Interaction between the ligand and receptor

After the interaction between the ligand and receptor has reached equilibrium, dissociation kinetics are initiated either by dilution or by the introduction of unlabelled ligand which competes for the receptor binding sites. The purpose, in both cases, is to ensure that once the radiolabelled ligand has dissociated from the receptor, it is not able to reassociate with the receptor. This allows the following reaction to occur in isolation ... 

As shown in Figure 6, the solvent molecules tend to be ordered around the molecules and when the protein and the ligand bind, several of these molecules are liberated and become disordered (entropic effect). Therefore, upon complex formation water molecules are released, receptor and ligand lose degrees of freedom and the interaction between the ligand and the receptor is calculated. 

Figure 17.31 Death of virally infected host celis via the death receptor on the host cell to which is bound the death ligand on the surface of the cytotoxic T-cell. The interaction between the ligand and the receptor results in activation of caspases that induce apoptosis. The latter process results in disintegration of the cell, the results of which are apoptotic vesicles that are phagocytosed and destroyed by the macrophages.

The focus of 3D-QSAR is to identify and quantitatively characterize the interactions between the ligand and the receptor s active site. As the title of the field suggests, the main basis of the QSAR models are the molecules 3D atomic (Cartesian) coordinates. The interactions between the atomic 3D coordinates and the receptor are correlated to the bioactivities producing a 3D-QSAR model. There are several methods to achieve the creation of QSAR... 

No matter whether at the interface of foreign materials or under in vivo conditions, cell adhesion is always accomplished via interactions between extracellular ligands and receptors on the cell surface. Typical species of cell adhesion receptors are integrins, proteoglycans, and selectins. Accordingly,... 

We wished to develop a macroscopic model of the interactions between molecular ligands and receptors. Molecular recognition is a broad subject that describes selective assembly in chemistry and biology, with examples from DNA-protein complex formation to asymmetric catalysis. The principle behind molecular recognition dictates that the molecules that mate have complementary shapes and interfacial characteristics. Our extension of this principle to the mesoscale involved the self-assembly of objects that matched both... 

In principle, MD simulations provide the most natural route to the explicit consideration of water molecules. In the MD docking approach described by Mangoni et al., explicit water molecules are indeed used (165). It was found, though, that the presence of explicit water molecules shields the interactions between the ligand and the receptor. Consequently, different weights were applied to the ligand-receptor and ligand-solvent interactions, respectively, to cope with this complica-... 

Figure 5 Schematic representation of vasopressin binding to the VIA receptor. Dotted lines indicate the postulated interactions between the ligand and the receptor residues located in the transmembrane domain of the receptor. The residue numbering is coded as in Figure 4, with the exception of TyrllS which corresponds to the official VIA receptor label. The site directed mutation and the decrease (x fold) in affinity of vasopressin for this mutant are indicated near each residue.

Molecular shape is related to several physico-chemical processes, such as transport phenomena as well as entropy contributions, and interaction capability between the ligand and receptor. 

Furthermore, even if the biological receptor is known and structurally determined, modern techniques such as virtual screening and docking experiments or de novo design systems have to take into account several alternative conformations of the small molecules under investigation to estimate and rank different binding modes and constants with locally optimized electrostatic and steric interactions between the ligand and its receptor [8]. 

In QSARs, the biological activity is also produced by the interaction between the ligand and the biological receptor of an organism. The only difference is that the ligand in QSARs is a chemical species, and the biological receptor is the biotic ligand. 

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