Super-resolution architecture of mammalian centriole distal appendages reveals distinct blade and matrix functional components.

Distal appendages (DAPs) are nanoscale, pinwheel-like structures protruding from the distal end of the centriole that mediate membrane docking during ciliogenesis, marking the cilia base around the ciliary gate. Here we determine a super-resolved multiplex of 16 centriole-distal-end components. Surprisingly, rather than pinwheels, intact DAPs exhibit a cone-shaped architecture with components filling the space between each pinwheel blade, a new structural element we term the distal appendage matrix (DAM). Specifically, CEP83, CEP89, SCLT1, and CEP164 form the backbone of pinwheel blades, with CEP83 confined at the root and CEP164 extending to the tip near the membrane-docking site. By contrast, FBF1 marks the distal end of the DAM near the ciliary membrane. Strikingly, unlike CEP164, which is essential for ciliogenesis, FBF1 is required for ciliary gating of transmembrane proteins, revealing DAPs as an essential component of the ciliary gate. Our findings redefine both the structure and function of DAPs.

Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons.

Actin and spectrin play important roles in neurons, but their organization in axons and dendrites remains unclear. We used stochastic optical reconstruction microscopy to study the organization of actin, spectrin, and associated proteins in neurons. Actin formed ringlike structures that wrapped around the circumference of axons and were evenly spaced along axonal shafts with a periodicity of ~180 to 190 nanometers. This periodic structure was not observed in dendrites, which instead contained long actin filaments running along dendritic shafts. Adducin, an actin-capping protein, colocalized with the actin rings. Spectrin exhibited periodic structures alternating with those of actin and adducin, and the distance between adjacent actin-adducin rings was comparable to the length of a spectrin tetramer. Sodium channels in axons were distributed in a periodic pattern coordinated with the underlying actin-spectrin-based cytoskeleton.

On conduction in a bacterial sodium channel.

Voltage-gated Na⁺-channels are transmembrane proteins that are responsible for the fast depolarizing phase of the action potential in nerve and muscular cells. Selective permeability of Na⁺ over Ca²âº or K⁺ ions is essential for the biological function of Na⁺-channels. After the emergence of the first high-resolution structure of a Na⁺-channel, an anionic coordination site was proposed to confer Na⁺ selectivity through partial dehydration of Na⁺ via its direct interaction with conserved glutamate side chains. By combining molecular dynamics simulations and free-energy calculations, a low-energy permeation pathway for Na⁺ ion translocation through the selectivity filter of the recently determined crystal structure of a prokaryotic sodium channel from Arcobacter butzleri is characterised. The picture that emerges is that of a pore preferentially occupied by two ions, which can switch between different configurations by crossing low free-energy barriers. In contrast to K⁺-channels, the movements of the ions appear to be weakly coupled in Na⁺-channels. When the free-energy maps for Na⁺ and K⁺ ions are compared, a selective site is characterised in the narrowest region of the filter, where a hydrated Na⁺ ion, and not a hydrated K⁺ ion, is energetically stable.

Schwann cells inhibit ectopic clustering of axonal sodium channels.

The clustering of voltage-gated sodium channels at the axon initial segment (AIS) and nodes of Ranvier is essential for the initiation and propagation of action potentials in myelinated axons. Sodium channels localize to the AIS through an axon-intrinsic mechanism driven by ankyrin G, while clustering at the nodes requires cues from myelinating glia that interact with axonal neurofascin186 (Sherman et al., 2005; Dzhashiashvili et al., 2007; Yang et al., 2007). Here, we report that in zebrafish mutants lacking Schwann cells in peripheral nerves (erbb2, erbb3, and sox10/colorless), axons form numerous aberrant sodium channel clusters throughout their length. Morpholino knockdown of ankyrin G, but not neurofascin, reduces the number of sodium channel clusters in Schwann cell-deficient mutants, suggesting that these aberrant clusters form by an axon-intrinsic mechanism. We also find that gpr126 mutants, in which Schwann cells are arrested at the promyelinating stage (Monk et al., 2009), are deficient in the clustering of neurofascin at the nodes of Ranvier. When Schwann cell migration in gpr126 mutants is blocked, there is an increase in the number of neurofascin clusters in peripheral axons. Our results suggest that Schwann cells inhibit the ability of ankyrin G to cluster sodium channels at ectopic locations, restricting its activity to the AIS and nodes of Ranvier.

Direct visualization of the trimeric structure of the ASIC1a channel, using AFM imaging.

There has been confusion about the subunit stoichiometry of the degenerin family of ion channels. Recently, a crystal structure of acid-sensing ion channel (ASIC) 1a revealed that it assembles as a trimer. Here, we used atomic force microscopy (AFM) to image unprocessed ASIC1a bound to mica. We detected a mixture of subunit monomers, dimers and trimers. In some cases, triple-subunit clusters were clearly visible, confirming the trimeric structure of the channel, and indicating that the trimer sometimes disaggregated after adhesion to the mica surface. This AFM-based technique will now enable us to determine the subunit arrangement within heteromeric ASICs.

More gating charges are needed to open a Shaker K+ channel than are needed to open an rBIIA Na+ channel.

This study presents what is, to our knowledge, a novel technique by means of which the ratio of the single gating charges of voltage-gated rat brain IIA (rBIIA) sodium and Shaker potassium ion channels was estimated. In the experiment, multiple tandems of enhanced green fluorescent protein were constructed and inserted into the C-terminals of Na(+) and K(+) ion channels. cRNA of Na(+) and K(+) ion channels was injected and expressed in Xenopus laevis oocytes. The two electrode voltage-clamp technique allowed us to determine the total gating charge of sodium and potassium ion channels, while a relative measure of the amount of expressed channels could be established on the basis of the quantification of the fluorescence intensity of membrane-bound channels marked by enhanced green fluorescent proteins. As a result, gating charge and fluorescence intensity were found to be positively correlated. A relative comparison of the single gating charges of voltage-gated sodium and potassium ion channels could thus be established: the ratio of the single gating charges of the Shaker potassium channel and the rBIIA sodium channel was found to be 2.5 +/- 0.4. Assuming the single channel gating charge of the Shaker K(+) channel to be approximately 13 elementary charges (well supported by other studies), this leads to approximately six elementary charges for the rBIIA sodium channel, which includes a fraction of gating charge that is missed during inactivation.

Nanoscale organization of the MEC-4 DEG/ENaC sensory mechanotransduction channel in Caenorhabditis elegans touch receptor neurons.

Hearing, touch and proprioception are thought to involve direct activation of mechano-electrical transduction (MeT) channels. In Caenorhabditis elegans touch receptor neurons (TRNs), such channels contain two pore-forming subunits (MEC-4 and MEC-10) and two auxiliary subunits (MEC-2 and MEC-6). MEC-4 and MEC-10 belong to a large superfamily of ion channel proteins (DEG/ENaCs) that form nonvoltage-gated, amiloride-sensitive Na+ channels. In TRNs, unique 15-protofilament microtubules and an electron-dense extracellular matrix have been proposed to serve as gating tethers critical for MeT channel activation. We combined high-pressure freezing and serial-section immunoelectron microscopy to determine the position of MeT channels relative to putative gating tethers. MeT channels were visualized using antibodies against MEC-4 and MEC-2. This nanometer-resolution view of a sensory MeT channel establishes structural constraints on the mechanics of channel gating. We show here that MEC-2 and MEC-5 collagen, a putative extracellular tether, occupy overlapping but distinct domains in TRN neurites. Although channels decorate all sides of TRN neurites; they are not associated with the distal endpoints of 15-protofilament microtubules hypothesized to be gating tethers. These specialized microtubules, which are unique to TRNs, assemble into a cross-linked bundle connected by a network of kinked filaments to the neurite membrane. We speculate that the microtubule bundle converts external point loads into membrane stretch which, in turn, facilitates MeT channel activation.

Adaptive Brownian dynamics for shape estimation of sodium ion channels.

Ion channels are protein macromolecules that form biological nanotubes across the membranes of living cells. Given many possible geometrical shapes of an ion channel, we propose a computational scheme of selecting the model that best replicates experimental observations, using adaptive Brownian dynamics simulations together with discrete optimization algorithms. Brownian dynamics simulations emulate the propagation of individual ions through the sodium channel nanotube at a femto time second time scale and Angstrom unit (10(-10) meter) spatial scale.

Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line.

Human embryonic kidney (HEK) 293 cells were characterised as an expression system for voltage-activated cationic channels. Current density for cationic channels intrinsically expressed in HEK 293 cells as well as cell ultrastructure was described after 7-11, 29-30 and 49-63 days of cell culture. Slowly activating outward potassium current with the current density varying between +10 and +26 pA/pF was observed in 72% to 95% of investigated cells. Rapidly inactivating outward potassium current with the current density varying between +7 and +10 pA/pF was present in 38% to 48% of all cells. 30% of cells exhibited voltage-activated calcium channel with the current density less than -1 pA/pF. Tetrodotoxin-sensitive sodium current with amplitudes between -1.4 and -2.2 pA/pF was initially present in 5% of cells, nevertheless, after 49-63 days of cell culture this proportion increased to 35%. Ultrastructure of HEK 293 cell surface, but not of cell's interior changed during cell culture. The longer the time after thawing the more microvilli and protrusions appear on the cell surface. Irregular cell contours hinder the cells to appose and only small patches of membranes form attachments. Staining of cells with a polycationic dye ruthenium red initially increased and decreased again following prolonged period of time in culture indicating regression of negatively charged layers of the cell surface coat. We suggest that the optimal time window for patch clamp experiment is between days 7 and 63 of cell culture due to alterations of cell surface.

Electron cryomicroscopic visualization of PomA/B stator units of the sodium-driven flagellar motor in liposomes.

A motor protein complex of the bacterial flagellum, PomA/B from Vibrio alginolyticus, was reconstituted into liposomes and visualized by electron cryomicroscopy. PomA/B is a sodium channel, composed of two membrane proteins, PomA and PomB, and converts ion flux to the rotation of the flagellar motor. Escherichia coli and Salmonella have a homolog called MotA/B, which utilizes proton instead of sodium ion. PomB and MotB have a peptidoglycan-binding motif in their C-terminal region, and therefore PomA/B and MotA/B are regarded as the stator. Energy filtering electron cryomicroscopy enhanced the image contrast of the proteins reconstituted into liposomes and showed that two extramembrane domains with clearly different sizes stick out of the lipid bilayers on opposite sides. Image analysis combined with gold labeling and deletion of the peptidoglycan-binding motif revealed that the longer one, approximately 70 A long, is likely to correspond to the periplasmic domain, and the other, about half size, to the cytoplasmic domain.

BetaIVSigma1 spectrin stabilizes the nodes of Ranvier and axon initial segments.

Saltatory electric conduction requires clustered voltage-gated sodium channels (VGSCs) at axon initial segments (AIS) and nodes of Ranvier (NR). A dense membrane undercoat is present at these sites, which is thought to be key for the focal accumulation of channels. Here, we prove that betaIVSigma1 spectrin, the only betaIV spectrin with an actin-binding domain, is an essential component of this coat. Specifically, betaIVSigma1 coexists with betaIVSigma6 at both AIS and NR, being the predominant spectrin at AIS. Removal of betaIVSigma1 alone causes the disappearance of the nodal coat, an increased diameter of the NR, and the presence of dilations filled with organelles. Moreover, in myelinated cochlear afferent fibers, VGSC and ankyrin G clusters appear fragmented. These ultrastructural changes can explain the motor and auditory neuropathies present in betaIVSigma1 -/- mice and point to the betaIVSigma1 spectrin isoform as a master-stabilizing factor of AIS/NR membranes.

Functional innervation in tissue engineered models for in vitro study and testing purposes.

The biotechnology industry is rapidly expanding and the emerging field of tissue engineering is projected to have a high impact in the near future. Recently the field of cellular, drug, and prosthetic delivery has melded with the field of tissue engineering to make simulated tissues. In addition to their roles as tissue substitutes for transplantation, these simulated tissues may provide more accurate models and environments for toxicology testing and the study of peripheral nerves. The current study demonstrates the importance of innervation, in general, for the function of engineered tissues. We observe that the presence of nerves in a tissue engineered (TE) human cornea model enhances the growth of the epithelium and the formation of its protective mucin layer. Innervation also confers protection to the epithelium from chemical insult, as determined by the level of post-treatment epithelial cell death. We demonstrate differential responses of the nerves to chemical stimuli by changes in intracellular sodium as measured by 2-photon microscopy. The 2-photon imaging techniques also allow for the visualization and study of the fine sensory axon fibers within the 3-dimensional tissue. This work demonstrates a role for innervation in the protective quality and function of the engineered tissue, and the potential to use the nerves themselves as indicators of the severity of an insult. These results are important to consider for the development of any optimized TE models for in vitro study and testing purposes.

Automatic particle pickup method using a neural network has high accuracy by applying an initial weight derived from eigenimages: a new reference free method for single-particle analysis.

The single-particle analysis is a structure-determining method for electron microscope (EM) images which does not require crystal. In this method, the projections are picked up and averaged by the images of similar Euler angles to improve the signal to noise ratio, and then create a 3-D reconstruction. The selection of a large number of particles from the cryo-EM micrographs is a pre-requisite for obtaining a high resolution. To pickup a low-contrast cryo-EM protein image, we have recently found that a three-layer pyramidal-type neural network is successful in detecting such a faint image, which had been difficult to detect by other methods. The connection weights between the input and hidden layers, which work as a matching filter, have revealed that they reflect characters of the particle projections in the training data. The images stored in terms of the connection weights were complex, more similar to the eigenimages which are created by the principal component analysis of the learning images rather than to the averages of the particle projections. When we set the initial learning weights according to the eigenimages in advance, the learning period was able to be shortened to less than half the time of the NN whose initial weights had been set randomly. Further, the pickup accuracy increased from 90 to 98%, and a combination of the matching filters were found to work as an integrated matching filter there. The integrated filters were amazingly similar to averaged projections and can be used directly as references for further two-dimensional averaging. Therefore, this research also presents a brand-new reference-free method for single-particle analysis.

FRET between cardiac Na+ channel subunits measured with a confocal microscope and a streak camera.

When and where proteins associate is a central question in many biomolecular studies. Förster resonance energy transfer (FRET) measurements can be used to address this question when the interacting proteins are labeled with appropriate donor and acceptor fluorophores. We describe an improved method to determine FRET efficiency that uses a mode-locked laser, a confocal microscope and a streak camera. We applied this method to study the association of alpha and beta(1) subunits of the human cardiac sodium channel. The subunits were tagged with the cyan and yellow variants of the green fluorescent protein (GFP) and expressed in human embryonic kidney (HEK293) cells. Pronounced FRET between the channel subunits in the endoplasmic reticulum (ER) suggested that the subunits associate before they reach the plasma membrane. The described method allows simultaneous measurement of donor and acceptor fluorescence decays and provides an intrinsically validated estimate of FRET efficiency.

Topology representing network enables highly accurate classification of protein images taken by cryo electron-microscope without masking.

In single-particle analysis, a three-dimensional (3-D) structure of a protein is constructed using electron microscopy (EM). As these images are very noisy in general, the primary process of this 3-D reconstruction is the classification of images according to their Euler angles, the images in each classified group then being averaged to reduce the noise level. In our newly developed strategy of classification, we introduce a topology representing network (TRN) method. It is a modified method of a growing neural gas network (GNG). In this system, a network structure is automatically determined in response to the images input through a growing process. After learning without a masking procedure, the GNG creates clear averages of the inputs as unit coordinates in multi-dimensional space, which are then utilized for classification. In the process, connections are automatically created between highly related units and their positions are shifted where the inputs are distributed in multi-dimensional space. Consequently, several separated groups of connected units are formed. Although the interrelationship of units in this space are not easily understood, we succeeded in solving this problem by converting the unit positions into two-dimensional (2-D) space, and by further optimizing the unit positions with the simulated annealing (SA) method. In the optimized 2-D map, visualization of the connections of units provided rich information about clustering. As demonstrated here, this method is clearly superior to both the multi-variate statistical analysis (MSA) and the self-organizing map (SOM) as a classification method and provides a first reliable classification method which can be used without masking for very noisy images.

Sodium imaging of climbing fiber innervation fields in developing mouse Purkinje cells.

Maturation of specific neuronal connections in the mature nervous system includes elimination of redundant synapses formed earlier during development. In the cerebellum of adult animals, each Purkinje cell (PC) is innervated by a single climbing fiber (CF). In early postnatal development each PC is innervated by multiple CFs and elimination of synapses formed by supernumerary CFs occurs until monoinnervation is established at around postnatal day 20 (P20) in mice. It is not clear whether multiple CFs, or only a single CF, translocate from the cell body of immature PCs to the developing dendrite and, in case several CFs translocate, whether they share or segregate their innervation fields. To localize CF innervation fields, we imaged changes in postsynaptic sodium concentration resulting from CF-mediated postsynaptic currents. We found that more than one CF translocates from an innervation field on the cell body of the PC to the developing dendrite and that these CFs share rather than segregate their innervation fields. We concluded that both the soma and the proximal dendrite of the PC are territories of competition for the developing CFs and that the overlapping of their termination fields may be the prerequisite for a local process of elimination of all but one CF, as previously demonstrated in the developing neuromuscular junction.

Sodium channel Na(v)1.6 is expressed along nonmyelinated axons and it contributes to conduction.

Nodes of Ranvier in myelinated fibers exhibit a complex architecture in which specific molecules organize in distinct nodal, paranodal and juxtaparanodal domains to support saltatory conduction. The clustering of sodium channel Na(v)1.6 within the nodal membrane has led to its identification as the major nodal sodium channel in myelinated axons. In contrast, much less is known about the molecular architecture of nonmyelinated fibers. In the present study, Na(v)1.6 is shown to be a significant component of nonmyelinated PNS axons. In DRG C-fibers, Na(v)1.6 is distributed continuously from terminal receptor fields in the skin to the dorsal root entry zone in the spinal cord. Na(v)1.6 is also present in the nerve endings of corneal C-fibers. Analysis of compound action potential recordings from wildtype and med mice, which lack Na(v)1.6, indicates that Na(v)1.6 plays a functional role in nonmyelinated fibers where it contributes to action potential conduction. These observations indicate that Na(v)1.6 functions not only in saltatory conduction in myelinated axons but also in continuous conduction in nonmyelinated axons.

Development of nodes of Ranvier.

The architecture and function of the nodes of Ranvier depend on several specialized cell contacts between the axon and myelinating glial cells. These sites contain highly organized multimolecular complexes of ion channels and cell adhesion molecules, closely connected with the cytoskeleton. Recent findings are beginning to reveal how this organization is achieved during the development of myelinated nerves. The role of membrane proteins involved in axoglial interactions and of associated cytoplasmic molecules is being elucidated, while studies of mutant mice have underlined the importance of glial cells and the specific role of axonal proteins in the organization of axonal domains.