Coupling structure with function in acid-sensing ion channels: challenges in pursuit of proton sensors

Abstract

Acid-sensing ion channels (ASICs) are a class of trimeric cation-selective ion channels activated by changes in pH within the physiological range. They are widely expressed in the central and peripheral nervous systems where they participate in a range of physiological and pathophysiological situations such as learning and memory, pain sensation, fear and anxiety, substance abuse and cell death. ASICs are localized to cell bodies and dendrites, including the postsynaptic density, and within the last 5 years several examples of proton-evoked ASIC excitatory postsynaptic currents have emerged. Thus, ASICs have become bona fide neurotransmitter-gated ion channels, activated by the smallest neurotransmitter possible: protons. Here we review how protons are thought to drive the conformational changes associated with ASIC activation and desensitization. In particular, we weigh the evidence for and against the so-called 'acidic pocket' being a vital proton sensor and discuss the emerging role of the β11-12 linker as a desensitization switch or 'molecular clutch'. We also examine how proton-induced conformational changes pose unique challenges to classical molecular dynamics simulations, as well as some possible solutions. Given the emergence of new methodologies and structures, the coming years will probably see many advances in the study of acid-sensing ion channels.

Keywords: ASICs; acid-sensing ion channels; desensitization; gating; molecular dynamics.

Figure 1. Phylogeny, function and form of acid-sensing ion channels

(A) Phylogenetic tree of human ASIC subunits. hBASIC is also known as ASIC5. Gray colored subunits are not proton sensitive. (B) Representative response of hASIC1a in an outside-out patch recording. (B, inset) Curves for pH activation (blue) and steady-state desensitization (red) generated using the Hill equation with pH₅₀ values (and slopes) of 6.4 (2) and 7.1 (8), respectively. (C) cASIC1 monomer (PDB: 4NYK) with individual domains colored. (D) Close in view of acidic pocket (boxed region in C). (E) cASIC1 trimer (PDB: 4NYK) with subunits tinted in green, orange or blue. Acidic pocket, palm domain and GAS belt are marked. (F) Close in view of palm domain (boxed region in E). Labelled positions for D and F are listed in Table 1 using cASIC1 numbering.

Figure 2. Structural changes associated with ASIC gating

(A, B) Resting and MitTx-bound open states of cASIC1 (PDB: 5WKV and 4NTW, A and B) with single subunit shown in cylinder representation. (C) Overlay of single subunits from A and B. (D) Toxin-bound open state (PDB: 4NTW) colored based on root mean squared difference between the resting state in A and the open state, where warmer colors denote greater differences according to the color key.

Figure 3. Structural changes associated with ASIC desensitization

(A, B) MitTx-bound open and desensitized states of cASIC1 (PDBs: 4NTW and 4NYK, respectively) with single subunit shown in cylinder representation. (C) Structural alignment of single subunits from A and B. (D) Toxin-bound open state monomer (PDB: 4NTW) colored based on root mean squared difference between the desensitized state in B and the open state, where warmer colors denote greater differences according to the color key. (E) Open state colored based on RMSD from the desensitized state with two chains illustrated. (F) Close up view of the boxed region in E to highlight the β11–12 linker. (G) Rotation and expansion of the boxed region showing the re-orientation of the linker between open and desensitized structures.