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In biochemistry and molecular biology, a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. [1] The binding partner of the macromolecule is often referred to as a ligand. [2]
The first description of cooperative binding to a multi-site protein was developed by A.V. Hill. [4] Drawing on observations of oxygen binding to hemoglobin and the idea that cooperativity arose from the aggregation of hemoglobin molecules, each one binding one oxygen molecule, Hill suggested a phenomenological equation that has since been named after him:
Associative substitution closely resembles the S N 2 mechanism in organic chemistry. A typically smaller ligand can attach to an unsaturated complex followed by loss of another ligand. Typically, the rate of the substitution is first order in entering ligand L and the unsaturated complex. [19] A generalized example of ligand dissociation
The carbonyl ligand engages in a wide range of bonding modes in metal carbonyl dimers and clusters. In the most common bridging mode, denoted μ 2 or simply μ, the CO ligand bridges a pair of metals. This bonding mode is observed in the commonly available metal carbonyls: Co 2 (CO) 8, Fe 2 (CO) 9, Fe 3 (CO) 12, and Co 4 (CO) 12.
In DNA-ligand binding studies, the ligand can be a small molecule, ion, [1] or protein [2] which binds to the DNA double helix. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure. Binding occurs by intermolecular forces, such as ionic bonds, hydrogen bonds and Van der Waals forces.
Molecular binding occurs in biological complexes (e.g., between pairs or sets of proteins, or between a protein and a small molecule ligand it binds) and also in abiologic chemical systems, e.g. as in cases of coordination polymers and coordination networks such as metal-organic frameworks.
In inorganic chemistry, the cis effect is defined as the labilization (or destabilization) of CO ligands that are cis to other ligands. CO is a well-known strong pi-accepting ligand in organometallic chemistry that will labilize in the cis position when adjacent to ligands due to steric and electronic effects.
The binding constant, or affinity constant/association constant, is a special case of the equilibrium constant K, [1] and is the inverse of the dissociation constant. [2] It is associated with the binding and unbinding reaction of receptor (R) and ligand (L) molecules, which is formalized as: R + L ⇌ RL