1. Università degli Studi di Milano
Facoltà di Farmacia
Modelling the folding of transmembrane proteins using a novel fragmental approach: the human ghrelin receptor and the glutamate transporter EAAT1
Alessandro Pedretti & Giulio Vistoli

2. The fragmental approach1
Aminoacid sequence
of the transmembrane protein
Fragmentation in structural domains
Folding prediction of each fragment
Assembling using a global template

3. Global template

4. Ligand-protein complexes
The fragmental approach2
Side chains building
Rough model
Final model
MM/MD refinement
Molecular docking
Ligand-protein complexes
Lignads
Model validation

5. Spiroindane derivative
HGHS-R1a ligand binding sites
Glu 124
Polar
Arg 283
Apolar
Spiroindane derivative
EC50 = 0.6 nM
TM3
TM6

6. pEC50 = 6.06 (0.35) – 0.070 (0.01) x Scorepol
QSAR analysis
pEC50 = 6.06 (0.35) – (0.01) x Scorepol
n = 35; r2 = 0.57; q2 = 0.51 s = 0.29; F = 44.30
Scorepol (Kcal/mol)
pEC50
pEC50 = 5.96 (0.29) – (0.0087) Scorepol – (0.0033) Scoreapol
n = 35; r2 = 0.72; q2 = 0.67; s = 0.24; F = 42.06
pEC50 calculated
pEC50 experimental

7. Conclusions
The fragmental approach allows to obtain good models avoiding the construction of bovine rhodopsin clones.
The computational results are confirmed by the good correlation between the experimental data and the docking scores.
The method was successfully applied to the non-GPCR protein EAAT1, obtaining results confirmed by the experimental data.