Flexible architecture of IP3R1 by Cryo-EM

Understanding IP3R channels: From structural underpinnings to ligand-dependent conformational landscape

Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ubiquitously expressed large-conductance Ca2+-permeable channels predominantly localized to the endoplasmic reticulum (ER) membranes of virtually all eukaryotic cell types. IP3Rs work as Ca2+ signaling hubs through which diverse extracellular stimuli and intracellular inputs are processed and then integrated to result in delivery of Ca2+ from the ER lumen to generate cytosolic Ca2+ signals with precise temporal and spatial properties. IP3R-mediated Ca2+ signals control a vast repertoire of cellular functions ranging from gene transcription and secretion to the more enigmatic brain activities such as learning and memory. IP3Rs open and release Ca2+ when they bind both IP3 and Ca2+, the primary channel agonists. Despite overwhelming evidence supporting functional interplay between IP3 and Ca2+ in activation and inhibition of IP3Rs, the mechanistic understanding of how IP3R channels convey their gating through the interplay of two primary agonists remains one of the major puzzles in the field. The last decade has seen much progress in the use of cryogenic electron microscopy to elucidate the molecular mechanisms of ligand binding, ion permeation, ion selectivity and gating of the IP3R channels. The results of these studies, summarized in this review, provide a prospective view of what the future holds in structural and functional research of IP3Rs.

IP3 receptors: An "elementary" journey from structure to signals

Inositol 1,4,5-trisphosphate receptors (IP3Rs) are large tetrameric channels which sit mostly in the membrane of the endoplasmic reticulum (ER) and mediate Ca2+ release from intracellular stores in response to extracellular stimuli in almost all cells. Dual regulation of IP3Rs by IP3 and Ca2+ itself, upstream "licensing", and the arrangement of IP3Rs into small clusters in the ER membrane, allow IP3Rs to generate spatially and temporally diverse Ca2+ signals. The characteristic biphasic regulation of IP3Rs by cytosolic Ca2+ concentration underpins regenerative Ca2+ signals by Ca2+-induced Ca2+-release, while also preventing uncontrolled explosive Ca2+ release. In this way, cells can harness a simple ion such as Ca2+ as a near-universal intracellular messenger to regulate diverse cellular functions, including those with conflicting outcomes such as cell survival and cell death. High-resolution structures of the IP3R bound to IP3 and Ca2+ in different combinations have together started to unravel the workings of this giant channel. Here we discuss, in the context of recently published structures, how the tight regulation of IP3Rs and their cellular geography lead to generation of "elementary" local Ca2+ signals known as Ca2+ "puffs", which form the fundamental bottleneck through which all IP3-mediated cytosolic Ca2+ signals must first pass.

Conformational motions and ligand-binding underlying gating and regulation in IP3R channel

Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP3 and Ca2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP3R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP3, Ca2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP3R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.

Functional determination of calcium-binding sites required for the activation of inositol 1,4,5-trisphosphate receptors

Inositol 1,4,5-trisphosphate receptors (IP3Rs) initiate a diverse array of physiological responses by carefully orchestrating intracellular calcium (Ca2+) signals in response to various external cues. Notably, IP3R channel activity is determined by several obligatory factors, including IP3, Ca2+, and ATP. The critical basic amino acid residues in the N-terminal IP3-binding core (IBC) region that facilitate IP3 binding are well characterized. In contrast, the residues conferring regulation by Ca2+ have yet to be ascertained. Using comparative structural analysis of Ca2+-binding sites identified in two main families of intracellular Ca2+-release channels, ryanodine receptors (RyRs) and IP3Rs, we identified putative acidic residues coordinating Ca2+ in the cytosolic calcium sensor region in IP3Rs. We determined the consequences of substituting putative Ca2+ binding, acidic residues in IP3R family members. We show that the agonist-induced Ca2+ release, single-channel open probability (P0), and Ca2+ sensitivities are markedly altered when the negative charge on the conserved acidic side chain residues is neutralized. Remarkably, neutralizing the negatively charged side chain on two of the residues individually in the putative Ca2+-binding pocket shifted the Ca2+ required to activate IP3R to higher concentrations, indicating that these residues likely are a component of the Ca2+ activation site in IP3R. Taken together, our findings indicate that Ca2+ binding to a well-conserved activation site is a common underlying mechanism resulting in increased channel activity shared by IP3Rs and RyRs.

Communications between Mitochondria and Endoplasmic Reticulum in the Regulation of Metabolic Homeostasis

Mitochondria associated membranes (MAM), which are the contact sites between endoplasmic reticulum (ER) and mitochondria, have emerged as an important hub for signaling molecules to integrate the cellular and organelle homeostasis, thus facilitating the adaptation of energy metabolism to nutrient status. This review explores the dynamic structural and functional features of the MAM and summarizes the various abnormalities leading to the impaired insulin sensitivity and metabolic diseases.

Calcium Release Channels: Structure and Function of IP3 Receptors and Ryanodine Receptors

Ca²⁺-release channels are giant membrane proteins that control the release of Ca²⁺ from the endoplasmic and sarcoplasmic reticulum. The two members, ryanodine receptors (RyRs) and inositol-1,4,5-trisphosphate Receptors (IP₃Rs), are evolutionarily related and are both activated by cytosolic Ca²⁺. They share a common architecture, but RyRs have evolved additional modules in the cytosolic region. Their massive size allows for the regulation by tens of proteins and small molecules, which can affect the opening and closing of the channels. In addition to Ca²⁺, other major triggers include IP₃ for the IP₃Rs, and depolarization of the plasma membrane for a particular RyR subtype. Their size has made them popular targets for study via electron microscopic methods, with current structures culminating near 3Å. The available structures have provided many new mechanistic insights int the binding of auxiliary proteins and small molecules, how these can regulate channel opening, and the mechanisms of disease-associated mutations. They also help scrutinize previously proposed binding sites, as some of these are now incompatible with the structures. Many questions remain around the structural effects of post-translational modifications, additional binding partners, and the higher-order complexes these channels can make in situ. This review summarizes our current knowledge about the structures of Ca²⁺-release channels and how this informs on their function.

A Comparative Perspective on Functionally-Related, Intracellular Calcium Channels: The Insect Ryanodine and Inositol 1,4,5-Trisphosphate Receptors

Calcium (Ca²⁺) homeostasis is vital for insect development and metabolism, and the endoplasmic reticulum (ER) is a major intracellular reservoir for Ca²⁺. The inositol 1,4,5- triphosphate receptor (IP₃R) and ryanodine receptor (RyR) are large homotetrameric channels associated with the ER and serve as two major actors in ER-derived Ca²⁺ supply. Most of the knowledge on these receptors derives from mammalian systems that possess three genes for each receptor. These studies have inspired work on synonymous receptors in insects, which encode a single IP₃R and RyR. In the current review, we focus on a fundamental, common question: “why do insect cells possess two Ca²⁺ channel receptors in the ER?”. Through a comparative approach, this review covers the discovery of RyRs and IP₃Rs, examines their structures/functions, the pathways that they interact with, and their potential as target sites in pest control. Although insects RyRs and IP₃Rs share structural similarities, they are phylogenetically distinct, have their own structural organization, regulatory mechanisms, and expression patterns, which explains their functional distinction. Nevertheless, both have great potential as target sites in pest control, with RyRs currently being targeted by commercial insecticide, the diamides.

Cryo-EM structure of type 1 IP3R channel in a lipid bilayer

Type 1 inositol 1,4,5-trisphosphate receptor (IP₃R1) is the predominant Ca²⁺-release channel in neurons. IP₃R1 mediates Ca²⁺ release from the endoplasmic reticulum into the cytosol and thereby is involved in many physiological processes. Here, we present the cryo-EM structures of full-length rat IP₃R1 reconstituted in lipid nanodisc and detergent solubilized in the presence of phosphatidylcholine determined in ligand-free, closed states by single-particle electron cryo-microscopy. Notably, both structures exhibit the well-established IP₃R1 protein fold and reveal a nearly complete representation of lipids with similar locations of ordered lipids bound to the transmembrane domains. The lipid-bound structures show improved features that enabled us to unambiguously build atomic models of IP₃R1 including two membrane associated helices that were not previously resolved in the TM region. Our findings suggest conserved locations of protein-bound lipids among homotetrameric ion channels that are critical for their structural and functional integrity despite the diversity of structural mechanisms for their gating.

3D structure of full-length rat type 1 inositol 1,4,5-trisphosphate receptor reconstituted in lipid nanodisc is determined using single-particle cryo-electron microscopy. The study suggests conserved locations of protein-bound lipids among structurally diverse, homo-tetrameric ion channels.

Effect of Wilforine on the Calcium Signaling Pathway in Mythimna separata Walker Myocytes Using the Calcium Imaging Technique

Although the action site of wilforine is located in the muscle tissue of insects, the insecticidal mechanism of wilforine is not yet clear. This research explored the effects of wilforine on the calcium signaling pathway using the calcium imaging technique to reveal the insecticidal mechanism. It was confirmed that wilforine had strong cytotoxicity to Mythimna separata myocytes with the IC₅₀ values of 25.14 and 19.65 mg/L using CCK-8 and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide methods, respectively. The morphological development of M. separata myocytes was also affected. The calcium imaging technique showed that the intracellular calcium ion concentration ([Ca²⁺]_i) increased by 23.45% of the initial value after being treated with 100 nM wilforine. However, wilforine did not increase [Ca²⁺]_i after the myocytes were preincubated with thapsigargin, and the [Ca²⁺]_i could not be decreased by 50 μM ryanodine after being treated with 100 nM wilforine. These results indicated that the targets of wilforine are located in the sarcoplasmic reticulum, and ryanodine receptor (RyR) is an important action target of wilforine. Furthermore, wilforine can also activate the inositol triphosphate receptor (IP₃R), which was confirmed through the use of 2-aminoethyl diphenylborinate, an inhibitor of IP₃R. Connected with previous research studies, it can be concluded that wilforine affects the calcium signaling pathway by combining with RyR and IP₃R, causing calcium dyshomeostasis, which results in insect paralysis and death.

Allosteric response to ligand binding: Molecular dynamics study of the N-terminal domains in IP receptor

Inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) is a huge tetrameric intracellular Ca2+ channel that mediates cytoplasmic Ca2+ signaling. The structural basis of the gating in IP3R has been studied by X-ray crystallography and cryo-electron microscopy, focusing on the domain rearrangements triggered by IP3 binding. Here, we conducted molecular dynamics (MD) simulations of the three N-terminal domains of IP3R responsible for IP3 binding (IBC/SD; two domains of the IP3 binding core, IBCβ and IBCα, and suppressor domain, SD) as a model system to study the initial gating stage. The response upon removal of IP3 from the IP3-bound form of IBC/SD was traced in MD trajectories. The two IBC domains showed an immediate response of opening after removal of IP3, and SD showed a simultaneous opening motion indicating a tight dynamic coupling with IBC. However, when IBC remained in a more closed form, the dynamic coupling broke and SD exhibited a more amplified closing motion independently of IBC. This amplified SD motion was caused by the break of connection between SD and IBCβ at the hinge region, but was suppressed in the native tetrameric state. The analyses using Motion Tree and the linear response theory clarified that in the open form, SD and IBCα moved collectively relative to IBCβ with a response upon IP3 binding within the linear regime, whereas in the closed form, such collectiveness disappeared. These results suggest that the regulation of dynamics via the domain arrangement and multimerization is requisite for large-scale allosteric communication in IP3R gating machinery.

IP3 receptors – lessons from analyses ex cellula

Inositol 1,4,5-trisphosphate receptors (IP3Rs) are widely expressed intracellular channels that release Ca2+ from the endoplasmic reticulum (ER). We review how studies of IP3Rs removed from their intracellular environment (‘ex cellula’), alongside similar analyses of ryanodine receptors, have contributed to understanding IP3R behaviour. Analyses of permeabilized cells have demonstrated that the ER is the major intracellular Ca2+ store, and that IP3 stimulates Ca2+ release from this store. Radioligand binding confirmed that the 4,5-phosphates of IP3 are essential for activating IP3Rs, and facilitated IP3R purification and cloning, which paved the way for structural analyses. Reconstitution of IP3Rs into lipid bilayers and patch-clamp recording from the nuclear envelope have established that IP3Rs have a large conductance and select weakly between Ca2+ and other cations. Structural analyses are now revealing how IP3 binding to the N-terminus of the tetrameric IP3R opens the pore ∼7 nm away from the IP3-binding core (IBC). Communication between the IBC and pore passes through a nexus of interleaved domains contributed by structures associated with the pore and cytosolic domains, which together contribute to a Ca2+-binding site. These structural analyses provide evidence to support the suggestion that IP3 gates IP3Rs by first stimulating Ca2+ binding, which leads to pore opening and Ca2+ release.

Cryo-EM reveals ligand induced allostery underlying InsP3R channel gating

Inositol-1,4,5-trisphosphate receptors (InsP₃Rs) are cation channels that mobilize Ca²⁺ from intracellular stores in response to a wide range of cellular stimuli. The paradigm of InsP₃R activation is the coupled interplay between binding of InsP₃ and Ca²⁺ that switches the ion conduction pathway between closed and open states to enable the passage of Ca²⁺ through the channel. However, the molecular mechanism of how the receptor senses and decodes ligand-binding signals into gating motion remains unknown. Here, we present the electron cryo-microscopy structure of InsP₃R1 from rat cerebellum determined to 4.1 Å resolution in the presence of activating concentrations of Ca²⁺ and adenophostin A (AdA), a structural mimetic of InsP₃ and the most potent known agonist of the channel. Comparison with the 3.9 Å-resolution structure of InsP₃R1 in the Apo-state, also reported herein, reveals the binding arrangement of AdA in the tetrameric channel assembly and striking ligand-induced conformational rearrangements within cytoplasmic domains coupled to the dilation of a hydrophobic constriction at the gate. Together, our results provide critical insights into the mechanistic principles by which ligand-binding allosterically gates InsP₃R channel.

Membrane protein structural biology in the era of single particle cryo-EM

In the past few years, significant technological breakthroughs in single particle cryo-electron microscopy enabled a 'resolution revolution' of this technique. It also changed structural biology in an unprecedented way. For many biological macromolecules, obtaining well-ordered crystals of suitable size is no longer a prerequisite for determining their atomic structures. One of the most impacted areas is the structural biology of integral membrane proteins. New structures are now determined at a rapid pace. Despite these advances, further technological developments are still required to overcome new technical challenges that face membrane protein structural biology. In this review, I attempt to discuss some of these challenges.

PLC and IP3-evoked Ca2+ release initiate the fast block to polyspermy in Xenopus laevis eggs

The fast block to polyspermy is achieved in Xenopus laevis eggs by fertilization-induced depolarization. Wozniak et al. show that fertilization activates a signaling cascade involving phospholipase C, IP₃, and intracellular Ca²⁺ release, which induces depolarization via Ca²⁺-activated Cl⁻ efflux.

The prevention of polyspermy is essential for the successful progression of normal embryonic development in most sexually reproducing species. In external fertilizers, the process of fertilization induces a depolarization of the egg’s membrane within seconds, which inhibits supernumerary sperm from entering an already-fertilized egg. This fast block requires an increase of intracellular Ca²⁺ in the African clawed frog, Xenopus laevis, which in turn activates an efflux of Cl⁻ that depolarizes the cell. Here we seek to identify the source of this intracellular Ca²⁺. Using electrophysiology, pharmacology, bioinformatics, and developmental biology, we explore the requirement for both Ca²⁺ entry into the egg from the extracellular milieu and Ca²⁺ release from an internal store, to mediate fertilization-induced depolarization. We report that although eggs express Ca²⁺-permeant ion channels, blockade of these channels does not alter the fast block. In contrast, insemination of eggs in the presence of Xestospongin C—a potent inhibitor of inositol 1,4,5-trisphosphate (IP₃)-induced Ca²⁺ release from the endoplasmic reticulum (ER)—completely inhibits fertilization-evoked depolarization and increases the incidence of polyspermy. Inhibition of the IP₃-generating enzyme phospholipase C (PLC) with U73122 similarly prevents fertilization-induced depolarization and increases polyspermy. Together, these results demonstrate that fast polyspermy block after fertilization in X. laevis eggs is mediated by activation of PLC, which increases IP₃ and evokes Ca²⁺ release from the ER. This ER-derived Ca²⁺ then activates a Cl⁻ channel to induce the fast polyspermy block. The PLC-induced cascade of events represents one of the earliest known signaling pathways initiated by fertilization.

Routine single particle CryoEM sample and grid characterization by tomography

Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment.

An analysis of variability in genome organisation of intracellular calcium release channels across insect orders

Using publicly available genomic data, combined with RT-PCR validation, we explore structural genomic variation for two major ion channels across insect classes. We have manually curated ryanodine receptor (RyR) and inositol 1,4,5-trisphosphate receptor (IP₃R) ORFs and their corresponding genomic structures from 26 different insects covering major insect orders. We found that, despite high protein identity for both RyRs (>75%) and IP₃Rs (~67%), the overall complexity of the gene structure varies greatly between different insect orders with the simplest genes (fewest introns) found in Diptera and the most complex in Lepidoptera. Analysis of intron conservation patterns indicated that the majority of conserved introns are found close to the 5' end of the channels and in RyR around the highly conserved mutually exclusive splice site. Of the two channels the IP₃Rs appear to have a less well conserved organisation with a greater overall number of unique introns seen between insect orders. We experimentally validated two of the manually curated ORFs for IP₃Rs and confirmed an atypical (3799aa) IP₃R receptor in Myzus persicae, which is approximately 1000 amino acids larger than previously reported for IP₃Rs.

Endoplasmic Reticulum-Mitochondrial Contactology: Structure and Signaling Functions

Interorganellar contacts are increasingly recognized as central to the control of cellular behavior. These contacts, which typically involve a small fraction of the endomembrane surface, are local communication hubs that resemble synapses. We propose the term contactology to denote the analysis of interorganellar contacts. Endoplasmic reticulum (ER) contacts with mitochondria were recognized several decades ago; major roles in ion and lipid transfer, signaling, and membrane dynamics have been established, while others continue to emerge. The functional diversity of ER-mitochondrial (ER-mito) contacts is mirrored in their structural heterogeneity, with subspecialization likely supported by multiple, different linker-forming protein structures. The nanoscale size of the contacts has made studying their structure, function, and dynamics difficult. This review focuses on the structure of the ER-mito contacts, methods for studying them, and the roles of contacts in Ca²⁺ and reactive oxygen species (ROS) signaling.

Crystal structures of the TRIC trimeric intracellular cation channel orthologues

Ca²⁺ release from the sarcoplasmic reticulum (SR) and endoplasmic reticulum (ER) is crucial for muscle contraction, cell growth, apoptosis, learning and memory. The trimeric intracellular cation (TRIC) channels were recently identified as cation channels balancing the SR and ER membrane potentials, and are implicated in Ca²⁺ signaling and homeostasis. Here we present the crystal structures of prokaryotic TRIC channels in the closed state and structure-based functional analyses of prokaryotic and eukaryotic TRIC channels. Each trimer subunit consists of seven transmembrane (TM) helices with two inverted repeated regions. The electrophysiological, biochemical and biophysical analyses revealed that TRIC channels possess an ion-conducting pore within each subunit, and that the trimer formation contributes to the stability of the protein. The symmetrically related TM2 and TM5 helices are kinked at the conserved glycine clusters, and these kinks are important for the channel activity. Furthermore, the kinks of the TM2 and TM5 helices generate lateral fenestrations at each subunit interface. Unexpectedly, these lateral fenestrations are occupied with lipid molecules. This study provides the structural and functional framework for the molecular mechanism of this ion channel superfamily.

Structure of IP3R channel: high-resolution insights from cryo-EM

Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ubiquitously expressed intracellular Ca2+ channels and the major mediators of cellular Ca2+ signals generated by the release of Ca2+ ions from intracellular stores in response to a variety of extracellular stimuli. Despite established physiological significance and proven involvements of IP3R channels in many human diseases, detailed structural basis for signal detection by these ion channels and their gating remain obscure. Recently, single particle electron cryomicroscopy (cryo-EM) has yielded a long-awaited near-atomic resolution structure of the entire full-length type 1 IP3R. This structure provided exciting mechanistic insights into the molecular assembly of IP3R, revealing the pronounced structural conservation of Ca2+ release channels and raising many fundamental and controversial questions on their activation and gating. Here we summarize the major technological advances that propelled our cryo-EM analysis of IP3R to near-atomic resolution and discuss what the future holds for structural biology of Ca2+ release channels.

Single-particle cryo-EM-Improved ab initio 3D reconstruction with SIMPLE/PRIME

Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. We developed the SIMPLE open-source image-processing suite for analysing cryo-EM images of single-particles. A core component of SIMPLE is the probabilistic PRIME algorithm for identifying clusters of images in 2D and determine relative orientations of single-particle projections in 3D. Here, we extend our previous work on PRIME and introduce new stochastic optimization algorithms that improve the robustness of the approach. Our refined method for identification of homogeneous subsets of images in accurate register substantially improves the resolution of the cluster centers and of the ab initio 3D reconstructions derived from them. We now obtain maps with a resolution better than 10 Å by exclusively processing cluster centers. Excellent parallel code performance on over-the-counter laptops and CPU workstations is demonstrated.

IP3 receptor signaling and endothelial barrier function

The endothelium, a monolayer of endothelial cells lining vessel walls, maintains tissue-fluid homeostasis by restricting the passage of the plasma proteins and blood cells into the interstitium. The ion Ca²⁺, a ubiquitous secondary messenger, initiates signal transduction events in endothelial cells that is critical to control of vascular tone and endothelial permeability. The ion Ca²⁺ is stored inside the intracellular organelles and released into the cytosol in response to environmental cues. The inositol 1,4,5-trisphosphate (IP₃) messenger facilitates Ca²⁺ release through IP₃ receptors which are Ca²⁺-selective intracellular channels located within the membrane of the endoplasmic reticulum. Binding of IP₃ to the IP₃Rs initiates assembly of IP₃R clusters, a key event responsible for amplification of Ca²⁺ signals in endothelial cells. This review discusses emerging concepts related to architecture and dynamics of IP₃R clusters, and their specific role in propagation of Ca²⁺ signals in endothelial cells.

IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography

The inositol 1,4,5-trisphosphate (IP₃) receptor (IP₃R) is an IP₃-gated ion channel that releases calcium ions (Ca²⁺) from the endoplasmic reticulum. The IP₃-binding sites in the large cytosolic domain are distant from the Ca²⁺ conducting pore, and the allosteric mechanism of how IP₃ opens the Ca²⁺ channel remains elusive. Here, we identify a long-range gating mechanism uncovered by channel mutagenesis and X-ray crystallography of the large cytosolic domain of mouse type 1 IP₃R in the absence and presence of IP₃ Analyses of two distinct space group crystals uncovered an IP₃-dependent global translocation of the curvature α-helical domain interfacing with the cytosolic and channel domains. Mutagenesis of the IP₃R channel revealed an essential role of a leaflet structure in the α-helical domain. These results suggest that the curvature α-helical domain relays IP₃-controlled global conformational dynamics to the channel through the leaflet, conferring long-range allosteric coupling from IP₃ binding to the Ca²⁺ channel.

From Stores to Sinks: Structural Mechanisms of Cytosolic Calcium Regulation

All eukaryotic cells have adapted the use of the calcium ion (Ca²⁺) as a universal signaling element through the evolution of a toolkit of Ca²⁺ sensor, buffer and effector proteins. Among these toolkit components, integral and peripheral proteins decorate biomembranes and coordinate the movement of Ca²⁺ between compartments, sense these concentration changes and elicit physiological signals. These changes in compartmentalized Ca²⁺ levels are not mutually exclusive as signals propagate between compartments. For example, agonist induced surface receptor stimulation can lead to transient increases in cytosolic Ca²⁺ sourced from endoplasmic reticulum (ER) stores; the decrease in ER luminal Ca²⁺ can subsequently signal the opening surface channels which permit the movement of Ca²⁺ from the extracellular space to the cytosol. Remarkably, the minuscule compartments of mitochondria can function as significant cytosolic Ca²⁺ sinks by taking up Ca²⁺ in a coordinated manner. In non-excitable cells, inositol 1,4,5 trisphosphate receptors (IP₃Rs) on the ER respond to surface receptor stimulation; stromal interaction molecules (STIMs) sense the ER luminal Ca²⁺ depletion and activate surface Orai1 channels; surface Orai1 channels selectively permit the movement of Ca²⁺ from the extracellular space to the cytosol; uptake of Ca²⁺ into the matrix through the mitochondrial Ca²⁺ uniporter (MCU) further shapes the cytosolic Ca²⁺ levels. Recent structural elucidations of these key Ca²⁺ toolkit components have improved our understanding of how they function to orchestrate precise cytosolic Ca²⁺ levels for specific physiological responses. This chapter reviews the atomic-resolution structures of IP₃R, STIM1, Orai1 and MCU elucidated by X-ray crystallography, electron microscopy and NMR and discusses the mechanisms underlying their biological functions in their respective compartments within the cell.

Inositol 1,4,5-trisphosphate receptor type 1 autoantibodies in paraneoplastic and non-paraneoplastic peripheral neuropathy

BACKGROUND

Recently, we described a novel autoantibody, anti-Sj/ITPR1-IgG, that targets the inositol 1,4,5-trisphosphate receptor type 1 (ITPR1) in patients with cerebellar ataxia. However, ITPR1 is expressed not only by Purkinje cells but also in the anterior horn of the spinal cord, in the substantia gelatinosa and in the motor, sensory (including the dorsal root ganglia) and autonomic peripheral nervous system, suggesting that the clinical spectrum associated with autoimmunity to ITPR1 may be broader than initially thought. Here we report on serum autoantibodies to ITPR1 (up to 1:15,000) in three patients with (radiculo)polyneuropathy, which in two cases was associated with cancer (ITPR1-expressing adenocarcinoma of the lung, multiple myeloma), suggesting a paraneoplastic aetiology.

METHODS

Serological and other immunological studies, and retrospective analysis of patient records.

RESULTS

The clinical findings comprised motor, sensory (including severe pain) and autonomic symptoms. While one patient presented with subacute symptoms mimicking Guillain-Barré syndrome (GBS), the symptoms progressed slowly in two other patients. Electrophysiology revealed delayed F waves; a decrease in motor and sensory action potentials and conduction velocities; delayed motor latencies; signs of denervation, indicating sensorimotor radiculopolyneuropathy of the mixed type; and no conduction blocks. ITPR1-IgG belonged to the complement-activating IgG1 subclass in the severely affected patient but exclusively to the IgG2 subclass in the two more mildly affected patients. Cerebrospinal fluid ITPR1-IgG was found to be of predominantly extrathecal origin. A ³H-thymidine-based proliferation assay confirmed the presence of ITPR1-reactive lymphocytes among peripheral blood mononuclear cells (PBMCs). Immunophenotypic profiling of PBMCs protein demonstrated predominant proliferation of B cells, CD4 T cells and CD8 memory T cells following stimulation with purified ITPR1 protein. Patient ITPR1-IgG bound both to peripheral nervous tissue and to lung tumour tissue. A nerve biopsy showed lymphocyte infiltration (including cytotoxic CD8 cells), oedema, marked axonal loss and myelin-positive macrophages, indicating florid inflammation. ITPR1-IgG serum titres declined following tumour removal, paralleled by clinical stabilization.

CONCLUSIONS

Our findings expand the spectrum of clinical syndromes associated with ITPR1-IgG and suggest that autoimmunity to ITPR1 may underlie peripheral nervous system diseases (including GBS) in some patients and may be of paraneoplastic origin in a subset of cases.

Synthesis of dimeric analogs of adenophostin A that potently evoke Ca2+ release through IP3 receptors

Syntheses and Ca²⁺ release potentials of four dimeric analogs of adenophostin A (AdA) through activation of type 1 IP₃R are reported. These analogs are full agonists of IP₃R and are equipotent to AdA, the most potent agonist of IP₃R.

Inositol 1,4,5-trisphosphate receptors (IP₃Rs) are tetrameric intracellular channels through which many extracellular stimuli initiate the Ca²⁺ signals that regulate diverse cellular responses. There is considerable interest in developing novel ligands of IP₃R. Adenophostin A (AdA) is a potent agonist of IP₃R and since some dimeric analogs of IP₃R ligands are more potent than the corresponding monomer; we considered whether dimeric AdA analogs might provide agonists with increased potency. We previously synthesized traizolophostin, in which a simple triazole replaced the adenine of AdA, and showed it to be equipotent to AdA. Here, we used click chemistry to synthesize four homodimeric analogs of triazolophostin, connected by oligoethylene glycol chains of different lengths. We evaluated the potency of these analogs to release Ca²⁺ through type 1 IP₃R and established that the newly synthesized dimers are equipotent to AdA and triazolophostin.

Denoising and covariance estimation of single particle cryo-EM images

The problem of image restoration in cryo-EM entails correcting for the effects of the Contrast Transfer Function (CTF) and noise. Popular methods for image restoration include 'phase flipping', which corrects only for the Fourier phases but not amplitudes, and Wiener filtering, which requires the spectral signal to noise ratio. We propose a new image restoration method which we call 'Covariance Wiener Filtering' (CWF). In CWF, the covariance matrix of the projection images is used within the classical Wiener filtering framework for solving the image restoration deconvolution problem. Our estimation procedure for the covariance matrix is new and successfully corrects for the CTF. We demonstrate the efficacy of CWF by applying it to restore both simulated and experimental cryo-EM images. Results with experimental datasets demonstrate that CWF provides a good way to evaluate the particle images and to see what the dataset contains even without 2D classification and averaging.

A Stochastic Hill Climbing Approach for Simultaneous 2D Alignment and Clustering of Cryogenic Electron Microscopy Images

A critical step in the analysis of novel cryogenic electron microscopy (cryo-EM) single-particle datasets is the identification of homogeneous subsets of images. Methods for solving this problem are important for data quality assessment, ab initio 3D reconstruction, and analysis of population diversity due to the heterogeneous nature of macromolecules. Here we formulate a stochastic algorithm for identification of homogeneous subsets of images. The purpose of the method is to generate improved 2D class averages that can be used to produce a reliable 3D starting model in a rapid and unbiased fashion. We show that our method overcomes inherent limitations of widely used clustering approaches and proceed to test the approach on six publicly available experimental cryo-EM datasets. We conclude that, in each instance, ab initio 3D reconstructions of quality suitable for initialization of high-resolution refinement are produced from the cluster centers.

Chapter 4 - Inositol 1,4,5-Trisphosphate Receptor Ubiquitination

Inositol 1,4,5-trisphosphate receptors (IP3Rs) are large (∼300kDa) proteins that associate into tetrameric ion channels in the endoplasmic reticulum (ER) membrane. Activation and opening of the channel upon binding of IP3 and Ca(2+) allows the flow of Ca(2+) ions from stores within the ER lumen to the cytosol, thereby promoting a number of Ca(2+)-dependent cellular events, such as secretion, neurotransmitter release, and cell division. Intriguingly, it appears that the same conformational change that IP3Rs undergo during activation makes them a target for degradation by the ubiquitin-proteasome pathway and that this mode of processing allows the cell to tune its internal Ca(2+) response to extracellular signals. Here, we review recent studies showing that activated IP3Rs interact with an array of proteins that mediate their degradation, that IP3Rs are modified by a complex array of ubiquitin conjugates, that this ubiquitination and degradation functions to regulate IP3-mediated Ca(2+) responses in the cell, and that mutations to different proteins involved in IP3R degradation result in a set of similar diseases.

Single-particle electron microscopy in the study of membrane protein structure

Single-particle electron microscopy (EM) provides the great advantage that protein structure can be studied without the need to grow crystals. However, due to technical limitations, this approach played only a minor role in the study of membrane protein structure. This situation has recently changed dramatically with the introduction of direct electron detection device cameras, which allow images of unprecedented quality to be recorded, also making software algorithms, such as three-dimensional classification and structure refinement, much more powerful. The enhanced potential of single-particle EM was impressively demonstrated by delivering the first long-sought atomic model of a member of the biomedically important transient receptor potential channel family. Structures of several more membrane proteins followed in short order. This review recounts the history of single-particle EM in the study of membrane proteins, describes the technical advances that now allow this approach to generate atomic models of membrane proteins and provides a brief overview of some of the membrane protein structures that have been studied by single-particle EM to date.

Gating machinery of InsP3R channels revealed by electron cryomicroscopy

Inositol-1,4,5-trisphosphate receptors (InsP3Rs) are ubiquitous ion channels responsible for cytosolic Ca(2+) signalling and essential for a broad array of cellular processes ranging from contraction to secretion, and from proliferation to cell death. Despite decades of research on InsP3Rs, a mechanistic understanding of their structure-function relationship is lacking. Here we present the first, to our knowledge, near-atomic (4.7 Å) resolution electron cryomicroscopy structure of the tetrameric mammalian type 1 InsP3R channel in its apo-state. At this resolution, we are able to trace unambiguously ∼85% of the protein backbone, allowing us to identify the structural elements involved in gating and modulation of this 1.3-megadalton channel. Although the central Ca(2+)-conduction pathway is similar to other ion channels, including the closely related ryanodine receptor, the cytosolic carboxy termini are uniquely arranged in a left-handed α-helical bundle, directly interacting with the amino-terminal domains of adjacent subunits. This configuration suggests a molecular mechanism for allosteric regulation of channel gating by intracellular signals.

Crystal structures of ryanodine receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant

Ryanodine receptors (RyRs) form calcium release channels located in the membranes of the sarcoplasmic and endoplasmic reticulum. RyRs play a major role in excitation-contraction coupling and other Ca²⁺-dependent signalling events, and consist of several globular domains that together form a large assembly. Here we describe the crystal structures of the SPRY1 and tandem-repeat domains at 1.2–1.5 Å resolution, which reveal several structural elements not detected in recent cryo-EM reconstructions of RyRs. The cryo-EM studies disagree on the position of SPRY domains, which had been proposed based on homology modelling. Computational docking of the crystal structures, combined with FRET studies, show that the SPRY1 domain is located next to FK506-binding protein (FKBP). Molecular dynamics flexible fitting and mutagenesis experiments suggest a hydrophobic cluster within SPRY1 that is crucial for FKBP binding. A RyR1 disease mutation, N760D, appears to directly impact FKBP binding through interfering with SPRY1 folding.

The ryanodine receptor (RyR) is a large multi-domain ion channel that functions to release calcium from the endoplasmic or sarcoplasmic reticulum. Here the authors present crystal structures of the SPRY1 and tandem repeat domains of RyR, allowing precise positioning of the domains and linking disease mutations to RyR function.

Regulatory Mechanisms of Endoplasmic Reticulum Resident IP3 Receptors

Dysregulated calcium signaling and accumulation of aberrant proteins causing endoplasmic reticulum stress are the early sign of intra-axonal pathological events in many neurodegenerative diseases, and apoptotic signaling is initiated when the stress goes beyond the maximum threshold level of endoplasmic reticulum. The fate of the cell to undergo apoptosis is controlled by Ca2(+) signaling and dynamics at the level of the endoplasmic reticulum. Endoplasmic reticulum resident inositol 1,4,5-trisphosphate receptors (IP3R) play a pivotal role in cell death signaling by mediating Ca2(+) flux from the endoplasmic reticulum into the cytosol and mitochondria. Hence, many prosurvival and prodeath signaling pathways and proteins affect Ca2(+) signaling by directly targeting IP3R channels, which can happen in an IP3R-isoform-dependent manner. Here, in this review, we summarize the regulatory mechanisms of inositol triphosphate receptors in calcium regulation and initiation of apoptosis during unfolded protein response.

Generation and functions of second messengers microdomains

A compelling example of the mechanisms by which the cells can organize and decipher complex and different functional activities is the convergence of a multitude of stimuli into signalling cascades, involving only few intracellular second messengers. The possibility of restricting these signalling events in distinct microdomains allows a fine and selective tuning of very different tasks. In this review, we will discuss the mechanisms that control the formation and the spatial distribution of Ca(2+) and cAMP microdomains, providing some examples of their functional consequences.

Single-particle cryo-EM of the ryanodine receptor channel in an aqueous environment

Ryanodine receptors (RyRs) are tetrameric ligand-gated Ca2+ release channels that are responsible for the increase of cytosolic Ca2+ concentration leading to muscle contraction. Our current understanding of RyR channel gating and regulation is greatly limited due to the lack of a high-resolution structure of the channel protein. The enormous size and unwieldy shape of Ca2+ release channels make X-ray or NMR methods difficult to apply for high-resolution structural analysis of the full-length functional channel. Single-particle electron cryo-microscopy (cryo-EM) is one of the only effective techniques for the study of such a large integral membrane protein and its molecular interactions. Despite recent developments in cryo-EM technologies and break-through single-particle cryo-EM studies of ion channels, cryospecimen preparation, particularly the presence of detergent in the buffer, remains the main impediment to obtaining atomic-resolution structures of ion channels and a multitude of other integral membrane protein complexes. In this review we will discuss properties of several detergents that have been successfully utilized in cryo-EM studies of ion channels and the emergence of the detergent alternative amphipol to stabilize ion channels for structure-function characterization. Future structural studies of challenging specimen like ion channels are likely to be facilitated by cryo-EM amenable detergents or alternative surfactants.

Antibodies to the inositol 1,4,5-trisphosphate receptor type 1 (ITPR1) in cerebellar ataxia

We report on a serum autoantibody associated with cerebellar ataxia. Immunohistochemical studies of sera from four patients referred for autoantibody testing revealed binding of high-titer (up to 1:5,000) IgG antibodies, mainly IgG1, to the molecular layer, Purkinje cell layer, and white matter on mouse, rat, porcine, and monkey cerebellum sections. The antibody bound to PC somata, dendrites, and axons, resulting in a binding pattern similar to that reported for anti-Ca/anti-ARHGAP26, but did not react with recombinant ARHGAP26. Extensive control studies were performed to rule out a broad panel of previously described paraneoplastic and non-paraneoplastic anti-neural autoantibodies. The characteristic binding pattern as well as double staining experiments suggested inositol 1,4,5-trisphosphate receptor type 1 (ITPR1) as the target antigen. Verification of the antigen included specific neutralization of the tissue reaction following preadsorption with ITPR1 (but not ARHGAP26) and a dot-blot assay with purified ITPR1 protein. By contrast, anti-ARHGAP26-positive sera did not bind to ITPR1. In a parallel approach, a combination of histoimmunoprecipitation and mass spectrometry also identified ITPR1 as the target antigen. Finally, a recombinant cell-based immunofluorescence assay using HEK293 cells expressing ITPR1 and ARHGAP26, respectively, confirmed the identification of ITPR1. Mutations of ITPR1 have previously been implicated in spinocerebellar ataxia with and without cognitive decline. Our findings suggest a role of autoimmunity against ITPR1 in the pathogenesis of autoimmune cerebellitis and extend the panel of diagnostic markers for this disease.

Structural insights into endoplasmic reticulum stored calcium regulation by inositol 1,4,5-trisphosphate and ryanodine receptors

The two major calcium (Ca²⁺) release channels on the sarco/endoplasmic reticulum (SR/ER) are inositol 1,4,5-trisphosphate and ryanodine receptors (IP3Rs and RyRs). They play versatile roles in essential cell signaling processes, and abnormalities of these channels are associated with a variety of diseases. Structural information on IP3Rs and RyRs determined using multiple techniques including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (EM), has significantly advanced our understanding of the mechanisms by which these Ca²⁺ release channels function under normal and pathophysiological circumstances. In this review, structural advances on the understanding of the mechanisms of IP3R and RyR function and dysfunction are summarized. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.

Aberrant calcium signaling by transglutaminase-mediated posttranslational modification of inositol 1,4,5-trisphosphate receptors

The inositol 1,4,5-trisphosphate receptor (IP3R) in the endoplasmic reticulum mediates calcium signaling that impinges on intracellular processes. IP3Rs are allosteric proteins comprising four subunits that form an ion channel activated by binding of IP3 at a distance. Defective allostery in IP3R is considered crucial to cellular dysfunction, but the specific mechanism remains unknown. Here we demonstrate that a pleiotropic enzyme transglutaminase type 2 targets the allosteric coupling domain of IP3R type 1 (IP3R1) and negatively regulates IP3R1-mediated calcium signaling and autophagy by locking the subunit configurations. The control point of this regulation is the covalent posttranslational modification of the Gln2746 residue that transglutaminase type 2 tethers to the adjacent subunit. Modification of Gln2746 and IP3R1 function was observed in Huntington disease models, suggesting a pathological role of this modification in the neurodegenerative disease. Our study reveals that cellular signaling is regulated by a new mode of posttranslational modification that chronically and enzymatically blocks allosteric changes in the ligand-gated channels that relate to disease states.

Contribution of Ca2+ release channels to hippocampal synaptic plasticity and spatial memory: potential redox modulation

SIGNIFICANCE

Memory is an essential human cognitive function. Consequently, to unravel the cellular and molecular mechanisms responsible for the synaptic plasticity events underlying memory formation, storage and loss represents a major challenge of present-day neuroscience.

RECENT ADVANCES

This review article first describes the wide-ranging functions played by intracellular Ca2+ signals in the activity-dependent synaptic plasticity processes underlying hippocampal spatial memory, and next, it focuses on how the endoplasmic reticulum Ca2+ release channels, the ryanodine receptors, and the inositol 1,4,5-trisphosphate receptors contribute to these processes. We present a detailed examination of recent evidence supporting the key role played by Ca2+ release channels in synaptic plasticity, including structural plasticity, and the formation/consolidation of spatial memory in the hippocampus.

CRITICAL ISSUES

Changes in cellular oxidative state particularly affect the function of Ca2+ release channels and alter hippocampal synaptic plasticity and the associated memory processes. Emphasis is placed in this review on how defective Ca2+ release, presumably due to increased levels of reactive oxygen species, may cause the hippocampal functional defects that are associated to aging and Alzheimer's disease (AD).

FUTURE DIRECTIONS

Additional studies should examine the precise molecular mechanisms by which Ca2+ release channels contribute to hippocampal synaptic plasticity and spatial memory formation/consolidation. Future studies should test whether redox-modified Ca2+ release channels contribute toward generating the intracellular Ca2+ signals required for sustained synaptic plasticity and hippocampal spatial memory, and whether loss of redox balance and oxidative stress, by altering Ca2+ release channel function, presumably contribute to the abnormal memory processes that occur during aging and AD.

Toward a high-resolution structure of IP₃R channel

The ability of cells to maintain low levels of Ca(2+) under resting conditions and to create rapid and transient increases in Ca(2+) upon stimulation is a fundamental property of cellular Ca(2+) signaling mechanism. An increase of cytosolic Ca(2+) level in response to diverse stimuli is largely accounted for by the inositol 1,4,5-trisphosphate receptor (IP3R) present in the endoplasmic reticulum membranes of virtually all eukaryotic cells. Extensive information is currently available on the function of IP3Rs and their interaction with modulators. Very little, however, is known about their molecular architecture and therefore most critical issues surrounding gating of IP3R channels are still ambiguous, including the central question of how opening of the IP3R pore is initiated by IP3 and Ca(2+). Membrane proteins such as IP3R channels have proven to be exceptionally difficult targets for structural analysis due to their large size, their location in the membrane environment, and their dynamic nature. To date, a 3D structure of complete IP3R channel is determined by single-particle cryo-EM at intermediate resolution, and the best crystal structures of IP3R are limited to a soluble portion of the cytoplasmic region representing ∼15% of the entire channel protein. Together these efforts provide the important structural information for this class of ion channels and serve as the basis for further studies aiming at understanding of the IP3R function.

Asymmetric perturbations of signalling oligomers

This review focuses on rapid and reversible noncovalent interactions for symmetric oligomers of signalling proteins. Symmetry mismatch, transient symmetry breaking and asymmetric perturbations via chemical (ligand binding) and physical (electric or mechanic) effects can initiate the signalling events. Advanced biophysical methods can reveal not only structural symmetries of stable membrane-bound signalling proteins but also asymmetric functional transition states. Relevant techniques amenable to distinguish between symmetric and asymmetric architectures are discussed including those with the capability of capturing low-populated transient conformational states. Typical examples of signalling proteins are overviewed for symmetry breaking in dimers (GPCRs, growth factor receptors, transcription factors); trimers (acid-sensing ion channels); tetramers (voltage-gated cation channels, ionotropic glutamate receptor, CNG and CHN channels); pentameric ligand-gated and mechanosensitive channels; higher order oligomers (gap junction channel, chaperonins, proteasome, virus capsid); as well as primary and secondary transporters. In conclusion, asymmetric perturbations seem to play important functional roles in a broad range of communicating networks.

Inositol 1,4,5-trisphosphate receptor-isoform diversity in cell death and survival

Cell-death and -survival decisions are critically controlled by intracellular Ca(2+) homeostasis and dynamics at the level of the endoplasmic reticulum (ER). Inositol 1,4,5-trisphosphate (IP3) receptors (IP3Rs) play a pivotal role in these processes by mediating Ca(2+) flux from the ER into the cytosol and mitochondria. Hence, it is clear that many pro-survival and pro-death signaling pathways and proteins affect Ca(2+) signaling by directly targeting IP3R channels, which can happen in an IP3R-isoform-dependent manner. In this review, we will focus on how the different IP3R isoforms (IP3R1, IP3R2 and IP3R3) control cell death and survival. First, we will present an overview of the isoform-specific regulation of IP3Rs by cellular factors like IP3, Ca(2+), Ca(2+)-binding proteins, adenosine triphosphate (ATP), thiol modification, phosphorylation and interacting proteins, and of IP3R-isoform specific expression patterns. Second, we will discuss the role of the ER as a Ca(2+) store in cell death and survival and how IP3Rs and pro-survival/pro-death proteins can modulate the basal ER Ca(2+) leak. Third, we will review the regulation of the Ca(2+)-flux properties of the IP3R isoforms by the ER-resident and by the cytoplasmic proteins involved in cell death and survival as well as by redox regulation. Hence, we aim to highlight the specific roles of the various IP3R isoforms in cell-death and -survival signaling. This article is part of a Special Issue entitled: Calcium signaling in health and disease. Guest Editors: Geert Bultynck, Jacques Haiech, Claus W. Heizmann, Joachim Krebs, and Marc Moreau.

Rotationally invariant image representation for viewing direction classification in cryo-EM

We introduce a new rotationally invariant viewing angle classification method for identifying, among a large number of cryo-EM projection images, similar views without prior knowledge of the molecule. Our rotationally invariant features are based on the bispectrum. Each image is denoised and compressed using steerable principal component analysis (PCA) such that rotating an image is equivalent to phase shifting the expansion coefficients. Thus we are able to extend the theory of bispectrum of 1D periodic signals to 2D images. The randomized PCA algorithm is then used to efficiently reduce the dimensionality of the bispectrum coefficients, enabling fast computation of the similarity between any pair of images. The nearest neighbors provide an initial classification of similar viewing angles. In this way, rotational alignment is only performed for images with their nearest neighbors. The initial nearest neighbor classification and alignment are further improved by a new classification method called vector diffusion maps. Our pipeline for viewing angle classification and alignment is experimentally shown to be faster and more accurate than reference-free alignment with rotationally invariant K-means clustering, MSA/MRA 2D classification, and their modern approximations.

Structure of thermally activated TRP channels

Temperature sensation is important for adaptation and survival of organisms. While temperature has the potential to affect all biological macromolecules, organisms have evolved specific thermosensitive molecular detectors that are able to transduce temperature changes into physiologically relevant signals. Among these thermosensors are ion channels from the transient receptor potential (TRP) family. Prime candidates include TRPV1-4, TRPA1, and TRPM8 (the so-called "thermoTRP" channels), which are expressed in sensory neurons and gated at specific temperatures. Electrophysiological and thermodynamic approaches have been employed to determine the nature by which thermoTRPs detect temperature and couple temperature changes to channel gating. To further understand how thermoTRPs sense temperature, high-resolution structures of full-length thermoTRPs channels will be required. Here, we will discuss current progress in unraveling the structures of thermoTRP channels.

Intracellular calcium channels: inositol-1,4,5-trisphosphate receptors

The inositol-1,4,5-trisphosphate receptors (InsP3Rs) are the major intracellular Ca(2+)-release channels in cells. Activity of InsP3Rs is essential for elementary and global Ca(2+) events in the cell. There are three InsP3Rs isoforms that are present in mammalian cells. In this review we will focus primarily on InsP3R type 1. The InsP3R1 is a predominant isoform in neurons and it is the most extensively studied isoform. Combination of biophysical and structural methods revealed key mechanisms of InsP3R function and modulation. Cell biological and biochemical studies lead to identification of a large number of InsP3R-binding proteins. InsP3Rs are involved in the regulation of numerous physiological processes, including learning and memory, proliferation, differentiation, development and cell death. Malfunction of InsP3R1 play a role in a number of neurodegenerative disorders and other disease states. InsP3Rs represent a potentially valuable drug target for treatment of these disorders and for modulating activity of neurons and other cells. Future studies will provide better understanding of physiological functions of InsP3Rs in health and disease.

Themes and variations in ER/SR calcium release channels: structure and function

Calcium (Ca(2+)) release from reticular stores is a vital regulatory signal in eukaryotes. Recent structural data on large NH(2)-terminal regions of IP(3)Rs and RyRs and their tetrameric arrangement in the full-length context reveal striking mechanistic similarities in Ca(2+) release channel function. A common ancestor found in unicellular genomes underscores the fundamentality of these elements to Ca(2+) release channels.