Atom-by-atom engineering of voltage-gated ion channels: magnified insights into function and pharmacology

Improved ANAP incorporation and VCF analysis reveal details of P2X7 current facilitation and a limited conformational interplay between ATP binding and the intracellular ballast domain

The large intracellular C-terminus of the pro-inflammatory P2X7 ion channel receptor (P2X7R) is associated with diverse P2X7R-specific functions. Cryo-EM structures of the closed and ATP-bound open full-length P2X7R recently identified a membrane-associated anchoring domain, an open-state stabilizing "cap" domain, and a globular "ballast domain" containing GTP/GDP and dinuclear Zn²⁺-binding sites with unknown functions. To investigate protein dynamics during channel activation, we improved incorporation of the environment-sensitive fluorescent unnatural amino acid L-3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (ANAP) into Xenopus laevis oocyte-expressed P2X7Rs and performed voltage clamp fluorometry. While we confirmed predicted conformational changes within the extracellular and the transmembrane domains, only 3 out of 41 mutants containing ANAP in the C-terminal domain resulted in ATP-induced fluorescence changes. We conclude that the ballast domain functions rather independently from the extracellular ATP binding domain and might require activation by additional ligands and/or protein interactions. Novel tools to study these are presented.

Structural Pharmacology of Voltage-Gated Sodium Channels

Voltage-gated sodium (Na_V) channels initiate and propagate action potentials in excitable tissues to mediate key physiological processes including heart contraction and nervous system function. Accordingly, Na_V channels are major targets for drugs, toxins and disease-causing mutations. Recent breakthroughs in cryo-electron microscopy have led to the visualization of human Na_V1.1, Na_V1.2, Na_V1.4, Na_V1.5 and Na_V1.7 channel subtypes at high-resolution. These landmark studies have greatly advanced our structural understanding of channel architecture, ion selectivity, voltage-sensing, electromechanical coupling, fast inactivation, and the molecular basis underlying Na_V channelopathies. Na_V channel structures have also been increasingly determined in complex with toxin and small molecule modulators that target either the pore module or voltage sensor domains. These structural studies have provided new insights into the mechanisms of pharmacological action and opportunities for subtype-selective Na_V channel drug design. This review will highlight the structural pharmacology of human Na_V channels as well as the potential use of engineered and chimeric channels in future drug discovery efforts.

Exploring structural dynamics of a membrane protein by combining bioorthogonal chemistry and cysteine mutagenesis

The functional mechanisms of membrane proteins are extensively investigated with cysteine mutagenesis. To complement cysteine-based approaches, we engineered a membrane protein with thiol-independent crosslinkable groups using azidohomoalanine (AHA), a non-canonical methionine analogue containing an azide group that can selectively react with cycloalkynes through a strain-promoted azide-alkyne cycloaddition (SPAAC) reaction. We demonstrate that AHA can be readily incorporated into the Shaker Kv channel in place of methionine residues and modified with azide-reactive alkyne probes in Xenopus oocytes. Using voltage-clamp fluorometry, we show that AHA incorporation permits site-specific fluorescent labeling to track voltage-dependent conformational changes similar to cysteine-based methods. By combining AHA incorporation and cysteine mutagenesis in an orthogonal manner, we were able to site-specifically label the Shaker Kv channel with two different fluorophores simultaneously. Our results identify a facile and straightforward approach for chemical modification of membrane proteins with bioorthogonal chemistry to explore their structure-function relationships in live cells.

Living cells can sense cues from their environment via molecules located at the interface between the inside and the outside of the cell. These molecules are mostly proteins and are made up of building blocks known as amino acids. To understand how these proteins work, fluorescent probes can be attached to amino acids within them – which can then tell when different parts of proteins move in response to a signal. Scientists often target fluorescent probes at the amino acid cysteine, because it has a chemically reactive side group and is rare enough so that unique positions can be labeled in the protein of interest. However, being able to target other amino acids would allow scientists to ask, and potentially solve, more precise questions about these proteins.

Methionine is another amino acid that has a low abundance in most proteins. Previous research has shown that the cell’s normal protein-building machinery can incorporate synthetic versions of methionine into proteins. This suggested that the introduction of chemically reactive alternatives to methionine could offer a way to label membrane proteins with fluorescent probes and free up the cysteines to be targeted with other approaches. Gupta et al. set out to develop a straightforward method to achieve this and started with a well-studied membrane protein, called Shaker, and cells from female African clawed frogs, which are widely used to study membrane proteins.

Gupta et al. found that the cells could readily take up a chemically reactive methionine alternative called azidohomoalanine (AHA) from their surrounding solution and incorporate it within the Shaker protein. The AHA took the place of the methionines that are normally found in Shaker, and just like in cysteine-based methods, fluorescent probes could be easily attached to the AHAs in this membrane protein. Shaker is a protein that allows potassium ions to flow across the cell membrane by changing shape in response to the membrane voltage. The fluorescence from those probes also changed with the membrane voltage in a way that was comparable to cysteine-mediated approaches. This indicated that the AHA modification could also be used to track structural changes in the Shaker protein. Finally, Gupta et al. showed that AHA- and cysteine-mediated labeling approaches could be combined to attach two different fluorescent probes onto the Shaker protein.

This method will expand the toolbox for researchers studying the relationship between the structure and function of membrane proteins in live cells. In future, it could be applied more widely once the properties of the fluorescent probes for AHA-mediated labeling can be optimized.