- Describe the basic structure of Nav and Kv ion channels (number of subunits or repeats, number of membrane-crossing alpha helices per repeat/subunit) and whether this pattern is common to all known ion channels.
- Ion channels have 4 membrane spanning domains.
- In K+ potassium channels, they’re composed of 4 separate polypeptides.
- Na+ and Ca2+ channels, there are 4 units spanning the membrane (made of 4 units each) that are linked together (instead of being separate) = I, II, III, and IV.
- Each domain contains 6 alpha helices (S1-6). ((connection between 3-4 are the inactivation domain in Na))
- opening of activation gate likely corresponds to hinge like motion of the S6 segment around conserved glycines.
- S4 helices have positively charged residues, or basic residues, every 3rd position (lys or arg) –> sense voltage in the environment.
- S5 and S6 helices, and their connecting P loop (pore loop), assemble to form the conducting pathway and selectivity filter (that makes sure correct ion passes through).
Not all ion channels are like this.
- NT receptors are generally coupled to ion channels (ionotropic) or activate 2nd messenger pathways that can affect different ion channels (metabotropic).
- –>Pentamer ligand-gated channels (like GABAR, GlyR, nAChR, 5HTR) –>heteropentamers with 4 transmembrane alpha helices per subunit (M1-M4). M2 helices surround the ion-conducting pathway; selective for Cl-, with slight preference for Na over K.
- –>Tetrameric ligand gated channels (like ionotropic glutamate receptors) 4 subunits with 3 alpha-helices each. In NMDA receptors, 2 subunits bind glutamate, and 2 bind glycine.
- –>CLC chloride channels are dimers, and each subunit has an independently-gated pore. A different gate further controls both those pores simultaneously. Some of these channels can be H+/Cl- exchangers. CLC chloride channels are important for stabilizing resting MP.
- –> Aquaporin water channels = tetramers, and each subunit contains a water pore that excludes all ions = ‘anti-ion’ channel (this incudes protons). They have water pores and a gated, central ion pore. Generally expressed in kidney or other tissues where you need rapid movement of water.
- Describe the basic principles of channel selectivity, the features of ions that are important for selectivity, and the role of dehydration of the ions.
Selectivity varies on lots of factors like specificity, size, charge, dehydration, and multiple binding sites.
Channel may be specific for a certain type of ion:
- K channel prefers K to Na, 10,000:1
- Na channel prefers Na to K 12:1
- Ca channel prefers Ca to Na 3000:1
- nAChr channel prefers Na to K 1.3: 1 (so not as selective based on ion)
- Channels can select based on size; too large ions are rejected.
- Charge is important; cation vs. anion channels. Valence can be important.
- Dehydration –>ions stabilized in solution by water, which makes the ions larger in size. Channels have to dehydrate the ion before they can pass through the pore (but this is energetically unfavorable) –> ion gets stabilized within the pore via energetic interactions with the AAs. Can interact with positive/basic residues (lys, arg), negative/acidic residues (glu, asp), with backbone carbonyls (which are negative) or alpha helix dipoles (N terminal is positive, C terminal is negative).
- Multiple binding sites can increase selectivity; even if its just the slight differences in the strength of an interaction between a preferred vs. non-preferred ion can overall enhance selectivity for preferred ion.
- Describe specific structures of Nav and Kv channels that serve as the voltage sensors, the selectivity filter, and the activation/inactivation gates and describe where these gates are located with respect to the membrane orientation of Nav and Kv.
- Gating is controlled by membrane potential (Vm) and the S4 subunit.
- Going from negative to positive Vm, activation gate in potassium channel rotates around a center pivot point (controlled by voltage-sensor S4) to the open position and K ions flow out of the cell –>activation.
- When the inside of the cell is made negative, the gate rotates back into the closed position –> deactivation.
- So in potassium channels we have activation and deactivation that responds to changes in Vm of the cell.
-In turn, Na channels have an activation gate and an inactivation gate, and yes inactivation is different then deactivation.
-When potentials switch from negative to positive, Na activation gate swings open and Na ions flow into the cell (here the process is still similar to that of K that we just learned about.
-Here, Inactivation gate is open at resting potential because the activation gate blocks its binding site within the pore.
-After the activation gate opens, the inactivation gate can bind to its site and ‘close’ –> inactivation –> current decays to 0 during a maintained depolarization. inactivation is like a teather ball
-Deactivation is when you have ‘removal of inactivation’ and the activation gate swings back into the closed position.
- So essentially the pattern goes like this activation, then inactivation, then removal of inactivation, then deactivation. In which one step must precede the other. Also note that activation and deactivation are fast processes, while inactivation and removal are slower.
-For sodium and potassium channels there seem to be conserved glycines involved in activation.
-Activation gates are likely the inner ends of the S6 helices that rotate (hinge-like) around conserved glycine residues.
- For Na channels, Inactivation gate formed by the linker between units III and IV (III-IV linker).
Vestibule on is an enlarged space ions must pass through before getting to the more narrow ‘selectivity filter’ part of the channel.
- Describe what structural features of Nav and Kv lead to “sidedness” of agents that act on these channels and to “state-dependence” of action.
- Selectivity filter on the extracellular side of the channel; vestibule near the intracellular side of the channel
- Some reagents site of action may only be on one side of the channel
Ex) TTX (tetrodoxin) = charged molecule that can’t cross the membrane, so when added to the ECF, it binds within the entrance of the pore (independent of the position of the activation or inactivation gates). No effect when added intracellularly because there’s no place for it to bind. only na not k.
Ex)Lidocaine. Equilibrates between its protonated and deprotonated forms. Protonated cannot cross the membrane; de-protonated form can. Protonated Lidocaine can block the channel from the intracellular side (produces anesthesia), but can only happen if Lidocaine can cross the vestibule (which requires activation gate be open and inactivation gate be open = state-dependent). Because Lidocaine binds within vestibule, it can be trapped there if the gates are closed.
