Question

How proteins bind ligands (specific examples/explaining of IMFs)? supply specific amino acids or prosthetic groups and demonstrating how they could interact with a ligand?

Answer 1

ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformation of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion or protein 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.

As an example, the specificity with which heme binds its various ligands changes when the heme is a component of myoglobin. When carbon monoxide binds to free heme molecules, it binds more than 20,000 times better than oxygen does, but it only binds 200 times better than oxygen when the heme is bound in myoglobin. The difference is most likely due to steric hindrance but there are other factors that have not yet been well-defined that may also affect the interaction of heme with carbon monoxide.