Probing Ion Channel Structure and Function Using Light-Sensitive Amino Acids.

Approaches to remotely control and monitor ion channel operation with light are expanding rapidly in the biophysics and neuroscience fields. A recent development directly introduces light sensitivity into proteins by utilizing photosensitive unnatural amino acids (UAAs) incorporated using the genetic code expansion technique. The introduction of UAAs results in unique molecular level control and, when combined with the maximal spatiotemporal resolution and poor invasiveness of light, enables direct manipulation and interrogation of ion channel functionality. Here, we review the diverse applications of light-sensitive UAAs in two superfamilies of ion channels (voltage- and ligand-gated ion channels; VGICs and LGICs) and summarize existing UAA tools, their mode of action, potential, caveats, and technical considerations to their use in illuminating ion channel structure and function.

Optogenetic Modulation of Ion Channels by Photoreceptive Proteins.

In these 15 years, researches to control cellular responses by light have flourished dramatically to establish "optogenetics" as a research field. In particular, light-dependent excitation/inhibition of neural cells using channelrhodopsins or other microbial rhodopsins is the most powerful and the most widely used optogenetic technique. New channelrhodopsin-based optogenetic tools having favorable characteristics have been identified from a wide variety of organisms or created through mutagenesis. Despite the great efforts, some neuronal activities are still hard to be manipulated by the channelrhodopsin-based tools, indicating that complementary approaches are needed to make optogenetics more comprehensive. One of the feasible and complementary approaches is optical control of ion channels using photoreceptive proteins other than channelrhodopsins. In particular, animal opsins can modulate various ion channels via light-dependent G protein activation. In this chapter, we summarize how such alternative optogenetic tools work and they will be improved.

Crystal structure of the channelrhodopsin light-gated cation channel.

Channelrhodopsins (ChRs) are light-gated cation channels derived from algae that have shown experimental utility in optogenetics; for example, neurons expressing ChRs can be optically controlled with high temporal precision within systems as complex as freely moving mammals. Although ChRs have been broadly applied to neuroscience research, little is known about the molecular mechanisms by which these unusual and powerful proteins operate. Here we present the crystal structure of a ChR (a C1C2 chimaera between ChR1 and ChR2 from Chlamydomonas reinhardtii) at 2.3 Å resolution. The structure reveals the essential molecular architecture of ChRs, including the retinal-binding pocket and cation conduction pathway. This integration of structural and electrophysiological analyses provides insight into the molecular basis for the remarkable function of ChRs, and paves the way for the precise and principled design of ChR variants with novel properties.

Optogenetics and pharmacogenetics: principles and applications.

Remote and selective spatiotemporal control of the activity of neurons to regulate behavior and physiological functions has been a long-sought goal in system neuroscience. Identification and subsequent bioengineering of light-sensitive ion channels (e.g., channelrhodopsins, halorhodopsin, and archaerhodopsins) from the bacteria have made it possible to use light to artificially modulate neuronal activity, namely optogenetics. Recent advance in genetics has also allowed development of novel pharmacological tools to selectively and remotely control neuronal activity using engineered G protein-coupled receptors, which can be activated by otherwise inert drug-like small molecules such as the designer receptors exclusively activated by designer drug, a form of chemogenetics. The cutting-edge optogenetics and pharmacogenetics are powerful tools in neuroscience that allow selective and bidirectional modulation of the activity of defined populations of neurons with unprecedented specificity. These novel toolboxes are enabling significant advances in deciphering how the nervous system works and its influence on various physiological processes in health and disease. Here, we discuss the fundamental elements of optogenetics and chemogenetics approaches and some of the applications that yielded significant advances in various areas of neuroscience and beyond.

Restoration of visual function by expression of a light-gated mammalian ion channel in retinal ganglion cells or ON-bipolar cells.

Most inherited forms of blindness are caused by mutations that lead to photoreceptor cell death but spare second- and third-order retinal neurons. Expression of the light-gated excitatory mammalian ion channel light-gated ionotropic glutamate receptor (LiGluR) in retinal ganglion cells (RGCs) of the retina degeneration (rd1) mouse model of blindness was previously shown to restore some visual functions when stimulated by UV light. Here, we report restored retinal function in visible light in rodent and canine models of blindness through the use of a second-generation photoswitch for LiGluR, maleimide-azobenzene-glutamate 0 with peak efficiency at 460 nm (MAG0(460)). In the blind rd1 mouse, multielectrode array recordings of retinal explants revealed robust and uniform light-evoked firing when LiGluR-MAG0(460) was targeted to RGCs and robust but diverse activity patterns in RGCs when LiGluR-MAG0(460) was targeted to ON-bipolar cells (ON-BCs). LiGluR-MAG0(460) in either RGCs or ON-BCs of the rd1 mouse reinstated innate light-avoidance behavior and enabled mice to distinguish between different temporal patterns of light in an associative learning task. In the rod-cone dystrophy dog model of blindness, LiGluR-MAG0(460) in RGCs restored robust light responses to retinal explants and intravitreal delivery of LiGluR and MAG0(460) was well tolerated in vivo. The results in both large and small animal models of photoreceptor degeneration provide a path to clinical translation.

Study of light-induced MscL gating by EPR spectroscopy.

A number of techniques developed to investigate protein structure and function depend on chemically modifying and/or labeling of proteins. However, in the case of homooligomeric proteins, the presence of multiple identical subunits obstructs the introduction of residue-specific labels to only one or several subunits, selectively. Here, in order to study the initial conformational changes of a homopentameric mechanosensitive ion channel during its gating, we developed a method for labeling a defined number of subunits of the channel with two different cysteine-specific compounds simultaneously. The first one is a light-sensitive channel activator that determines the degree of openness of the ion channel upon irradiation. The second one is a spin label, containing an unpaired electron, which allows following the resulting structural changes upon channel gating by electron paramagnetic resonance spectroscopy. With this method, we could open MscL into different sub-open states. As the number of light switches per channel increased, the intersubunit spin-spin interactions became less, indicating changes in intersubunit proximities and opening of the channel. The ability of controlled activation of MscL into different open states with a noninvasive trigger and following the resulting conformational changes by spectroscopy will pave the way for detailed spectroscopic studies in the area of mechanosensation.

Flipping the Photoswitch: Ion Channels Under Light Control.

Nature has incorporated small photochromic molecules, colloquially termed 'photoswitches', in photoreceptor proteins to sense optical cues in phototaxis and vision. While Nature's ability to employ light-responsive functionalities has long been recognized, it was not until recently that scientists designed, synthesized and applied synthetic photochromes to manipulate many of which open rapidly and locally in their native cell types, biological processes with the temporal and spatial resolution of light. Ion channels in particular have come to the forefront of proteins that can be put under the designer control of synthetic photochromes. Photochromic ion channel controllers are comprised of three classes, photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and photochromic crosslinkers (PXs), and in each class ion channel functionality is controlled through reversible changes in photochrome structure. By acting as light-dependent ion channel agonists, antagonist or modulators, photochromic controllers effectively converted a wide range of ion channels, including voltage-gated ion channels, 'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperature-sensitive ion channels, into man-made photoreceptors. Control by photochromes can be reversible, unlike in the case of 'caged' compounds, and non-invasive with high spatial precision, unlike pharmacology and electrical manipulation. Here, we introduce design principles of emerging photochromic molecules that act on ion channels and discuss the impact that these molecules are beginning to have on ion channel biophysics and neuronal physiology.

Optimal pulse length of insonification for Piezo1 activation and intracellular calcium response.

Ultrasound (US) neuromodulation, especially sonogenetics, has been demonstrated with potential applications in noninvasive and targeted treatment of various neurological disorders. Despite the growing interest, the mechanism for US neuromodulation remains elusive, and the optimal condition for eliciting a neural response with minimal adverse effect has not been identified. Here, we investigate the Piezo1 activation and intracellular calcium response elicited by acoustical streaming induced shear stress under various US exposure conditions. We find that Piezo1 activation and resultant intracellular calcium response depend critically on shear stress amplitude and pulse length of the stimulation. Under the same insonification acoustic energy, we further identify an optical pulse length that leads to maximum cell deformation, Piezo1 activation, and calcium response with minimal injury, confirmed by numerical modeling of Piezo1 channel gating dynamics. Our results provide insight into the mechanism of ultrasonic activation of Piezo1 and highlight the importance of optimizing US exposure conditions in sonogenetics applications.

Photoswitching of model ion channels in lipid bilayers.

Membrane proteins can be regulated by alterations in material properties intrinsic to the hosting lipid bilayer. Here, we investigated whether the reversible photoisomerization of bilayer-embedded diacylglycerols (OptoDArG) with two azobenzene-containing acyl chains may trigger such regulatory events. We observed an augmented open probability of the mechanosensitive model channel gramicidin A (gA) upon photoisomerizing OptoDArG's acyl chains from trans to cis: integral planar bilayer conductance brought forth by hundreds of simultaneously conducting gA dimers increased by typically >50% - in good agreement with the observed increase in single-channel lifetime. Further, (i) increments in the electrical capacitance of planar lipid bilayers and protrusion length of aspirated giant unilamellar vesicles into suction pipettes, as well as (ii) changes of small-angle X-ray scattering of multilamellar vesicles indicated that spontaneous curvature, hydrophobic thickness, and bending elasticity decreased upon switching from trans- to cis-OptoDArG. Our bilayer elasticity model for gA supports the causal relationship between changes in gA activity and bilayer material properties upon photoisomerization. Thus, we conclude that photolipids are deployable for converting bilayers of potentially diverse origins into light-gated actuators for mechanosensitive proteins.

Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design.

Microbial rhodopsins are photoreceptive membrane proteins, which are used as molecular tools in optogenetics. Here, a machine learning (ML)-based experimental design method is introduced for screening rhodopsins that are likely to be red-shifted from representative rhodopsins in the same subfamily. Among 3,022 ion-pumping rhodopsins that were suggested by a protein BLAST search in several protein databases, the ML-based method selected 65 candidate rhodopsins. The wavelengths of 39 of them were able to be experimentally determined by expressing proteins with the Escherichia coli system, and 32 (82%, p = 7.025 × 10-5) actually showed red-shift gains. In addition, four showed red-shift gains >20 nm, and two were found to have desirable ion-transporting properties, indicating that they would be potentially useful in optogenetics. These findings suggest that data-driven ML-based approaches play effective roles in the experimental design of rhodopsin and other photobiological studies. (141/150 words).

Bioinspired smart gating of nanochannels toward photoelectric-conversion systems.

Learning from nature has inspired the creation of intelligent materials to better understand and imitate biology. Recent studies on bioinspired responsive surfaces that can switch between different states are shown, which open up new avenues for the development of smart materials in two dimensions. Based on this strategy, biomimetic nanochannel systems have been produced by introducing responsive molecules, which closely mimic the gating mechanism of biological nanochannels and show potential applications in many fields such as photoelectric-conversion systems demonstrated in this paper.

Ionizing radiation decreases veratridine-stimulated uptake of sodium in rat brain synaptosomes.

Veratridine-stimulated uptake of sodium-22 in brain synaptosomes was significantly reduced by ionizing radiation over a dose range of 10 to 1000 rads. The response was dose-dependent and involved a decrease in the maximum effect of veratridine on uptake. The central nervous system may be more sensitive to ionizing radiation than generally thought, perhaps through a loss of the ability of the sodium channel to respond properly to stimulation.

Evidence that transduction of electromagnetic field is mediated by a force receptor.

Low-strength magnetic fields triggered onset and offset evoked potentials, indicating that the detection process was a form of sensory transduction; whether the field interacted directly with an ion channel or indirectly via a signaling cascade is unknown. By analogy with electrosensory transduction in lower life forms, we hypothesized that the evoked potentials were initiated by a force exerted by the induced electric field on an ion channel in the plasma membrane. We applied a rapid magnetic stimulus (0.2 ms) and found that it produced evoked potentials indistinguishable in latency, magnitude, and frequency from those found previously when the stimulus was 50 times slower. The ability of the field-detection system in human subjects to respond to the rapid stimulus supported the theory that the receptor potentials necessary for production of evoked potentials originated from a direct interaction between the field and an ion channel in the plasma membrane that resulted in a change in the average probability of the channel to be in the open state.

Sensitized photoinactivation of minigramicidin channels in bilayer lipid membranes.

The method of sensitized photoinactivation based on the photosensitized damage of gramicidin A (gA) molecules was applied here to study ionic channels formed by minigramicidin (the 11-residue analogue of gramicidin A) in a planar bilayer lipid membrane (BLM) of different thickness. Irradiation of BLM with a single flash of visible light in the presence of a photosensitizer (aluminum phthalocyanine or Rose Bengal) generating singlet oxygen provoked a decrease in the minigramicidin-induced electric current across BLM, the kinetics of which had the characteristic time of several seconds, as observed with gA. For gA, there is good correlation between the characteristic time of photoinactivation and the single-channel lifetime. In contrast to the covalent dimer of gA characterized by extremely long single-channel lifetime and the absence of current relaxation upon flash excitation, the covalent head-to-head dimer of minigramicidin displayed the flash-induced current decrease with the kinetics being strongly dependent on the membrane thickness. The current decrease became slower both upon increasing the concentration of the minigramicidin covalent dimer and upon including cholesterol in the membrane composition. These data in combination with the quadratic dependence of the current on the peptide concentration can be rationalized by hypothesizing that the macroscopic current across BLM measured at high concentrations of the peptide is provided by dimers of minigramicidin covalent dimers in the double beta(5.7)-helical conformation having the lifetime of about 0.4 s, while single channels with the lifetime of 0.01 s, observed at a very low peptide concentration, correspond to the single-stranded beta(6.3)-helical conformation. Alternatively the results can be explained by clustering of channels at high concentrations of the minigramicidin covalent dimer.

Fiber-coupled light-emitting diode for localized photostimulation of neurons expressing channelrhodopsin-2.

Channelrhodopsin-2 (ChR2) is a blue-light-gated ion channel that can be used to stimulate genetically defined neurons reproducibly, rapidly and non-invasively. Existing approaches for delivering light to cells expressing ChR2 rely upon microscopes, lasers, arc lamps and shutters, all of which are relatively expensive and are not readily scalable for use on more than one brain region or animal at a time. In this paper, we describe an inexpensive method for delivering blue light locally and with millisecond precision to cells expressing ChR2. We accomplished this by coupling the light from a high-intensity blue light-emitting diode (LED; XLamp XR-E from CREE) into an optical fiber. When positioned in proximity to ChR2-expressing HEK293 cells, this fiber-coupled LED provided localized illumination of up to 32mW/mm2 and generated ChR2 photocurrents as efficiently as wide-field mercury arc lamp illumination. This fiber-coupled LED was also used to photostimulate action potentials in ChR2-expressing dorsal root ganglia (DRG) sensory neurons. LED light power and pulse frequency were controlled with an inexpensive, custom-built amplifier circuit. This scalable fiber-coupled LED system can be used to deliver light independent of the microscope objective and could, in principle, deliver light in parallel to multiple brain regions or to multiple genetically engineered animals.

Mechanisms and Mitochondrial Redox Signaling in Photobiomodulation.

Photobiomodulation (PBM) involves the use of red or near-infrared light at low power densities to produce a beneficial effect on cells or tissues. PBM therapy is used to reduce pain, inflammation, edema, and to regenerate damaged tissues such as wounds, bones, and tendons. The primary site of light absorption in mammalian cells has been identified as the mitochondria and, more specifically, cytochrome c oxidase (CCO). It is hypothesized that inhibitory nitric oxide can be dissociated from CCO, thus restoring electron transport and increasing mitochondrial membrane potential. Another mechanism involves activation of light or heat-gated ion channels. This review will cover the redox signaling that occurs in PBM and examine the difference between healthy and stressed cells, where PBM can have apparently opposite effects. PBM has a marked effect on stem cells, and this is proposed to operate via mitochondrial redox signaling. PBM can act as a preconditioning regimen and can interact with exercise on muscles.

Optical switches and triggers for the manipulation of ion channels and pores.

Like fluorescence sensing techniques, methods to manipulate proteins with light have produced great advances in recent years. Ion channels have been one of the principal protein targets of photoswitched manipulation. In combination with fluorescence detection of cell signaling, this has enabled non-invasive, all-optical experiments on cell and tissue function, both in vitro and in vivo. Optical manipulation of channels has also provided insights into the mechanism of channel function. Optical control elements can be classified according to their molecular reversibility as non-reversible phototriggers where light breaks a chemical bond (e.g. caged ligands) and as photoswitches that reversibly photoisomerize. Synthetic photoswitches constitute nanoscale actuators that can alter channel function using three different strategies. These include (1) nanotoggles, which are tethered photoswitchable ligands that either activate channels (agonists) or inhibit them (blockers or antagonists), (2) nanokeys, which are untethered (freely diffusing) photoswitchable ligands, and (3) nanotweezers, which are photoswitchable crosslinkers. The properties of such photoswitches are discussed here, with a focus on tethered photoswitchable ligands. The recent literature on optical manipulation of ion channels is reviewed for the different channel families, with special emphasis on the understanding of ligand binding and gating processes, applications in nanobiotechnology, and with attention to future prospects in the field.

Self-consistent molecular dynamics formulation for electric-field-mediated electrolyte transport through nanochannels.

A self-consistent molecular dynamics (SCMD) formulation is presented for electric-field-mediated transport of water and ions through a nanochannel connected to reservoirs or baths. The SCMD formulation is compared with a uniform field MD approach, where the applied electric field is assumed to be uniform, for 2nm and 3.5nm wide nanochannels immersed in a 0.5M KCl solution. Reservoir ionic concentrations are maintained using the dual-control-volume grand canonical molecular dynamics technique. Simulation results with varying channel height indicate that the SCMD approach calculates the electrostatic potential in the simulation domain more accurately compared to the uniform field approach, with the deviation in results increasing with the channel height. The translocation times and ionic fluxes predicted by uniform field MD can be substantially different from those predicted by the SCMD approach. Our results also indicate that during a 2ns simulation time K+ ions can permeate through a 1nm channel when the applied electric field is computed self-consistently, while the permeation is not observed when the electric field is assumed to be uniform.

Stimulating Neurons with Heterologously Expressed Light-Gated Ion Channels.

Heterologous expression of ion channels that can be directly gated by light has made it possible to stimulate almost any excitable cell with light. Optogenetic stimulation has been particularly powerful in the neurosciences, as it allows the activation of specific, genetically defined neurons with precise timing. Organotypic hippocampal slice cultures are a favored preparation for optogenetic experiments. They can be cultured for many weeks and, after transfection with optogenetic actuators and sensors, allow the study of individual synapses or small networks. The absence of any electrodes allows multiple imaging sessions over the course of several days and even chronic stimulation inside the incubator. These timescales are not accessible in electrophysiological experiments. Here, we introduce the production of organotypic hippocampal slice cultures and their transduction or transfection with optogenetic tools. We then discuss the options for light stimulation.

The roles of trp and calcium in regulating photoreceptor function in Drosophila.

Invertebrate photoreceptors use the ubiquitous inositol-lipid signaling pathway for phototransduction. This pathway depends on Ca2+ release from internal stores and on Ca2+ entry via light-activated channels to replenish the loss of Ca2+ in those stores. The Drosophila transient receptor potential (TRP) protein is essential for the high Ca2+ permeability and other biophysical properties of these light-activated channels, which affect both excitation and adaptation in photoreceptor cells. Physiological and heterologous expression studies indicate that TRP is a putative subunit of a surface membrane channel that can be activated by depletion of internal Ca2+ stores. Furthermore, trp is an archetypal member of a multigene family whose products share a structure that is highly conserved throughout evolution, from worms to humans.