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The P2Y1 purinoceptor cloned from chick brain (Webb, T. et al (1993) FEBS Lett.,
324, 219-225) is a 362 amino acid, 41 kDa protein. To locate residues
tentatively involved in ligand recognition a molecular model of the P2Y
purinoceptor has been constructed. The model was based on the primary sequence
and structural homology with the G-protein coupled photoreceptor rhodopsin, in
analogy to the method proposed by Ballesteros and Weinstein ((1995) Meth.
Neurosci. 25, 366-428). Transmembrane helices were constructed from the amino
acid sequence, minimized individually, and positioned in a helical bundle. The
helical bundle was then minimized using the Amber forcefield in Discover (BIOSYM
Technologies) to obtain the final model. Several residues that have been shown
to be critical in ligand binding in other GPCRs are conserved in the P2Y1
purinoceptor. According to our model the side chains of these conserved residues
are facing the internal cleft in which ligand binding likely occurs. The model
also suggests four basic residues (H121 in TM3, H266 and K269 in TM6 and R299 in
TM7) near the extracellular surface that might be involved in ligand binding.
These basic residues might be essential in coordinating the triphosphate chain
of the endogenous ligand adenosine 5'-triphosphate (ATP). Potential binding
sites for agonists have been explored by docking several derivatives (including
newly synthesized N6-derivatives) into the model. The N6-phenylethyl substituent
is tolerated pharmacologically, and in our model this substituent occupies a
region predominantly defined by aromatic residues such as F51 (TM1), Y100 (TM2)
and F120 (TM3). The dimethylated analogue of ATP, N6,N6-dimethyl-adenosine
5'-triphosphate, is less well tolerated pharmacologically, and our model
predicts that the attenuated activity is due to interference with hydrogen
bonding capacity to Q296 (TM7).
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