Structural and molecular modeling features of P2X receptors

Abstract

Currently, adenosine 5'-triphosphate (ATP) is recognized as the extracellular messenger that acts through P2 receptors. P2 receptors are divided into two subtypes: P2Y metabotropic receptors and P2X ionotropic receptors, both of which are found in virtually all mammalian cell types studied. Due to the difficulty in studying membrane protein structures by X-ray crystallography or NMR techniques, there is little information about these structures available in the literature. Two structures of the P2X4 receptor in truncated form have been solved by crystallography. Molecular modeling has proven to be an excellent tool for studying ionotropic receptors. Recently, modeling studies carried out on P2X receptors have advanced our knowledge of the P2X receptor structure-function relationships. This review presents a brief history of ion channel structural studies and shows how modeling approaches can be used to address relevant questions about P2X receptors.

Figure 1.

Cartoon representation of the three different families of ion channels. Pentameric: (A) Structure of the nicotinic acetylcholine receptor (PDB code: 2BG9); (B) A ligand-gated ion channel from Erwinia chrysanthemi (PDB code 2VL0); (C) An open pore conformation of a bacterial ligand-gated ion channel(PDB code 3EAM); Trimeric: (D) Crystal structure of the adenosine adenosine 5′-triphosphate(ATP)-gated zebrafish P2X4 ion channel in agonist-bound (PDB code 4DW1); Tetrameric: (E) Structure of the AMPA subtype ionotropic glutamate receptor (PDB code 3KG2). The figure also includes a representation of the biological membrane showing the actual proportions of the transmembrane channel. The images below the membrane represent the top view, taking the membrane as a reference. The numbers show the approximate diameter of the narrowest region of the pore.

Figure 2.

Top (A) and side (B) view representation of a P2X4 ion channel, taking the membrane as reference. Residues D91, D99, D307, E310 and D323 lie along the assumed ion pathway and are shown in red. Three monomeric units (pink, green and blue form a trimeric configuration in which these negatively charged amino acids can form a strong positive gradient that supports ion migration into the cell; (C) Dolphin like shape of P2X4 subunit; The highlighted region in (D) shows the putative ATP binding site (N296, R298, K316, K70, K72, F188 and T189), as suggested by Hattori et al. [21]. The binding cleft is located between two adjacent chains. Figure created using APBS (APBS version 1.3 [52]) and PyMOL (The PyMOL Molecular Graphics System version 1.5.0.4 [53]).

Figure 3.

(A) and (B) are shown the Open (ATP bound) and closed side view of P2X7R built from the P2XR4 structure, respectively; (C) and (D) are shown the Open and closed top view (from outside the cell membrane), showing the diameter of the gate, respectively.

Figure 4.

Side view of two adjacent units, showing a putative ATP binding site, transposed from the P2X4 crystal structure.

Figure 5.

Detailed views of the open (A) and closed (B) P2X7R channel. The measured diameter of the channel in the open structure is about 7.6 Ǻ, but wider openings may be attained.