Binding site
[2] Ligands may include other proteins (resulting in a protein–protein interaction),[3] enzyme substrates,[4] second messengers, hormones, or allosteric modulators.
Electric charge, steric shape and geometry of the site selectively allow for highly specific ligands to bind, activating a particular cascade of cellular interactions the protein is responsible for.
[12][13][14] Enzymes incur catalysis by binding more strongly to transition states than substrates and products.
[15][11] Types of enzymes that can perform these actions include oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases.
Allosteric binding induces conformational changes that may increase the protein's affinity for substrate.
[21] In the context of the blood, an example of competitive binding is carbon monoxide which competes with oxygen for the active site on heme.
Recent research shows that binding site structure has profound consequences for the biology of protein complexes (evolution of function, allostery).
Considering the cryptic binding sites increases the size of the potentially “druggable” human proteome from ~40% to ~78% of disease-associated proteins.
[29] The binding sites have been investigated by: support vector machine applied to "CryptoSite" data set,[29] Extension of "CryptoSite" data set,[30] long timescale molecular dynamics simulation with Markov state model and with biophysical experiments,[31] and cryptic-site index that is based on relative accessible surface area.
Curves can be characterized by their shape, sigmoidal or hyperbolic, which reflect whether or not the protein exhibits cooperative or noncooperative binding behavior respectively.
The Michaelis Menten equation is derived based on steady-state conditions and accounts for the enzyme reactions taking place in a solution.
Thus, the study of binding sites is relevant to many fields of research, including cancer mechanisms,[36] drug formulation,[37] and physiological regulation.
[40] This interaction inhibits the synthesis of tetrahydrofolate, shutting off production of DNA, RNA and proteins.
[40] Inhibition of this function represses neoplastic growth and improves severe psoriasis and adult rheumatoid arthritis.
Beta blockers (β-Blockers) are antihypertensive agents that block the binding of the hormones adrenaline and noradrenaline to β1 and β2 receptors in the heart and blood vessels.
These receptors normally mediate the sympathetic "fight or flight" response, causing constriction of the blood vessels.
Botulinum toxin, known commercially as Botox, is a neurotoxin that causes flaccid paralysis in the muscle due to binding to acetylcholine dependent nerves.
