Table 1.
Templates used for homology modeling of TRPs and the packing of LBD of TRPV1 and TRPM8 channels.
| Protein | Method used | Structure or structural template with PDB identifier | Packing of LBD | References | |
|---|---|---|---|---|---|
| TRPV1 | Homology modeling | - S1–S6 | 2R9R (Kv1.2) | n/d | Brauchi et al., 2007 |
| - C- termini | 1Q3E (HCN2) | ||||
| TRPV1 | Homology modeling | - N-termini (TMP kinase) | 1E9C | Loose | Fernández-Ballester and Ferrer-Montiel, 2008 |
| - Ankyrin domain (TRPV1 ARD) | 2PNN | ||||
| - S1–S6 (Kv1.2) | 2R9R | ||||
| - Proximal C-termini (synthetic) | 1WL5 | ||||
| - Distal C- termini1 (HCN2 channel) | Q3E | ||||
| TRPV1 | CryoEM | - Ankyrin domain (TRPV1 ARD) | 2PNN | n/d | Moiseenkova-Bell et al., 2008 |
| - S1–S6 (Kv1.2) | 2R9R | ||||
| TRPM8 | Homology modeling | 13 different protein fragments. Including: | Loose | Pedretti et al., 2009 | |
| - S3 and S4 (Kv1.2) | 2R9R | ||||
| - C- termini (HCN2-cAMP) | 1Q50 | ||||
| TRPM8 | TRPM8 and TRPM8-ago nist MD simulations | TRPV1 homology model by Pedretti et al. (2009). | Loose | Pedretti et al., 2011 | |
| TRPV1 | Fluorescence spectroscopy and CryoEM | - Ankyrin domain | 2PNN | Constrained | De-la-Rosa et al., 2013 |
| - S1–S6 | 2R9R | ||||
| TRPM8 TRPV1 | Homology modeling and further testing by chimeric constructs | Independently: | Constrained | Kalia and Swartz, 2013 | |
| (Kv1.2) | 2R9R | ||||
| (MLotiK) | 3CL1 | ||||
| TRPV1 | CryoEM for apo TRPV1 channel | 2R9P | – | Liao et al., 2013 | |
| TRPV1 | CryoEM for RTX/DkTx bonded TRPV1 channel | 2R9Q | – | Cao et al., 2013b | |
| TRPV1 | CryoEM for capsaicin bonded TRPV1 channel | 2R9R | – | Cao et al., 2013b | |
n/d, not described.
An extensive overview on the structure of TRP channels fragments with high resolution data can be found in “Structural Biology of TRP channels,” by Li et al. (2011).