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A tethered intracellular particle blocks an open ion channel from the cytoplasmic side. In classical Shaker-type channels the particle is N-terminal: removing it suppresses fast inactivation, while cytoplasmic application of a corresponding peptide can restore block. The pore-blocking mechanism differs from ordinary activation-gate closure.

A localized region with calcium concentration differing from the surrounding compartment, for example close to an open ion channel. A whole-cell average can miss such local signals.

The cell membrane, also called the plasma membrane, is the selective boundary separating a biological cell's cytoplasm from its surroundings. Both prokaryotes and eukaryotes have a cell membrane. Where a cell wall is present, it is a distinct structure outside the cell membrane; the two names are not synonyms. This separation lets a biological cell maintain internal conditions while exchanging material through membrane transport. See NHGRI: cell membrane.

The familiar architecture is a lipid bilayer containing membrane proteins. In a phospholipid-based lipid bilayer, two membrane leaflets face opposite ways: hydrophilic heads face the water on each side, while hydrophobic tails face one another in the interior. The heads are therefore exposed both outside and inside the biological cell. This arrangement combines a water-facing surface with a barrier to many water-soluble solutes; the schematic represents organization rather than an atomistic structure. See Alberts et al., Molecular Biology of the Cell: the lipid bilayer.

Selective permeability means that different substances cross at different rates under comparable conditions. Small nonpolar molecules can pass through a lipid bilayer by diffusion, while ions encounter a strong barrier without a suitable route. An ion channel supplies a selective water-filled pathway when open; a carrier protein binds a solute and changes shape to expose it to the other side. These membrane proteins therefore add specific routes to the barrier. An open ion channel permits passive transport, whereas a carrier protein can mediate either passive transport or active transport. See Alberts et al.: principles of membrane transport.

The useful combination is retention plus controlled exchange: a completely impermeable boundary would prevent uptake, whereas unrestricted mixing would erase differences in concentration and membrane potential. The fluid mosaic model connects these functions to an organized but mobile lipid bilayer containing proteins.

A cell-surface receptor detects an extracellular signal at the cell membrane. Its changed state affects the intracellular side, coupling reception to signal transduction or directly to an ion channel's opening.

A chemical synapse transmits a signal by releasing neurotransmitter from a presynaptic neuron to act on postsynaptic receptors across a synaptic cleft. The two cell membranes remain separate. A typical fast transmission sequence is:

See Chemical Synapses and 3.1 Synapses. The fast pathway uses synaptic vesicles prepared near release sites; it does not require a distant synaptic vesicle to travel across the terminal after every action potential. See Basic Neurochemistry: calcium entry and vesicles at release sites. Some chemical synapses release neurotransmitter in response to graded presynaptic membrane potential changes rather than action potentials.

Neurotransmitter clearance limits how long released neurotransmitter remains available. Depending on the neurotransmitter and location, diffusion away, uptake through membrane transport proteins into the sending or neighboring biological cells, and breakdown by enzymes contribute. Receptor binding and unbinding also affect response duration. Recovering synaptic vesicle membrane is a separate recycling task; uptake of released neurotransmitter is not the return of an intact synaptic vesicle. See General Principles of Cell Communication.

This electrical-to-chemical-to-electrical sequence offers several places to adjust a signal: synaptic release probability, receptor availability and neurotransmitter clearance can change its strength or duration. It helps explain why synaptic plasticity can modify communication between neurons, and why an arriving action potential need not cause a postsynaptic action potential.

Otto Loewi's 1936 Nobel lecture describes his 1921 experiment: fluid from a frog heart whose nerves had been stimulated produced the corresponding response when transferred to another heart. The transferable substance established chemical mediation in that preparation. This was evidence for released chemical signaling, not yet an identification of synaptic vesicle fusion and not a claim that every synapse is chemical. See Loewi, The Chemical Transmission of Nerve Action, Nobel lecture, 12 December 1936.

An ion channel that conducts chloride and, for some family members, other anions. Members differ in voltage dependence and physiological role; an anion channel is distinct from a coupled anion exchanger.

An availability change associated with the outer pore and selectivity filter of certain potassium ion channels. Its kinetics and structural origin differ from ball-and-chain inactivation, although the two processes can interact.

Cytosol dialysis is exchange between the cytosol and pipette solution through the opening used in conventional whole-cell recording. Diffusion can change ion concentrations and dilute soluble regulators of ion channels. A diminishing response can therefore reflect the recording's alteration of the biological cell, rather than the experimental treatment.

A direct motivating example is the 1988 article Muscarinic activation of ionic currents measured by a new whole-cell recording method. In rat lacrimal gland biological cells, the acetylcholine response in conventional whole-cell recording lasted about five minutes. With a pore-forming substance in the patch pipette instead of open break-in, the response remained undiminished after one hour. The readout was activation of calcium-activated potassium and ${\mathrm{Cl}}^{-}$ ion electric currents; preserving the response supported a role for retained cytoplasmic components. The authors also tested the substance extracellularly and observed reversible increases in cation electrical conductance. This comparison motivates perforated patch recording, but does not show that every intracellular constituent or every ion channel response is preserved. ^[ref]

Practical controls are matched pipette and bath compositions, recording elapsed time after break-in, time-matched untreated preparations, and tracking both patch-clamp series resistance and baseline leakage. Comparing conventional whole-cell recording with perforated patch recording can separate loss of soluble components from an intended treatment effect, but only if electrical access is characterized in both. These are controls suggested by the mechanisms above, not a new set of measured results.

Neuroscientist and biophysicist whose research includes ion channels.^[ref]

Facilitated diffusion is passive transport through a membrane transport protein, such as an ion channel or carrier protein, down the relevant electrochemical gradient. The protein supplies a route; it does not by itself provide free energy for uphill transfer.

A G protein-coupled receptor is a cell-surface receptor that relays activation through a G protein on the intracellular side of the cell membrane. The activated G protein can regulate an enzyme or ion channel, so a GPCR supplies a concrete metabotropic receptor example: ligand recognition and the eventual response are connected through distinct components. Different G proteins couple to different targets. See Alberts et al., Molecular Biology of the Cell, 4th edition: signaling through G-protein-linked cell-surface receptors.

A conductance-based Hodgkin-Huxley model couples membrane potential to voltage-dependent channel-gating variables. It explains generation of action potentials through regenerative and opposing ionic electric currents, while its parameters and channel assumptions determine its biological domain of validity.

In the classical model, $m$ describes sodium activation, $h$ describes availability against sodium inactivation, and $n$ describes potassium activation. Each follows two-state ion-channel gating, with its own voltage-dependent rates. The available electrical conductances areThe barred quantities are maximum electrical conductances. The factors have the interpretation of independent permissive gates in an ion channel: three activation factors and a distinct inactivation-availability factor for sodium, and four identical activation factors for potassium. Large $h$ means availability; small $h$ means inactivation. These are model assumptions, not a literal structural description of every ion channel. See Gerstner, Kistler, Naud and Paninski, Neuronal Dynamics (2014), §2.2: model definition and stochastic opening.

With inward-positive electric current, a single-compartment form isHere $C$ is membrane capacitance, $I_{\mathrm{ext}}$ is imposed inward electric current, $g_L$ is leak electrical conductance, and each $E$ is a reversal potential. Use consistent units, and either whole-compartment quantities throughout or quantities per membrane area throughout. Opening changes electrical conductance; the reversal potential and present membrane potential determine the associated electric current. Coupling this equation to the voltage-dependent gates makes a generally nonlinear system of ordinary differential equations; a gate's fixed-voltage limit alone does not specify its evolving state during an action potential.

The original quantitative account is ^[ref]. The contrast with the leaky integrate-and-fire model is useful: here an action potential emerges from evolving ionic electric currents, whereas the simpler model records a threshold event and imposes a reset.

A permissive gate allows conduction when it is open. Suppose an ion channel conducts only when all $q$ gates are open, where $q$ is a positive integer. If the gate-open events are mutually independent events and each has the same open probability $p$ at the time considered, thenThis follows from the multiplication rule for independent events. Identical transition rates alone do not guarantee independence: the initial gate states must also be independently prepared, and the model must not couple their transitions. Gates sharing a fluctuating membrane potential can be correlated; the simple product requires an appropriate independence assumption, for example independent gates at an externally fixed voltage.

At $p=0.5$, channels requiring $q=1,2,4$ permissive gates have open probabilities $0.5$, $0.25$ and $0.0625$. For four independent gates there are $2^4=16$ possible open/closed configurations, equally probable at $p=0.5$; only the all-open configuration conducts. Thus $0.5$ is the gate-open probability, while $0.0625$ is the whole-channel open probability. Neither is a fractional state of one observed channel. Among $160$ independently prepared identical four-gate channels, the expected value of the open count is $160/16=10$, although an actual count fluctuates.

For unequal independent gate-open probabilities $p_j$, use $P_{\mathrm{open}}={\prod }_j{p}_j$ rather than $p^q$. This is the distinction behind the Hodgkin-Huxley model's $m^{3}h$: $m$ and $h$ are different activation and inactivation-availability variables, rather than one common $p$. Its $n^4$ uses four identical activation factors. Independence and the all-open requirement are model assumptions; correlated gates or alternative conducting configurations require a different calculation. The simple product is useful because a modest gate-open probability can produce sharply suppressed whole-channel availability without any additional gate interaction.

An IP3 receptor is an intracellular ligand-gated ion channel, rather than the extracellular signal's cell-surface receptor. Its opening is regulated by both IP3 and cytosolic calcium: IP3 binding is not a command that fixes one constant release rate. Mammalian IP3 receptors have three subtypes, with possible mixed assemblies and splice variants; these need not have identical regulation or cellular roles. The 2010 authored account distinguishes established channel behavior from then-unresolved structural explanations.^[ref]

An inside-out patch is an excised membrane patch whose cytosol side faces the bath. Bath changes can therefore test effects on the intracellular face of an ion channel, with the extracellular face exposed to pipette solution.

An ion channel is a membrane protein that provides a selective pathway for ions across a cell membrane. An open pore permits passive transport down the relevant electrochemical gradient; it does not supply the free energy for uphill transport as a pump involved in active transport does. Two things are needed for a net electric current: an available pathway and an electrochemical potential difference. Opening a pore alone need not produce a net electric current. See Ion Channels and the Electrical Properties of Membranes.

The selective permeability of an ion channel depends on interactions between its pore and the passing ions, not simply on a hole's diameter. Some ion channels strongly favor potassium over sodium; others admit several kinds of positively charged ions. Thus selective does not necessarily mean exclusive to one ion species. See Purves et al., Neuroscience, 2nd edition (2001): molecular structure of ion channels and the mixed-channel example in Purves et al.: principles derived from studies of the neuromuscular junction.

Gating is the opening and closing of an ion channel's pathway. A voltage-gated ion channel responds to membrane potential; an ionotropic receptor can respond to a bound ligand. Gating changes the available electrical conductance, while the electrochemical gradient supplies the drive for passive transport. For a fixed reversal potential in the simple model below, opening more identical ion channels increases the magnitude of the electric current at a fixed nonzero drive, without choosing its sign independently of membrane potential. The two-state ion-channel gating model describes how the open fraction can change. See the Alberts reference above.

For a worked approximation, hold an open population's electrical conductance at $g=10\mathrm{nS}$ and its reversal potential at $E_{\mathrm{rev}}=-80\mathrm{mV}$. Use $V=V_{\mathrm{inside}}-V_{\mathrm{outside}}$ for membrane potential and inward-positive conventional current:At $V=-100,-80,-60\mathrm{mV}$, respectively, the electric currents are $+200,0,-200\mathrm{pA}$, since $1\mathrm{nS}\times 1\mathrm{mV}=1\mathrm{pA}$. Positive electric current means net positive electric charge entering, or net negative electric charge leaving; it does not mean that every ion moves inward. For a pore passing only positive ions, the three results mean net inward passage, no net passage, and net outward passage. These stipulated values describe an illustrative Ohmic approximation, not measured properties of a particular ion channel; see reversal potential for the current plot and limitations.

The useful connection is between a molecular gate and a controllable electric current. A ligand can change electrical conductance through an ionotropic receptor, or membrane potential can change it through a voltage-gated ion channel, connecting recognition and electrical signaling. In a historical landmark, Erwin Neher and Bert Sakmann reported currents from individual ion channels in frog muscle membranes in 1976. See Neher and Sakmann, Single-channel currents recorded from membrane of denervated frog muscle fibres, Nature 260, 799–802 (1976).

A disease in which altered ion channel number, transport or gating contributes to abnormal cell function. A causal account connects measured channel behavior to cellular activity, rather than inferring mechanism from a sequence variant alone.

A transient electrical current associated with displacement of voltage-sensor charge during ion channel gating, distinct from current carried through an open permeation pathway. Its voltage dependence and changes following sensor mutations constrain the charge motions that couple membrane potential to opening.

Ion-channel inactivation is loss of availability for conduction, distinct from simply closing an otherwise activatable ion channel. Recovery depends on channel type and membrane potential; incomplete recovery of sodium-selective voltage-gated ion channels contributes to a neuronal refractory period.

The probability that an ion channel is in a conducting open state under specified conditions. For N equivalent channels, each carrying open-state electric current i, the mean total electric current is $N{P}_{O}i$. An ensemble open fraction and the fraction of time one channel remains open coincide under suitable stationary and ergodic assumptions. A two-state ion-channel gating model is one model of this probability, not its definition.