TRPV1 Structural Rearrangements Revealed

The apo-structure of TRPV1 was docked into the 3D density maps of capsaicin- and RTX/DkTx-bound structures as a rigid body. The S1-S4 domain fits nicely into both maps, therefore only slight adjustments were performed at this part of the model. On the other hand, the S4-S5 linker, pore module (S5-P-S6) and TRP domain of the TRPV1 apo-structure exhibit substantial deviation from both maps, indicating structural rearrangements during ligand binding. This part of the model was rebuilt in Coot ^{53 (link),54 (link)} using the apo-structure as a reference. The density map for the pore module of capsaicin bound structure is of sufficient quality to assign most side chains in this region, allowing us to obtain an accurate pore profile by calculating pore radii using HOLE program^{55 (link)}. However, density for the TRP domain, especially the part that immediately follows S6, does not allow for side chain resolution, likely reflecting the dynamic nature of this region during gating. Nonetheless, the invariant W697 in helical TRP domain shows excellent density and serves as a landmark to orient the entire helix. The map of RTX/DkTx bound structure is of sufficient quality to build the model without ambiguity. A polyalanine model (a total of 31 aa) based on the NMR structure of hanatoxin (pdb code: 1D1H) ^{56 (link)} was docked onto the DkTx density with slight adjustment.