Figure 1

Three-dimensional models for Tre1⁺ and Tre1^sctt . mtre1 and msctt are the models generated with GPCR-ModSim and gtre1 and gsctt are the models generated with GPCR-ITASSER. mtre1 and gtre1 are models for Tre1⁺ and msctt and gsctt are models for Tre1^sctt. The N-termini are colored blue and the C-termini are colored red. (A) The best models chosen from the GPCR-ModSim and GPCR-ITASSER. (B) A closer view of helices 5 and 6 (yellow and gold) denoted by arrowheads, and intracellular loop 2 (green) shown by arrows. In the gtre1 and gsctt models, helices 5 and 6 are extended compared to the other 5 helices. Intracellular loop 2 is unstructured in mtre1 but contains a short helix in gtre1. (C) The resulting models after 262 ns (mtre1), 258 ns (msctt), 270 ns (gtre1) or 276 ns (gsctt) of MD simulations with the protein embedded in a POPE lipid bilayer. The differences in helical length of helices 5 and 6 and the structure of intracellular loop 2 between the initial structures generated by GPCR-ModSim and GPCR-ITASSER are still present after the MD.