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. 2019 Jun 18;52(6):1643-1652.
doi: 10.1021/acs.accounts.9b00075. Epub 2019 May 31.

Structural and Evolutionary Insights Point to Allosteric Regulation of TRP Ion Channels

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Structural and Evolutionary Insights Point to Allosteric Regulation of TRP Ion Channels

Jacob K Hilton et al. Acc Chem Res. .

Abstract

The familiar pungent taste of spicy food, the refreshing taste of mint, and many other physiological phenomena are mediated by transient receptor potential (TRP) ion channels. TRP channels are a superfamily of ion channels that are sensitive to diverse chemical and physical stimuli and play diverse roles in biology. In addition to chemical regulation, some family members also sense common physical stimuli, such as temperature or pressure. Since their discovery and cloning in the 1990s and 2000s, understanding the molecular mechanisms governing TRP channel function and polymodal regulation has been a consistent but challenging goal. Until recently, a general lack of high-resolution TRP channel structures had significantly limited a molecular understanding of their function. In the past few years, a flood of TRP channel structures have been released, made possible primarily by advances in cryo-electron microscopy (cryo-EM). The boon of many structures has unleashed unparalleled insight into TRP channel architecture. Substantive comparative studies between TRP structures provide snapshots of distinct states such as ligand-free, stabilized by chemical agonists, or antagonists, partially illuminating how a given channel opens and closes. However, the now ∼75 TRP channel structures have ushered in surprising outcomes, including a lack of an apparent general mechanism underlying channel opening and closing among family members. Similarly, the structures reveal a surprising diversity in which chemical ligands bind TRP channels. Several TRP channels are activated by temperature changes in addition to ligand binding. Unraveling mechanisms of thermosensation has proven an elusive challenge to the field. Although some studies point to thermosensitive domains in the transmembrane region of the channels, results have sometimes been contradictory and difficult to interpret; in some cases, a domain that proves essential for thermal sensitivity in one context can be entirely removed from the channel without affecting thermosensation in another context. These results are not amenable to simple interpretations and point to allosteric networks of regulation within the channel structure. TRP channels have evolved to be fine-tuned for the needs of a species in its environmental niche, a fact that has been both a benefit and burden in unlocking their molecular features. Functional evolutionary divergence has presented challenges for studying TRP channels, as orthologs from different species can give conflicting experimental results. However, this diversity can also be examined comparatively to decipher the basis for functional differences. As with structural biology, untangling the similarities and differences resulting from evolutionary pressure between species has been a rich source of data guiding the field. This Account will contextualize the existing biochemical and functional data with an eye to evolutionary data and couple these insights with emerging structural biology to better understand the molecular mechanisms behind chemical and physical regulation of TRP channels.

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Figures

Figure 1.
Figure 1.. TRP channel evolutionary relationships and representative structures.
Left, a phylogenetic tree of human TRP channels, including an ancestral non-mammalian TRPN1 channel (Gray). Yellow stars indicate that a structure of either the human or an ortholog channel has been determined. To date, at least two structures have been determined from each human TRP subfamily, with exception of TRPA1, where there is a lone human subfamily member. Representative structures have been determined for the entire vanilloid (TRPV) subfamily. The structures reveal a conserved general transmembrane architecture with highly diverse extramembrane loops and N- and C-terminal domains. The collective structural information has shaped understanding of how TRP channels gate in response to chemical and physical stimuli. TRPA is for ankyrin, -V for vanilloid, -M for melastatin, -C for canonical, -ML for mucolipin, -P for polycystic.
Figure 2.
Figure 2.. The conserved transmembrane architecture of TRP ion channels.
A TRP channel monomer (left panels) contains six transmembrane helices, including two conserved structural domains. The S1-S4 ligand sensing domain (blue) is a four-helix bundle of first four transmembrane helices, S1 to S4. The last two transmembrane helices, S5 and S6, form the pore domain (PD, red) where the tetramer of the PD forms the conductance pathway of the channel. The S1-S4 domain and the PD are linked by an S4-S5 linker (orange). Two additional conserved helices are the pore helix (PH, purple) and the amphipathic TRP helix (cyan). A functional channel is composed of a domain-swapped tetramer, with the PD helices interacting with adjacent subunits (right panels). Structural and functional studies suggest that allosteric networks between binding, temperature sensing, and other stimuli regulate these channels.
Figure 3.
Figure 3.. Insights from evolutionary studies.
A) TRPM8 and TRPV1 show distinct patterns of coevolution. Using GREMLIN software the 100 highest probability predicted coevolving residues were plotted on homology models of the human TRPV1 (red) and TRPM8 (blue) TMD regions (including helices S1-S6), with pseudo-bonds shown between coevolving pairs. The analysis identifies coevolution of the intracellular S1-S4 domain to the pore domain. However, patterning differences of the evolutionary constraints suggests there are distinct mechanisms and allosteric networks. B) The frequency of exonic human TRPM8 single-nucleotide polymorphisms (SNPs) as a function of residue number. A decreased SNPs frequency in the TMD indicates that this region is less tolerant of mutations. Data were aggregated from the Ensembl database searching exclusively deposited human genomes.
Figure 4.
Figure 4.. Allosteric coupling in ligand and temperature activation.
Panel A shows structures of 2-APB bound TRPV3 and TRPV6 in gold and cyan respectively. Between the two structural studies, four 2-APB binding sites have been identified in related TRPV channels. These coupled with functional studies suggest that in 2-APB ligand regulation of TRP channels allostery is key to modulating function. Panel B identifies residues essential to exchanging cold-sensing properties between TRPM8 channels from hibernating and non-hibernating rodents. The six residues are far away in space indicating that allosteric networks are key to deciphering these outcomes. Comparing these six mutations with human TRPM8 show that not only are allosteric networks important but also that there must be compensating pairs of residues that impact allostery.
Figure 5.
Figure 5.. Diverse S1-S4 gating-coupled movements identified from TRPV structural studies.
In TRPV1, the S1-S4 domain remains immobile while a residing lipid (black rectangle) is replaced by a vanilloid ligand (red circle). In TRPV2, the S1-S4 domain, along with intracellular ankyrin repeat domains, rotates when the lower gate opens. In TRPV3, the S1-S4 domain tilts towards the PD when the agonist 2-APB (yellow diamond) binds to the S1-S4 domain. TRPV4 gating details are presently unclear, but a unique S1-S4 arrangement causes the S3 helix to contact S6 helix. In TRPV5, the S1-S4 domain tilts away from the PD when the antagonist econazole (dark green hexagon) enters the binding pocket, causing the lower gate to close. In TRPV6, the inhibitor 2-APB (yellow diamond) causes the S3 helix to move toward S4-S5 linker to close the lower gate.

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