There is evidence that the P2X1 receptor subunit is involved in apoptosis, platelet aggregation, and smooth muscle contraction. The conformation of the membrane-embedded, ligand-gated mouse P2X1 glycoprotein, a monovalent-bivalent cation channel-forming receptor, is predicted. The first step is based on secondary structure prediction. The secondary structure is converted into a three-dimensional geometry. Then, the secondary and tertiary structures are optimized by using the quantum chemistry RHF/3-21G minimal basic set and the all-atom molecular mechanics AMBER96 force field. The fold of the membrane-embedded protein is simulated by a suitable dielectric. The structure is refined using a conjugate gradient minimizer (Fletcher-Reeves modification of the Polak- Ribiere method). Although the mouse P2X1 receptor subunit is more complex (388 amino acids) than the KcsA protein (160 amino acids), the overall folds are similar. The geometry optimized P2X1 receptor subunit is freely available for academic researchers on e-mail request (PDB format).
Keywords: Structural bioinformatics, ATP-activated purinergic receptor, P2X receptor, Cation channel, KcsA protein
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