Ligand binding receptor spheres

Zwanzig, R. (1990). Diffusion-controlled ligand binding to spheres partially covered by receptors an effective medium treatment, Proc. Natl. Acad. Sci. USA, 87, 5856-5857. 

Figure 2 In DOCK, the receptor is geometrically described using overlapping spheres of different sizes that are complementary to the molecular surface of the ligand-binding site. The ligand is described with spheres inside its surface. During the docking process protein and ligand spheres are matched.

Figure 3 Overview of the receptor-ligand binding process. All species involved are solvated by water (symbolized by gray spheres). The binding free energy difference between the bound and unbound state is a sum of enthalpic components (breaking and formation of hydrogen bonds, formation of specific hydrophobic contacts), and entropic components (release of water from hydrophobic surfaces to solvent, loss of conformational mobility of receptor and ligand).

Figure 9. Sphere generation approach to determine the geometric requirements of a binding site. The binding site is formed from six atoms (filled circles). The molecular surface is shown by a thick black line. The receptor sphere (which will contain the bound ligand) are constructed with centers along the surface normals (19).

Figure 4 Schematic representation of the S-HTj receptor subunit. The sphere represents the ligand binding area, in contact with three loops of the receptor subimit. The upper line of the boxed sequences, corresponds to the sequence of the 5-HTg receptor subunit [99] and was numbered starting from the first methionine of the signal sequence. The 3 other lines correspond to the nicotinic, glycine and GabaA a-subimit sequences, respectively. In the Mil domain, the sequence of the nicotinic a7-subunit was inserted between the S-HTg and the three other sequences.

Figure 5.7 Neighbor-joining trees of the sequence homology of each binding site for monoamine-related GPCRs. The underlying sequence blocks correspond to transmembrane residues identified within the 6-A contact spheres of 5-HT (panel A), propranolol (panel B) and 8-OH-DPAT (panel C), respectively, in the rho-dopsin-based models of the 5-HT1A receptor-ligand complexes. Details as in the legend for Figure 5.2.

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