Receptor dimensionality

Suppose now that the sites are not independent, but that addition of a second (and subsequent) ligand next to a previously bound one (characterized by an equilibrium constant K ) is easier than the addition of the first ligand. In the case of a linear receptor B, the problem is fonnally equivalent to the one-dimensional Ising model of ferromagnetism, and neglecting end effects, one has [M] ... 

Desjarlais R L, R P Sheridan, G L Seibel, J S Dixon, ID Kuntz and R Venkataraghavan 1988. Using Shap Complementarity as an Initial Screen in Designing Ligands for a Receptor Binding Site of Know Three-Dimensional Structure. Journal of Medicinal Chemistry 31 722-729. 

DP Mamott, IG Dougall, P Meghani, Y-J Liu, DR Flower. Lead generation using pharmacophore mapping and three-dimensional database searching Application to muscarinic M3 receptor antagonists. J Med Chem 42 3210-3216, 1999. 

Given the difficulty of obtaining three-dimensional crystals of membrane proteins, it is not surprising that the electron microscope technique is now widely used to study large membrane-bound complexes such as the acetylcholine receptor, rhodopsin, ion pumps, gap junctions, water channels and light-harvesting complexes, which crystallize in two dimensions. 

Metal-directed self-assembly of two- and three-dimensional synthetic receptors (macroheterocycles involving transition metal atoms, among them chelated atoms) 98CSR417. 

A receptor is a surface membrane component, usually a protein, which regulates some biological event in response to reversible binding of a relatively small molecule40 . The precise three-dimensional structures of the binding sites of receptors still remain unknown today. Thus, this section mainly describes the correlation of shape similarity between the molecules which would bind to a given receptor with their biological activity. 

Ryanodine Receptor. Figure 1 Three-dimensional architecture of the RyR1 by cryo-electron microscopy, (a), top view (from the T-tubule) (b), bottom view (from the SR lumen) (c), side view (parallel to the SR membrane). The binding sites of FKBP12, apo-CaM and Ca -CaM are indicated in the side view. Courtesy of Dr. M. Samso (modified from Samso etal. (2005) Nat Struct Mol Biol 12 539-544). 

The physiologic LRG interaction actually involves at least five types of components ligand, receptor, intact G or G protein subunits (a and Py), GTP (which promotes LRG dissociation and activation), and GDP (which promotes LR dissociation from G but not G dissociation into its subunits). Little about the dynamics of these processes is known. The LRG states may be visualized, in shorthand, as a 3-dimensional array (Figure 1). A large number of questions concerning LRG states remain to be addressed ... 

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Xue L, Stahura FL, Godden JW, Bajorath J. Mini-fingerprints detect similar activity of receptor ligands previously recognized only by three-dimensional pharmacophore-based methods. J Chem Inf Comp Sci 2001 41 394-401. 

Varady J, Wu X, Fang X, Min J, Hu Z, Levant B, Wang S. Molecular modeling of the three-dimensional structure of dopamine 3 (D3) subtype receptor discovery of novel and potent D3 ligands through a hybrid pharmacophore-and structure-based database searching approach. / Med Chem 2003 46 4377-92. 

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