their expression pattern and functional role in the worm. Here we present the single particle cryo-electron microscopy structure of the native TMC-2 complex isolated from C. elegans. The complex is composed of two copies each of the pore-forming TMC-2 subunit, the calcium and integrin binding protein CALM-1 and the transmembrane inner ear protein TMIE. Comparison of the TMC-2 complex to the recently published cryo-EM structure of the C. elegans TMC-1 complex reveals differences in subunit composition and highlights conserved protein-lipid interactions, as well as other structural features, that together suggest a mechanism for TMC-mediated mechanosensory transduction. Significance StatementOne mechanism by which organisms sense their environment is through the perception of mechanical stimuli such as sound, touch, and vibration. Transmembrane channel-like (TMC) proteins are ion channels whose function has been linked to a variety of mechanosensitive processes, including hearing and balance in vertebrates and touch sensation in worms. The molecular mechanisms by which TMCs respond to mechanical stimuli are unknown. Here we present the structure of the TMC-2 complex isolated from worms. Comparison of the TMC-2 complex to the recently solved structure of the worm TMC-1 complex highlights common structural features that are likely important for sensing mechanical stimuli yet also illuminates key differences that may explain the distinct functional roles of TMC-1 and TMC-2 in the worm.

biochemistry↗

bioRxiv2023

Regulated assembly and neurosteroid modulation constrain GABAA receptor pharmacology in vivo

Type A GABA receptors (GABAARs) are the principal inhibitory receptors in the brain and the target of a wide range of clinical agents, including anesthetics, sedatives, hypnotics, and antidepressants. However, our understanding of GABAAR pharmacology has been hindered by the vast number of pentameric assemblies that can be derived from a total 19 different subunits and the lack of structural knowledge of clinically relevant receptors. Here, we isolate native murine GABAAR assemblies containing the widely expressed 1 subunit, and elucidate their structures in complex with drugs used to treat insomnia (zolpidem and flurazepam) and postpartum depression (the neurosteroid allopregnanolone). Using cryo-EM analysis and single-molecule photobleaching experiments, we uncover only three structural populations in the brain: the canonical 1{beta}2{gamma}2 receptor containing two 1 subunits and two unanticipated assemblies containing one 1 and either an 2, 3 or 5 subunit. Both of the noncanonical assemblies feature a more compact arrangement between the transmembrane and extracellular domains. Interestingly, allopregnanolone is bound at the transmembrane /{beta} subunit interface, even when not added to the sample, revealing an important role for endogenous neurosteroids in modulating native GABAARs. Together with structurally engaged lipids, neurosteroids produce global conformational changes throughout the receptor that modify both the pore diameter and binding environments for GABA and insomnia medications. Together, our data reveal that GABAAR assembly is a strictly regulated process that yields a small number of structurally distinct complexes, defining a structural landscape from which subtype-specific drugs can be developed.

neuroscience↗

bioRxiv2022

Purification and biochemical analysis of native AMPA receptors from three different mammalian species

The majority of fast, excitatory synaptic transmission in the central nervous system (CNS) is mediated by -amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs), which are glutamate-activated ion channels integral to synaptic plasticity, motor coordination, learning, and memory. AMPARs are multiprotein assemblies comprised of a tetrameric receptor core that co-assembles with a broad range of peripheral auxiliary proteins which shape subcellular localization and signaling properties of the resulting complexes. Structure determination of AMPARs has traditionally relied on recombinant expression systems; however, these methods are not well suited to elucidate the diverse array of AMPAR assemblies that are differentially expressed in mammalian brains. While recent studies of native receptor complexes have advanced our understanding of endogenous assemblies, receptors thus far have only been isolated from rodent brain tissue. Here, we employed an immunoaffinity purification strategy to isolate native AMPARs from the brains of three different mammals - pigs, sheep, and cows. Compared to rodents; pigs, sheep, and cows are from a unique clade of mammals - ungulates, that share a closer genomic identity with humans. We determined the molecular size, overall yield, and purity of native AMPARs isolated from these three mammals, thereby demonstrating that structural determination and biochemical analysis is possible from a clade of mammals evolutionarily distinct from rodents.

biochemistry↗

bioRxiv2022

Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants

The serotonin transporter (SERT) is a member of the SLC6 neurotransmitter transporter family that mediates serotonin reuptake at presynaptic nerve terminals. SERT is the target of both therapeutic antidepressant drugs and illicit psychostimulant substances such as cocaine and methamphetamines, which are small molecules that perturb normal serotonergic transmission by interfering with serotonin transport. Despite decades of studies, important functional aspects of SERT such as the oligomerization state of native SERT and its interactions with potential proteins remain unresolved. Here we develop methods to isolate SERT from porcine brain (pSERT) using a mild, non-ionic detergent, utilize fluorescence- detection size-exclusion chromatography to investigate its oligomerization state and interactions with other proteins, and employ single-particle cryo-electron microscopy to elucidate the structures of pSERT in complexes with methamphetamine or cocaine, providing structural insights into psychostimulant recognition and accompanying pSERT conformations. Methamphetamine and cocaine both bind to SERT central site, stabilizing the transporter in an outward open conformation. We also identify densities attributable to multiple cholesterol or cholesteryl hemisuccinate (CHS) molecules, as well as to a detergent molecule bound to SERT allosteric site. Under our conditions of isolation, we find that pSERT is best described as a monomeric entity, isolated without interacting proteins, and is ensconced by multiple cholesterol or CHS molecules. SignificanceThe serotonin transporter (SERT) is the target of antidepressants and illicit psychostimulants. Despite its importance in the nervous, cardiovascular and gastrointestinal systems, there is no direct knowledge of SERTs oligomerization state(s) and interactions with other proteins. Here, we develop methods to isolate porcine SERT (pSERT) from native brain tissue in the presence of a mild, non-ionic detergent, and investigated its properties by biochemical, structural and computational methods. We show how cocaine and methamphetamine exert their pharmacological effect on SERT, binding to a site halfway across the membrane-spanning region of the transporter, stabilizing pSERT in an outward open conformation. pSERT is best described as a monomeric entity, requiring neither oligomerization or additional proteins for its structure or function.

biophysics↗

bioRxiv2022

Structure of C. elegans TMC-1 complex illuminates auditory mechanosensory transduction

The initial step in the sensory transduction pathway underpinning hearing and balance in mammals involves the conversion of force into the gating of a mechanosensory transduction (MT) channel. Despite the profound socioeconomic impacts of hearing disorders and the fundamental biological significance of understanding MT, the composition, structure and mechanism of the MT complex has remained elusive. Here we report the single particle cryo-EM structure of the native MT TMC-1 complex isolated from C. elegans. The 2-fold symmetric complex is composed of 2 copies each of the pore-forming TMC-1 subunit, the calcium-binding protein CALM-1 and the transmembrane inner ear protein TMIE. CALM-1 makes extensive contacts with the cytoplasmic face of the TMC-1 subunits while the single-pass TMIE subunits reside on the periphery of the complex, poised like the handles of an accordion. A subset of particles in addition harbors a single arrestin-like protein, ARRD-6, bound to a CALM-1 domain. Single- particle reconstructions and molecular dynamics simulations show how the MT complex deforms the membrane bilayer and suggest crucial roles for lipid-protein interactions in the mechanism by which mechanical force is transduced to ion channel gating.

biochemistry↗

bioRxiv2022

Aminomethanesulfonic acid illuminates the boundary between full and partial agonists of the pentameric glycine receptor

To clarify the determinants of agonist efficacy in pentameric ligand-gated ion channels we examined a new compound, aminomethanesulfonic acid (AMS), a molecule intermediate in structure between glycine and taurine. Despite wide availability, to date there are no reports of AMS action on glycine receptors, perhaps because AMS is unstable at physiological pH. Here we show that at pH 5, AMS is an efficacious agonist, eliciting in zebrafish 1 glycine receptors a maximum single channel open probability of 0.85, much greater than that of {beta}-alanine (0.54) or taurine (0.12), and second only to that of glycine itself (0.96). Thermodynamic cycle analysis of the efficacy of these closely related agonists shows supra-additive interaction between changes in the length of the agonist molecule and the size of the anionic moiety. Single particle cryo-EM structures of AMS-bound glycine receptors show that the AMS-bound agonist pocket is as compact as with glycine, and three-dimensional classification demonstrates that the channel populates the open and the desensitized states, like glycine, but not the closed intermediate state associated with the weaker partial agonists, {beta}-alanine and taurine. Because AMS is on the cusp between full and partial agonists, it provides a new tool to help us understand agonist action in the pentameric superfamily of ligand-gated ion channels.

biophysics↗

bioRxiv2021

Molecular structure and conformation of stereocilia tip-links elucidated by cryo-electron tomography

Mechanosensory transduction (MT), the conversion of mechanical stimuli into electrical signals, underpins hearing and balance and is carried out within hair cells in the inner ear. Hair cells harbor actin-filled stereocilia, arranged in rows of descending heights, where the tips of stereocilia are connected to their taller neighbors by a filament composed of protocadherin 15 (PCDH15) and cadherin 23 (CDH23), deemed the tip-link. Tension exerted on the tip-link opens an ion channel at the tip of the shorter stereocilia, thus converting mechanical force into an electrical signal. While biochemical and structural studies have provided insights into the molecular composition and structure of isolated portions of the tip-link, the architecture, location and conformational states of intact tip-links, on stereocilia, remains unknown. Here we report in situ cryo-electron microscopy imaging of the tip-link in mouse stereocilia. We observe individual PCDH15 molecules at the tip and shaft of stereocilia and determine their stoichiometry, conformational heterogeneity, and their complexes with CDH23. The PCDH15/CDH23 complexes occur in clusters, frequently with more than one copy of PCDH15 at the tip of stereocilia, suggesting that tip-links might consist of more than one copy of the PCDH15/CDH23 heterotetramer and by extension, might include multiple MT complexes.

neuroscience↗

bioRxiv2020

Conserved His-Gly motif of acid-sensing ion channels resides in a reentrant loop implicated in gating and ion selectivity

Acid-sensing ion channels (ASICs) are proton-gated members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels and are expressed throughout central and peripheral nervous systems. The homotrimeric splice variant ASIC1a has been implicated in nociception, fear memory, mood disorders and ischemia. Here we extract full-length chicken ASIC1a (cASIC1a) from cell membranes using styrene maleic acid (SMA) copolymer, yielding structures of ASIC1a channels in both high pH resting and low pH desensitized conformations by single-particle cryo-electron microscopy (cryo-EM). The structures of resting and desensitized channels reveal a reentrant loop at the amino terminus of ASIC1a that includes the highly conserved His-Gly (HG) motif. The reentrant loop lines the lower ion permeation pathway and buttresses the Gly-Ala-Ser (GAS) constriction, thus providing a structural explanation for the role of the His-Gly dipeptide in the structure and function of ASICs.

biochemistry↗

bioRxiv2020

Chemical and structural investigation of the paroxetine-human serotonin transporter complex

Antidepressants target the serotonin transporter (SERT) by inhibiting serotonin reuptake. Structural and biochemical studies aiming to understand the binding of small-molecules to conformationally dynamic transporters like SERT often require thermostabilizing mutations and antibodies to stabilize a specific conformation. Such modifications to SERT have led to questions about the relationships of these structures to the bona fide conformation and inhibitor binding poses of the wild-type transporter. To address these concerns, we characterized wild-type SERT with truncated N- and C-termini and thermostabilized variants of SERT bound with paroxetine using x-ray crystallography, single particle cryo-EM and biochemical techniques. Moreover, using a C-H functionalization approach to synthesize enantiopure analogues, we replaced the halide of the fluorophenyl group in paroxetine with either bromine or iodine. We then exploited the anomalous scattering of Br and I to define the pose of the respective paroxetine analog. These structures provide mutually consistent insights into how paroxetine and its analogs bind to the central substrate-binding site of SERT, stabilize the outward-open conformation, and inhibit serotonin transport.

biochemistry↗

bioRxiv2019

Mechanism of gating and partial agonist action in the glycine receptor

The glycine receptor is a pentameric, neurotransmitter-activated ion channel that transitions between closed/resting, open and desensitized states. Glycine, a full agonist, produces an open channel probability (Po) of [~]1.0 while partial agonists, such as taurine and {gamma}-amino butyric acid (GABA) yield submaximal Po values. Despite extensive studies of pentameric Cys-loop receptors, there is little knowledge of the molecular mechanisms underpinning partial agonist action and how the receptor transitions from the closed to open and to desensitized conformations. Here we use electrophysiology and molecular dynamics (MD) simulations, together with a large ensemble of single particle cryo-EM reconstructions, to show how agonists populate agonist-bound yet closed channel states, thus explaining their lesser efficacy, yet also populate agonist-bound open and desensitized states. Measurements within the neurotransmitter binding pocket, as a function of bound agonist, provide a metric to correlate the extent of agonist-induced conformational changes to open channel probability across the Cys-loop receptor family.

neuroscience↗

bioRxiv2018

Anti-NMDA receptor encephalitis in mice induced by active immunization with conformationally-stabilized holoreceptors

Autoimmunity to membrane proteins in the central nervous system has been increasingly recognized as a cause of neuropsychiatric disease. A key recent development was the discovery of antibodies to NMDA receptors in limbic encephalitis, characterized by cognitive changes, memory loss, seizures and sometimes long-term morbidity or mortality. Treatment approaches and experimental studies have largely focused on the pathogenic role of these autoantibodies. Passive antibody transfer to mice has provided useful insights, but does not produce the full spectrum of the human disease. Here we describe a de novo autoimmune mouse model of anti-NMDA receptor encephalitis. Active immunization of immune competent mice with conformationally-stabilized, native-like NMDA receptors induced a fulminant encephalitis that was strikingly similar to the behavioral and pathologic characteristics of human cases. Our results provide evidence of neuroinflammation and immune cell infiltration as early and robust features of the autoimmune response. Use of transgenic mice indicated that mature T cells as well as antibody-producing cells were required for disease induction. Our results provide new insights into disease pathogenesis as well as a platform for testing mechanisms of disease initiation and therapeutic approaches.\n\nOne Sentence SummaryWe report an active immunization model of anti-NMDA receptor encephalitis in mice that recapitulates the features of the clinical disease, provides new insights into the pathophysiology, and offers a platform for investigation of new therapeutic interventions.

neuroscience↗

bioRxiv2018

Divalent cation and chloride ion sites of chicken acid sensing ion channel 1a elucidated by x-ray crystallography

Acid sensing ion channels (ASICs) are proton-gated ion channels that are members of the degenerin/epithelial sodium channel superfamily and are expressed throughout central and peripheral nervous systems. ASICs have been implicated in multiple physiological processes and are subject to numerous forms of endogenous and exogenous regulation that include modulation by Ca2+ and Cl- ions. However, the mapping of ion binding sites as well as a structure-based understanding of the mechanisms underlying ionic modulation of ASICs have remained elusive. Here we present ion binding sites of chicken ASIC1a in resting and desensitized states at high and low pH, respectively, determined by anomalous diffraction x-ray crystallography. The acidic pocket serves as a nexus for divalent cation binding at both low and high pH, while we observe divalent cation binding within the central vestibule on the resting channel at high pH only. Moreover, neutralization of residues positioned to coordinate divalent cations via individual and combined Glu to Gln substitutions reduced, but did not extinguish, modulation of proton-dependent gating by Ca2+. Additionally, we demonstrate that anion binding at the canonical thumb domain site is state-dependent and present a previously undetected anion site at the mouth of the extracellular fenestrations on the resting channel. Our results map anion and cation sites on ASICs across multiple functional states, informing possible mechanisms of modulation and providing a blueprint for the design of therapeutics targeting ASICs.

biophysics↗