Molecular mechanisms of thermal sensing by TRP ion channels

TRPV Ion channels are sophisticated molecular sensors that respond to distinct temperature thresholds. The recent surge in cryo-em structures has provided numerous insights into the structural rearrangements accompanying their opening and closing; however, the molecular mechanisms by which TRPV channels establish precise and robust temperature sensing remain elusive. This work employs molecular simulations, multi-ensemble contact analysis, graph theory, and machine learning techniques to reveal the temperature-sensitive residue-residue interactions driving allostery in TRPV3. We find that groups of residues exhibiting similar temperature-dependent contact frequency profiles cluster at specific channel regions. The dominant mode clusters on the ankyrin repeat domain and display a linear melting trend, while others show non-linear and sometimes increasing contact-frequency trends. These modes describe the residue-level temperature response patterns that underlie the channel's functional dynamics. With network analysis, we show that the community structure of the channel changes with temperature, providing a detailed description of temperature-dependent domain coupling. We also find a network of high centrality contacts that connects distant regions of the protomer to a point directly adjacent to the gate, serving as a means for the temperature-sensitive contact modes to regulate channel gating allosterically. Using a random forest model, we show that the contact states of specific temperature-sensitive modes are indeed predictive of the channel gate's state. Supporting the physical validity of these modes and networks are several residues identified with our analyses that are reported in the literature to be functionally critical. Our results offer a model for thermo-TRP channel function and demonstrate the utility of temperature-sensitive contact analysis.